Contacts of the helix formed by residues 82 - 111 (chain A) in PDB entry 2QQY
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 ASP 82 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ALA* 3.4 3.7 + - - +
81A GLU* 1.3 80.1 - - - +
83A VAL* 1.3 60.9 + - + +
84A ARG* 3.3 12.0 + - - +
85A GLU* 2.9 35.3 + - - +
86A MSE 2.9 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 3.9 13.9 - - + -
34A SER* 4.3 14.1 - - - +
37A TYR* 3.1 39.9 - - + +
41A LEU* 3.6 31.4 - - + -
82A ASP* 1.3 71.2 - - + +
84A ARG* 1.3 67.7 + - - +
86A MSE 3.1 14.6 + - + +
87A LEU* 2.9 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ASP* 3.3 11.4 + - - +
83A VAL* 1.3 75.8 - - - +
85A GLU* 1.3 59.5 + - + +
87A LEU* 3.0 11.4 + - - +
88A GLU* 2.8 54.6 + - - +
137A LEU 5.4 0.2 + - - -
138A LEU* 2.8 49.6 + - - +
139A ASN* 5.3 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLN 4.1 1.0 - - - +
80A ALA* 3.7 8.5 - - + -
81A GLU* 2.9 40.1 + - - +
82A ASP* 2.9 27.1 + - - +
84A ARG* 1.3 74.7 - - + +
86A MSE 1.3 65.4 + - - +
88A GLU* 4.3 8.3 - - - +
89A TYR* 2.9 64.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A HIS* 5.5 1.8 - - + +
29A ASN* 3.2 41.5 + - + +
32A THR* 3.5 26.0 - - - +
33A VAL* 3.8 36.3 - - + -
45A PHE* 3.8 15.7 - - + -
80A ALA* 3.6 22.4 - - + +
82A ASP* 2.9 19.8 + - - +
83A VAL* 3.3 14.8 - - + +
85A GLU* 1.3 75.1 - - - +
87A LEU* 1.3 61.6 + - - +
89A TYR* 4.1 1.9 - - - +
90A ALA* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 4.2 22.2 - - + -
44A PHE* 5.0 0.2 - - + -
45A PHE* 3.9 25.1 - - + -
83A VAL* 2.9 32.1 + - + +
84A ARG* 3.0 3.3 + - - +
86A MSE 1.3 75.3 - - - +
88A GLU* 1.3 63.3 + - - +
90A ALA* 3.4 3.1 + - - +
91A ARG* 3.0 23.7 + - - +
134A LEU* 3.8 27.5 - - + +
137A LEU* 4.5 20.2 - - + +
138A LEU* 3.6 27.9 - - + +
----------------------------------------------------------
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 ARG* 2.8 55.7 + - - +
85A GLU* 3.9 8.9 - - - +
87A LEU* 1.3 77.1 - - - +
89A TYR* 1.3 73.7 + - + +
91A ARG* 3.3 8.2 + - - +
92A GLN* 2.9 28.8 + - - +
138A LEU* 3.9 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A MSE 4.2 7.6 - - - +
78A LYS* 3.8 46.6 - - + +
79A GLN 3.7 22.2 - - - -
80A ALA* 4.2 9.2 - - + -
85A GLU* 2.9 51.7 + - + +
86A MSE 4.2 3.4 - - - +
88A GLU* 1.3 88.3 - - + +
90A ALA* 1.3 59.6 + - - +
92A GLN* 3.9 14.0 - - - +
93A SER* 3.0 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A MSE 3.7 27.2 - - + -
26A TYR* 4.0 14.1 + - + +
29A ASN* 4.7 4.3 - - - +
45A PHE* 5.0 2.2 - - + -
86A MSE 3.1 19.1 + - - +
87A LEU* 3.8 4.9 - - - +
89A TYR* 1.3 75.0 - - - +
91A ARG* 1.3 57.9 + - - +
93A SER* 3.4 2.8 + - - -
94A GLU* 2.9 34.5 + - - +
134A LEU* 3.8 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU 3.0 17.7 + - - +
88A GLU* 3.4 8.5 - - - +
90A ALA* 1.3 75.9 - - - +
92A GLN* 1.3 59.2 + - - +
94A GLU* 3.2 4.5 + - - +
95A TYR* 2.9 56.1 + - - +
131A MSE 3.6 31.9 - - + +
134A LEU* 3.6 23.2 - - + +
