Contacts of the helix formed by residues 93 - 117 (chain A) in PDB entry 1Q0K
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 93 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLN* 3.3 3.4 - - - +
91A SER* 2.9 12.7 + - - +
92A THR* 1.3 79.3 + - - +
94A PRO* 1.3 68.1 - - - +
95A ALA* 2.8 34.8 + - - +
96A THR* 2.8 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LYS* 3.6 19.0 - - + +
25A GLN* 3.4 13.2 - - + +
26A GLU* 3.5 47.3 - - + +
29A ALA* 5.5 6.1 - - + -
92A THR 3.3 7.2 - - - +
93A ASP* 1.3 89.4 - - - +
95A ALA* 1.3 55.0 + - - +
96A THR 3.3 0.2 - - - -
97A GLY 3.3 1.7 + - - -
98A GLN* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ASP* 2.8 24.1 + - - +
94A PRO* 1.3 77.1 - - - +
96A THR* 1.3 60.3 + - + +
98A GLN* 3.3 7.6 + - - +
99A LYS* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLN* 2.8 20.6 + - - -
84A ALA 4.3 3.1 - - - +
87A ALA* 4.5 11.2 - - + +
88A ALA* 3.4 20.8 - - - +
91A SER* 3.5 23.9 + - - +
93A ASP* 2.8 23.7 + - + +
95A ALA* 1.3 74.2 - - + +
97A GLY* 1.3 64.2 + - - +
99A LYS* 3.1 16.3 + - - +
100A ALA* 3.2 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA* 4.9 2.4 - - - +
21A VAL* 4.5 5.8 - - - -
22A LYS* 4.3 14.1 - - - +
25A GLN* 3.2 22.0 + - - -
88A ALA* 4.2 8.7 - - - -
94A PRO 3.7 0.4 - - - -
95A ALA 3.2 0.4 - - - -
96A THR* 1.3 84.4 + - - +
98A GLN* 1.3 56.1 + - - +
100A ALA* 3.3 6.6 + - - +
101A LEU* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LYS* 2.7 38.4 + - - +
94A PRO 2.9 18.4 + - - +
95A ALA* 3.6 9.0 - - - +
96A THR 3.2 0.2 - - - -
97A GLY* 1.3 73.9 - - - +
99A LYS* 1.3 60.3 + - - +
101A LEU* 3.3 18.8 + - - +
102A ASP* 2.8 55.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
84A ALA* 4.4 8.3 - - + -
95A ALA 2.9 14.4 + - - +
96A THR* 3.5 12.1 - - - +
98A GLN* 1.3 74.2 - - - +
100A ALA* 1.3 65.7 + - - +
102A ASP* 3.3 17.2 + - + +
103A TYR* 3.2 65.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA* 5.0 2.9 - - + -
81A ALA* 4.7 1.9 - - - +
84A ALA* 3.9 17.4 - - + +
85A LEU* 3.6 39.0 - - + +
88A ALA* 5.3 1.1 - - + -
96A THR 3.2 8.8 + - - +
97A GLY* 3.3 10.7 + - - +
99A LYS* 1.3 77.3 - - - +
101A LEU* 1.3 65.2 + - - +
103A TYR* 3.3 4.7 + - - +
104A ILE* 3.0 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 4.0 16.4 - - + +
18A ALA* 3.6 28.3 - - + +
19A GLU* 3.9 27.8 - - + +
22A LYS* 4.0 22.4 - - + -
97A GLY 3.0 17.9 + - - +
98A GLN* 3.6 30.1 - - - +
100A ALA* 1.3 76.2 - - - +
102A ASP* 1.3 62.2 + - - +
104A ILE* 3.4 5.7 + - + +
105A ALA* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLN* 2.8 48.3 + - - +
99A LYS* 3.4 21.4 - - + +
100A ALA 3.1 0.4 - - - -
101A LEU* 1.3 77.6 - - - +
103A TYR* 1.3 64.2 + - + +
105A ALA* 3.2 15.9 + - - +
106A GLN* 3.2 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU* 3.7 20.1 - - + +
80A GLU* 3.6 56.0 + - + +
81A ALA* 3.7 22.7 - - + -
84A ALA* 3.9 10.1 - - + -
99A LYS* 3.2 51.3 + - - -
100A ALA 3.3 4.0 + - - +
102A ASP* 1.3 77.9 - - + +
104A ILE* 1.3 65.8 + - - +
106A GLN* 3.0 20.6 + - - +
107A ILE* 2.9 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PRO* 4.3 11.8 - - + +
14A ALA* 4.0 20.9 - - + +
15A ARG* 4.1 30.1 - - + +
18A ALA* 3.6 31.0 - - + -
55A LEU* 4.1 25.6 - - + -
81A ALA* 5.0 1.6 - - + +
85A LEU* 4.9 7.6 - - + -
100A ALA* 3.0 18.0 + - + +
101A LEU* 3.7 7.2 - - - +
103A TYR* 1.3 75.8 - - - +
105A ALA* 1.3 53.2 + - - +
107A ILE* 3.3 8.0 + - - +
108A ASP* 2.7 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU 3.1 14.3 + - - +
