Contacts of the helix formed by residues 82 - 111 (chain A) in PDB entry 1KRQ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 82 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TRP* 3.5 15.9 - - - -
80A PHE 3.7 1.6 - - - -
81A LYS* 1.3 84.5 - - - +
83A LEU* 1.3 67.2 + - - +
84A LEU* 3.8 8.0 + - - +
85A ASP* 3.1 18.0 + - - +
86A VAL* 2.9 25.5 + - - +
151A LEU* 6.3 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TRP* 4.1 2.8 - - - -
31A CYS* 5.0 2.7 - - - -
36A LEU* 4.0 25.6 - - + +
39A ALA* 3.8 17.0 - - + -
82A SER* 1.3 76.0 - - - +
84A LEU* 1.3 62.7 + - - +
86A VAL* 3.2 7.6 + - - +
87A PHE* 3.1 51.6 + - + -
141A ILE* 4.0 19.1 - - + -
151A LEU* 3.8 32.8 - - + +
154A ALA* 3.8 29.6 - - + -
155A ASP* 4.5 4.9 - - - +
158A ILE* 4.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A SER* 3.3 6.8 + - - +
83A LEU* 1.3 76.7 - - - +
85A ASP* 1.3 67.5 + - - +
87A PHE 3.4 1.1 + - - +
88A GLU* 2.9 58.0 + - + +
138A VAL* 4.1 17.9 - - + -
141A ILE* 4.3 30.5 - - + +
142A LYS* 4.4 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PHE* 3.2 14.4 - - - +
81A LYS* 2.7 41.0 + - + +
82A SER* 3.1 25.5 + - - +
84A LEU* 1.3 79.5 - - - +
86A VAL* 1.3 60.9 + - - +
88A GLU* 3.2 13.2 + - - +
89A LYS* 3.0 56.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET* 3.6 18.4 - - + +
30A TRP* 3.7 27.6 - - + -
31A CYS* 4.4 5.6 - - - -
43A LEU* 3.8 28.0 - - + -
80A PHE* 3.7 26.9 - - + -
82A SER 2.9 18.1 + - - +
83A LEU* 3.4 9.4 - - - +
85A ASP* 1.3 77.5 - - - +
87A PHE* 1.3 63.5 + - + +
89A LYS* 3.3 4.0 + - - +
90A THR* 2.9 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ALA* 3.7 28.7 - - + -
42A PHE* 4.0 28.7 - + - -
43A LEU* 4.1 24.0 - - + -
83A LEU* 3.1 31.2 + - + +
84A LEU 3.4 2.0 + - - +
86A VAL* 1.3 81.3 - - + +
88A GLU* 1.3 63.3 + - - +
90A THR* 3.8 6.6 - - - -
91A TYR* 3.2 15.8 + - - +
134A PHE* 4.2 20.8 - + - +
137A ILE* 3.7 21.1 - - + -
138A VAL* 3.3 24.0 - - + +
141A ILE* 4.0 15.7 - - + -
158A ILE* 3.7 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 2.9 51.6 + - + +
85A ASP* 3.2 12.3 + - - +
87A PHE* 1.3 75.6 - - - +
89A LYS* 1.3 62.6 + - + +
91A TYR* 3.3 5.7 + - - +
92A GLU* 2.9 33.6 + - - +
138A VAL* 4.4 12.1 - - + +
142A LYS* 4.0 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 5.8 0.6 - - + +
27A MET* 3.6 18.4 - - + -
77A GLU* 3.8 21.5 + - - +
79A ASN 5.2 2.6 + - - -
80A PHE* 4.1 10.5 - - + +
81A LYS* 5.8 3.6 - - - +
85A ASP* 3.0 42.5 + - - +
86A VAL 3.5 6.3 - - - +
88A GLU* 1.3 78.7 - - + +
90A THR* 1.3 51.0 + - - +
92A GLU* 3.1 23.1 - - - +
93A HIS* 2.8 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.8 27.1 + - + -
27A MET* 3.2 19.8 - - - +
43A LEU* 4.2 9.4 - - + +
86A VAL* 2.9 19.7 + - - +
87A PHE* 3.9 9.9 - - - -
88A GLU 3.3 0.2 - - - -
89A LYS* 1.3 74.0 - - - +
91A TYR* 1.3 65.3 + - - +
93A HIS* 3.2 3.6 + - - +
94A GLU* 2.9 23.0 + - - +