135A ASP* 2.8 41.6 + - - +
138A LEU* 4.4 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LYS* 3.0 43.0 + - - +
88A GLU 2.9 15.2 + - - +
89A TYR* 3.9 12.3 - - - +
91A ARG* 1.3 74.8 - - - +
93A SER* 1.3 67.9 + - - +
95A TYR* 3.2 10.4 + - + +
96A GLU* 2.8 54.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLY 5.5 0.9 + - - -
22A ALA* 4.7 10.0 - - - +
25A MSE 3.8 25.4 - - - +
89A TYR 3.0 19.0 + - - -
90A ALA 3.5 4.2 + - - -
92A GLN* 1.3 78.4 - - - +
94A GLU* 1.3 58.7 + - - +
96A GLU* 3.4 13.6 + - - +
97A THR* 2.9 35.4 + - - -
100A ARG* 4.7 1.0 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
22A ALA* 5.4 1.9 - - - +
26A TYR* 2.6 34.7 + - - +
52A GLU* 4.3 4.9 - - - +
90A ALA 2.9 28.5 + - - +
91A ARG 3.5 6.5 - - - +
93A SER* 1.3 76.1 + - - +
95A TYR* 1.3 65.9 + - - +
97A THR* 3.3 6.5 + - - -
98A ILE* 3.0 30.2 + - - +
127A GLU* 2.5 35.5 - - - +
130A HIS* 3.5 21.9 + - + +
131A MSE 4.1 16.6 - - + +
134A LEU* 4.1 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ARG* 2.9 41.2 + - - +
92A GLN* 3.5 11.7 - - + +
94A GLU* 1.3 76.6 - - - +
96A GLU* 1.3 68.5 + - + +
98A ILE* 3.3 6.2 + - + +
99A LYS* 3.0 46.5 + - + +
131A MSE 4.0 17.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 5.8 2.4 - - - +
92A GLN* 2.8 54.9 + - + +
93A SER* 3.8 10.0 - - - +
95A TYR* 1.3 82.2 - - + +
97A THR* 1.3 65.1 + - - +
99A LYS* 3.4 7.3 + - - +
100A ARG* 3.1 48.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLY 5.1 5.9 + - - -
19A GLU* 4.2 11.0 - - + +
93A SER* 2.9 25.5 + - - -
94A GLU* 3.6 10.1 - - - -
96A GLU* 1.3 77.3 - - - +
98A ILE* 1.3 57.5 + - - +
100A ARG* 3.2 25.3 + - - +
101A TYR* 3.0 56.5 + - + -
127A GLU* 3.8 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU 3.0 22.5 + - - +
95A TYR* 3.7 4.3 - - + +
97A THR* 1.3 74.4 - - - +
99A LYS* 1.3 61.0 + - - +
101A TYR* 3.3 6.8 + - - +
102A GLU* 2.9 38.3 + - + +
124A ILE* 4.0 24.5 - - + +
127A GLU* 3.6 25.8 - - + +
128A THR* 3.6 34.5 - - - +
131A MSE 4.0 23.1 - - + -
----------------------------------------------------------
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 TYR* 3.0 38.2 + - + +
96A GLU* 3.7 8.7 - - - +
97A THR 3.4 0.2 - - - -
98A ILE* 1.3 77.4 - - - +
100A ARG* 1.3 62.0 + - + +
102A GLU* 3.4 7.3 + - - +
103A LYS* 3.1 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU* 4.2 24.0 + - - +
15A ASP* 3.4 29.2 + - - +
18A GLY* 3.9 21.7 - - - -
75A LEU* 4.1 20.1 - - - +
93A SER 4.7 2.0 + - - -
96A GLU* 3.1 39.6 + - - +
97A THR* 3.2 33.0 + - - +
99A LYS* 1.3 78.1 - - + +
101A TYR* 1.3 57.9 + - - +
103A LYS* 3.1 8.8 + - - +
104A ARG* 2.9 42.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASP* 3.5 33.9 - - + +
19A GLU* 2.7 26.2 + - + +
55A HIS* 5.2 0.4 - - - -
59A LEU* 3.3 21.7 - - + +
97A THR* 3.0 44.1 + - + +
98A ILE* 3.3 2.9 + - - +
100A ARG* 1.3 75.6 - - - +
102A GLU* 1.3 53.2 + - - +
104A ARG* 3.3 3.5 + - + +
105A LYS* 2.7 35.2 + - - +
120A LEU* 3.6 26.8 - - + +