102A ASP* 3.4 12.3 - - - +
103A TYR 3.2 0.4 - - - -
104A ILE* 1.3 79.4 - - - +
106A GLN* 1.3 57.0 + - + +
108A ASP* 3.6 7.5 - - - +
109A LYS* 3.1 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU* 3.4 31.6 - - + +
102A ASP* 3.4 17.6 - - - +
103A TYR* 3.0 23.2 + - - +
105A ALA* 1.3 77.0 - - + +
107A ILE* 1.3 64.6 + - - +
109A LYS* 3.3 9.9 + - - +
110A ILE* 3.2 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PRO* 5.2 2.2 - - + -
55A LEU* 4.1 17.9 - - + -
58A LEU* 4.4 18.6 - - + -
63A PHE* 4.3 23.1 - - + -
74A LEU* 5.0 1.3 - - + -
77A LEU* 3.6 23.1 - - + +
78A VAL* 3.9 25.4 - - + -
81A ALA* 3.7 29.6 - - + -
103A TYR 2.9 17.1 + - - +
104A ILE* 3.7 6.5 - - + +
106A GLN* 1.3 75.4 - - - +
108A ASP* 1.3 58.2 + - - +
110A ILE* 3.2 5.5 + - - +
111A PHE* 2.8 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASP* 4.5 1.0 - - - +
11A PRO* 3.2 27.4 - - + +
12A ALA 4.5 4.0 + - - -
15A ARG* 4.9 11.8 + - - -
104A ILE* 2.7 23.3 + - + +
105A ALA* 3.6 10.7 - - - +
106A GLN 3.2 0.2 - - - -
107A ILE* 1.3 73.2 - - - +
109A LYS* 1.3 62.5 + - - +
111A PHE* 3.1 6.7 + - - +
112A TRP* 3.0 57.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ALA 3.1 14.4 + - - +
106A GLN* 3.4 13.5 - - - +
107A ILE 3.2 0.2 - - - -
108A ASP* 1.3 78.6 + - - +
110A ILE* 1.3 64.9 + - + +
112A TRP* 3.5 5.1 + - - +
113A GLU* 3.1 49.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PHE* 4.2 19.3 - - + -
71A TYR* 3.9 40.6 - - + -
73A GLU* 4.0 22.2 - - + +
74A LEU* 4.2 14.1 - - + -
77A LEU* 3.9 27.1 - - + -
106A GLN 3.2 6.0 + - - +
107A ILE* 3.2 8.8 + - - +
109A LYS* 1.3 75.8 - - + +
111A PHE* 1.3 67.7 + - - +
113A GLU* 3.2 12.0 + - - +
114A THR* 3.1 21.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR* 3.5 35.2 - - + -
11A PRO* 3.3 33.4 - - + -
58A LEU* 4.1 7.9 - - + -
62A TYR* 3.6 43.5 - + - -
63A PHE* 4.2 11.4 - + + -
107A ILE* 2.8 14.1 + - + +
108A ASP 3.1 8.3 + - - +
110A ILE* 1.3 75.8 - - - +
112A TRP* 1.3 94.2 + + - +
114A THR* 2.4 25.3 + - - -
115A LYS* 3.2 31.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR 5.3 2.5 - - - -
10A ASP* 4.0 23.7 + - - -
108A ASP* 3.0 52.8 + - - +
109A LYS* 4.1 4.5 - - - +
111A PHE* 1.3 94.7 - + - +
113A GLU* 1.3 64.5 + - - +
115A LYS* 3.1 40.9 + - + +
116A LYS* 3.2 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A TYR* 2.7 44.1 + - - +
109A LYS* 3.1 46.5 + - + +
110A ILE* 3.2 9.4 + - - +
112A TRP* 1.3 76.8 - - - +
114A THR* 1.3 61.4 + - - +
116A LYS* 3.1 31.2 + - + +
117A ALA* 3.3 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A TYR* 2.8 28.7 + - - -
63A PHE* 4.1 13.2 - - + -
67A HIS* 3.7 33.9 + - + -
71A TYR* 4.0 20.9 - - + -
110A ILE 3.2 13.0 - - - +
111A PHE 2.4 24.3 + - - -
113A GLU* 1.3 76.9 - - - +
115A LYS* 1.3 56.2 + - - +
117A ALA* 2.8 27.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLY 4.9 9.9 + - - -
9A TYR* 5.5 4.9 + - - +
62A TYR* 3.2 29.2 + - - +
111A PHE* 3.2 34.9 - - + +
112A TRP* 3.3 39.5 - - + +
113A GLU 3.1 0.4 - - - -
114A THR* 1.3 79.1 - - - +
116A LYS* 1.3 60.9 + - + +
117A ALA* 3.2 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A TRP* 3.3 24.1 - - - +
113A GLU* 3.1 22.4 + - + +
115A LYS* 1.3 77.8 - - + +
117A ALA* 1.3 58.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A HIS* 5.4 2.8 + - - -
113A GLU 3.3 12.9 + - - +
114A THR* 2.8 22.6 - - - +
115A LYS 3.2 2.4 - - - -
116A LYS* 1.3 82.3 - - - +
----------------------------------------------------------
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