Contacts of the helix formed by residues 79 - 100 (chain B) in PDB entry 2Q7M
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 79 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B GLY 3.8 0.2 - - - -
78B CYS* 1.3 90.2 - - - +
80B GLN* 1.3 57.6 + - - +
81B VAL* 3.1 9.2 - - - -
82B PRO* 2.8 46.7 - - - +
83B ALA* 3.2 10.9 - - - +
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Residues in contact with GLN 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLY 3.6 4.3 + - - +
8B ASN* 3.2 33.9 - - + +
9B VAL 2.8 22.2 - - - +
10B VAL 3.1 1.0 - - - +
11B LEU* 2.8 53.0 - - - +
12B LEU* 3.6 19.9 - - + +
75B GLY 3.5 17.3 + - - +
79B SER* 1.3 71.2 - - - +
81B VAL* 1.3 62.2 + - + +
84B ALA* 3.2 23.8 + - - +
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 4.5 11.9 - - + -
79B SER* 4.4 6.1 - - - -
80B GLN* 1.3 81.3 - - + +
82B PRO* 1.3 81.2 - - + +
83B ALA 3.2 0.9 - - - -
84B ALA* 3.2 3.9 + - - +
85B PHE* 2.9 23.0 + - + +
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Residues in contact with PRO 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B SER* 2.8 42.4 - - - +
81B VAL* 1.3 104.3 - - + +
83B ALA* 1.3 67.0 + - - +
85B PHE* 3.0 7.2 + - + -
86B ALA* 2.8 28.9 + - - +
121B PHE* 4.3 8.4 - - + -
125B MET* 3.6 18.4 - - - -
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 4.1 2.0 - - + -
71B LEU* 3.1 19.0 - - - +
74B ALA 2.9 30.7 - - - +
75B GLY* 3.4 15.0 - - - +
79B SER 3.2 9.9 - - - +
82B PRO* 1.3 82.1 - - - +
84B ALA* 1.3 56.4 - - - +
87B GLY 3.1 21.5 + - - -
122B LEU* 3.7 5.4 - - + +
125B MET* 3.0 16.5 - - + +
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Residues in contact with ALA 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 3.4 33.2 - - + +
12B LEU* 3.6 13.0 - - + +
15B VAL* 4.1 9.1 - - + +
71B LEU* 4.3 4.5 - - - -
80B GLN 3.2 20.3 + - - +
81B VAL 3.2 4.3 + - - +
82B PRO 3.2 0.4 - - - -
83B ALA* 1.3 78.6 - - - +
85B PHE* 1.3 61.7 + - - +
87B GLY* 3.7 1.6 + - - -
88B LEU* 3.2 18.9 + - - +
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Residues in contact with PHE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B VAL* 2.9 16.8 + - + +
82B PRO* 3.7 7.0 - - + +
84B ALA* 1.3 73.0 - - - +
86B ALA* 1.3 60.4 + - - +
87B GLY 3.0 1.3 - - - -
88B LEU* 2.6 38.6 + - + +
89B MET* 3.0 38.3 + - + +
142F ASP* 5.1 15.3 - - + -
144F GLU* 4.0 32.1 - - + -
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PRO 2.8 12.3 + - - +
85B PHE* 1.3 74.0 - - - +
87B GLY* 1.3 60.5 + - - +
89B MET* 3.2 9.1 + - - -
90B TYR* 3.1 3.3 + - - +
118B ILE* 2.8 34.6 - - + +
121B PHE* 3.0 43.5 - - + -
122B LEU* 3.9 13.0 - - + -
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Residues in contact with GLY 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B VAL* 3.8 7.0 - - - -
67B PHE* 3.5 25.4 - - - -
71B LEU* 4.0 9.0 - - - -
83B ALA 3.1 17.3 + - - -
84B ALA 3.9 2.2 - - - -
85B PHE 3.0 1.0 - - - -