123A MSE 3.9 36.1 - - + -
124A ILE* 3.5 22.5 - - + +
127A GLU* 4.4 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ILE* 2.9 30.0 + - + +
99A LYS* 3.6 7.4 - - - +
101A TYR* 1.3 71.8 - - - +
103A LYS* 1.3 67.6 + - - +
105A LYS* 3.3 28.6 + - - +
106A GLU* 3.3 21.7 + - - +
124A ILE* 3.5 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLU* 4.9 1.2 + - - -
99A LYS 3.1 12.3 + - - +
100A ARG* 3.1 11.9 + - - +
102A GLU* 1.3 76.8 - - - +
104A ARG* 1.3 73.0 + - - +
106A GLU* 3.2 7.7 + - - +
107A GLN* 2.6 53.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.8 15.4 - - + +
11A GLY* 3.1 25.4 + - - -
12A LEU* 3.5 33.9 - - + +
14A GLU* 4.4 6.7 + - - -
15A ASP* 2.7 38.8 + - - +
100A ARG* 2.9 37.9 + - - +
101A TYR* 3.5 8.1 - - - +
103A LYS* 1.3 82.2 - - - +
105A LYS* 1.3 51.5 + - - +
107A GLN* 3.1 32.3 + - - +
108A ALA* 2.8 35.9 + - - +
120A LEU* 3.5 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A TYR 2.7 21.4 + - - +
102A GLU* 3.3 30.6 + - - +
104A ARG* 1.3 72.8 - - - +
106A GLU* 1.3 67.3 + - - +
108A ALA* 3.7 0.9 - - - +
109A ALA* 2.7 38.2 + - + +
117A VAL* 4.0 18.1 - - + +
120A LEU* 3.6 24.4 - - + +
121A GLU* 3.8 32.1 - - + +
124A ILE* 4.2 8.7 - - + -
----------------------------------------------------------
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 GLU 3.3 8.2 + - - +
103A LYS* 3.2 10.2 + - - +
105A LYS* 1.3 90.7 + - - +
107A GLN* 1.3 61.7 + - - +
109A ALA* 4.1 13.1 - - - +
110A ASN* 2.9 52.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ASP 5.9 0.2 - - - +
7A GLU* 3.4 41.4 + - + +
8A LEU* 4.0 18.3 - - + -
103A LYS* 2.6 40.8 + - - +
104A ARG* 3.1 42.4 + - - +
106A GLU* 1.3 74.0 - - - +
108A ALA* 1.3 65.4 + - - +
110A ASN* 3.3 7.1 + - - +
111A LEU* 3.2 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 4.2 5.7 - - + +
104A ARG 2.8 19.3 + - - +
105A LYS 3.9 1.3 - - - +
107A GLN* 1.3 69.5 - - - +
109A ALA* 1.3 67.0 + - - +
111A LEU* 3.2 8.6 + - - -
112A ASN 3.2 0.2 + - - -
113A MSE 2.9 30.3 + - + +
116A LEU* 3.7 35.9 - - + -
117A VAL* 3.7 17.3 - - + -
120A LEU* 3.9 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LYS* 2.7 25.1 + - + +
106A GLU* 4.1 19.1 - - - +
108A ALA* 1.3 72.0 - - - +
110A ASN* 1.3 58.3 + - - +
112A ASN* 2.8 25.7 + - - +
113A MSE 4.8 0.9 - - - +
117A VAL* 3.5 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ASP* 6.1 0.7 - - - +
106A GLU* 2.9 41.6 + - - +
107A GLN* 3.7 6.9 - - - +
108A ALA 3.3 0.4 - - - -
109A ALA* 1.3 76.6 - - - +
111A LEU* 1.3 59.4 + - + +
112A ASN* 3.3 8.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 4.6 2.7 - - - +
4A ASP* 3.8 46.2 - - + +
5A VAL* 4.3 12.6 - - + -
8A LEU* 3.9 28.3 - - + -
107A GLN* 3.2 18.6 + - + +
108A ALA 3.2 5.0 + - - +
109A ALA 3.1 0.8 - - - -
110A ASN* 1.3 78.1 - - + +
112A ASN* 1.3 73.8 + - - +
113A MSE 3.2 24.0 + - + +
----------------------------------------------------------
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