134A PHE* 3.3 39.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PHE 3.2 15.9 + - - +
88A GLU* 3.7 4.7 - - - +
90A THR* 1.3 78.7 - - - +
92A GLU* 1.3 63.1 + - - +
94A GLU* 3.1 5.3 + - + +
95A GLN* 3.0 53.2 + - + +
131A GLU* 3.7 35.3 + - + +
134A PHE* 4.1 14.8 - - + +
135A ARG* 3.4 52.5 + - + +
138A VAL* 4.3 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU* 2.9 16.4 + - - +
89A LYS* 3.1 27.5 - - - +
91A TYR* 1.3 77.9 - - - +
93A HIS* 1.3 62.1 + - - +
95A GLN* 3.2 14.4 + - - +
96A PHE* 3.1 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS* 4.7 3.1 + - + -
19A TYR* 3.8 23.0 - + - -
20A ALA* 3.2 35.0 - - + -
23A LEU* 3.6 23.1 - - + -
24A TYR* 3.1 21.2 + - + +
89A LYS 2.8 18.6 + - - +
90A THR* 3.7 6.3 - - - +
92A GLU* 1.3 73.9 - - - +
94A GLU* 1.3 62.4 + - - +
96A PHE* 3.2 26.3 + + + +
97A ILE* 3.0 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 2.5 28.7 + - - +
46A HIS* 3.3 16.3 + - - -
50A GLU* 3.7 4.9 - - - +
90A THR* 2.9 17.4 + - + +
91A TYR* 3.1 14.6 + - + +
93A HIS* 1.3 76.2 - - - +
95A GLN* 1.3 58.7 + - - +
97A ILE* 3.1 8.0 + - - +
98A THR* 2.9 31.2 + - - -
127A GLN* 3.2 30.0 + - - +
130A GLU* 3.7 16.4 - - - +
131A GLU* 4.7 9.4 - - + -
134A PHE* 3.7 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TYR* 3.0 49.3 + - + +
92A GLU* 3.2 12.4 + - - +
94A GLU* 1.3 75.4 - - - +
96A PHE* 1.3 63.1 + - - +
98A THR* 3.2 3.0 + - - -
99A LYS* 2.9 23.4 + - - +
131A GLU* 3.8 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS* 3.3 43.5 - - + -
19A TYR* 6.4 0.2 - + - -
92A GLU 3.1 12.9 + - - +
93A HIS* 3.3 34.5 - + + +
95A GLN* 1.3 76.7 - - - +
97A ILE* 1.3 61.5 + - + +
99A LYS* 3.2 10.0 + - + +
100A SER* 2.9 35.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLN* 4.5 7.2 - - - +
16A LYS* 5.2 7.0 - - + +
17A GLU* 4.1 17.9 - - - +
20A ALA* 3.9 14.1 - - + -
24A TYR* 4.3 4.7 - - - +
50A GLU* 4.0 16.6 - - - +
93A HIS* 3.0 41.7 + - + +
94A GLU* 3.1 11.2 + - - +
96A PHE* 1.3 80.1 - - + +
98A THR* 1.3 66.5 + - - +
100A SER* 3.2 8.9 + - - -
101A ILE* 3.0 28.2 + - + +
127A GLN* 3.7 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU 2.9 9.1 + - - -
95A GLN 3.2 7.2 + - - -
97A ILE* 1.3 74.7 - - - +
99A LYS* 1.3 66.3 + - - +
101A ILE* 2.9 15.4 + - + +
102A ASN* 2.9 28.6 + - - +
127A GLN* 3.2 37.0 + - + +
131A GLU* 2.7 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLN 2.9 13.3 + - - +
96A PHE* 3.2 14.3 + - + +
98A THR* 1.3 76.3 - - - +
100A SER* 1.3 64.2 + - - +
102A ASN* 3.1 13.9 + - - +
103A THR* 3.0 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLN* 3.5 20.6 - - - -
16A LYS* 3.3 33.6 - - - +
96A PHE* 2.9 23.6 + - - -
97A ILE* 3.5 10.7 - - - -
98A THR 3.2 0.4 - - - -
99A LYS* 1.3 77.2 - - - +
101A ILE* 1.3 61.8 + - - +
103A THR* 3.3 8.5 + - - -
104A LEU* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLN* 3.9 28.7 - - + +
17A GLU* 4.8 0.4 - - - +
97A ILE* 3.0 23.8 + - + +
98A THR* 2.9 10.1 + - + +
100A SER* 1.3 73.9 - - - +
102A ASN* 1.3 62.7 + - - +
104A LEU* 3.1 12.4 + - + +
105A VAL* 2.9 36.0 + - + +
120A LEU* 4.9 5.8 - - + +
123A TYR* 4.0 39.3 - - + -
124A VAL* 4.1 25.8 - - + +
127A GLN* 4.3 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A THR* 2.9 37.9 + - - +
99A LYS* 3.1 10.3 + - - +
101A ILE* 1.3 77.2 - - - +
103A THR* 1.3 58.1 + - - +
105A VAL* 3.1 8.7 + - - +
106A GLU* 2.9 31.1 + - - +
124A VAL* 5.4 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 6.3 4.0 - - + -
99A LYS* 3.0 15.3 + - - +
100A SER* 3.6 11.2 - - - -
102A ASN* 1.3 75.3 - - - +
104A LEU* 1.3 62.7 + - + +
106A GLU* 3.5 14.9 + - - +
107A HIS* 3.0 24.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.4 47.1 - - + +
10A LEU* 4.3 14.1 - - + +
13A GLN* 3.6 39.3 - - + +
100A SER 3.1 14.4 + - - +
101A ILE* 3.1 15.8 + - + +
103A THR* 1.3 75.2 - - + +
105A VAL* 1.3 64.5 + - - +
107A HIS* 3.3 2.6 + - - -
108A MET* 3.1 38.3 + - + +
120A LEU* 3.8 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ILE* 2.9 23.7 + - + +
102A ASN* 3.6 11.2 - - - +
104A LEU* 1.3 74.7 - - - +
106A GLU* 1.3 64.4 + - - +
108A MET* 3.0 18.8 + - - +
109A LEU* 3.2 15.8 + - + +
117A PHE* 3.3 30.2 - - + -
120A LEU* 4.2 16.8 - - + -
121A GLN* 4.4 4.5 - - - +
124A VAL* 3.8 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ASN 2.9 15.5 + - - +
103A THR* 3.6 14.8 - - - +
105A VAL* 1.3 77.7 - - - +
107A HIS* 1.3 64.5 + - - +
109A LEU* 3.1 10.3 + - + +
110A THR* 3.0 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A SER* 5.4 0.4 - - - -
5A GLU* 4.3 15.1 - - + +
6A VAL* 4.3 14.1 - - + +
9A LEU* 3.5 32.7 - - + +
103A THR* 3.0 16.8 + - + +
104A LEU 3.7 4.9 - - - +
106A GLU* 1.3 79.4 + - - +
108A MET* 1.3 63.1 + - - +
110A THR* 3.8 5.8 - - - -
111A HIS* 3.1 72.5 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL* 3.9 29.8 - - + -
9A LEU* 4.1 14.6 - - + -
10A LEU* 5.4 1.8 - - + -
104A LEU* 3.1 35.2 - - + +
105A VAL* 3.0 8.1 + - - +
107A HIS* 1.3 89.6 - - - +
109A LEU* 1.3 60.1 + - - +
112A LYS* 3.0 7.3 + - - -
113A ASP* 2.7 47.8 + - - +
114A TYR* 5.0 0.3 - - - -
116A THR* 3.6 33.7 - - + -
117A PHE* 4.0 15.5 - - + +
120A LEU* 4.2 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A VAL* 3.2 8.3 + - + +
106A GLU* 3.1 10.8 + - - +
108A MET* 1.3 77.8 - - - +
110A THR* 1.3 67.0 + - + +
112A LYS* 3.2 14.4 + - - +
114A TYR* 3.9 28.9 + - + -
117A PHE* 3.8 43.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLU* 3.0 27.7 + - + +
107A HIS* 3.3 8.1 + - - -
109A LEU* 1.3 78.5 - - + +
111A HIS* 1.3 90.1 + - - +
112A LYS* 3.2 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A SER* 5.9 1.8 - - - +
5A GLU* 5.3 5.4 - - + +
6A VAL* 5.9 1.6 - - + -
107A HIS* 3.1 52.7 + + + +
108A MET* 4.7 0.9 - - - +
110A THR* 1.3 106.8 + - - +
112A LYS* 1.3 70.5 + - - +
113A ASP* 3.3 6.9 + - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il