86B ALA* 1.3 76.0 - - - +
88B LEU* 1.3 58.4 + - - +
90B TYR* 3.5 12.6 - - - +
91B LEU* 3.2 17.0 - - - +
122B LEU* 4.1 2.9 - - - +
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 4.4 4.0 - - + -
18B ILE* 5.5 5.4 - - + -
84B ALA 3.2 13.6 + - - +
85B PHE* 2.6 30.7 + - + +
87B GLY* 1.3 70.7 - - - +
89B MET* 1.3 81.6 + - - +
91B LEU* 2.9 34.4 + - + +
92B PHE* 3.3 35.4 + - + -
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Residues in contact with MET 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B PHE* 3.0 46.4 + - + +
86B ALA* 3.9 7.6 - - - +
88B LEU* 1.3 83.2 - - - +
90B TYR* 1.3 55.7 + - - +
92B PHE* 2.6 47.3 + - + +
93B VAL* 2.8 20.1 + - + +
118B ILE* 3.0 19.5 - - + -
143F PHE* 6.4 2.5 - - + -
144F GLU* 5.7 7.2 - - - -
145F ASN 6.3 0.2 - - - +
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Residues in contact with TYR 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ALA* 2.9 39.3 + - + +
67B PHE* 3.3 53.2 - + + -
86B ALA 3.1 0.9 + - - +
87B GLY 3.5 10.5 - - - +
89B MET* 1.3 76.3 - - - +
91B LEU* 1.3 60.4 + - + +
93B VAL* 3.8 4.8 - - + +
94B ARG* 3.0 54.5 + - + +
114B PHE* 3.6 17.9 - + - -
115B GLY* 5.0 8.3 - - - -
118B ILE* 2.9 38.4 - - + +
119B ILE* 4.2 10.5 - - + -
501C 2CS 5.8 4.0 - - - -
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 3.4 26.5 - - + +
18B ILE* 3.5 28.5 - - + -
19B SER* 3.4 27.8 - - - -
22B GLN* 3.4 27.3 + - + +
67B PHE* 4.1 4.7 - - + -
87B GLY 3.2 20.4 + - - +
88B LEU* 2.9 20.4 + - + +
90B TYR* 1.3 93.1 - - + +
92B PHE* 1.3 64.2 + - + +
94B ARG* 4.0 1.6 - - - +
95B GLN* 3.4 17.3 + - - +
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Residues in contact with PHE 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 3.3 35.9 + - + -
89B MET* 2.6 40.8 + - + +
91B LEU* 1.3 75.0 - - + +
93B VAL* 1.3 64.3 + - + +
94B ARG 3.2 0.2 - - - -
95B GLN* 3.1 5.5 + - + -
96B LYS* 2.9 37.9 + - + +
145F ASN* 5.4 9.6 - - - -
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Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B MET* 2.8 24.0 + - + +
90B TYR* 3.8 9.2 - - + +
92B PHE* 1.3 74.3 - - + +
94B ARG* 1.3 52.4 + - - +
96B LYS* 3.1 6.7 + - + +
97B TYR* 2.7 40.5 + - + +
114B PHE* 4.6 12.1 - - + -
115B GLY* 4.3 27.8 - - - +
118B ILE* 4.5 8.1 - - + -
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Residues in contact with ARG 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B SER* 3.9 6.1 + - - -
22B GLN* 2.7 35.1 + - - +
23B ASN* 2.3 33.7 + - - -
26B PHE* 3.6 9.9 - - - -
60B CYS* 3.2 50.5 + - - -
64B TYR* 3.5 33.3 - - - +
90B TYR* 3.0 37.8 + - + +
91B LEU 4.0 0.7 - - - +
93B VAL* 1.3 76.3 - - - +
95B GLN* 1.3 57.1 + - - +
97B TYR* 4.0 3.0 - - - +
98B PHE* 2.9 34.3 + - - +
114B PHE* 3.4 27.6 - - + -
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Residues in contact with GLN 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B GLN* 2.9 22.5 + - - +
25B PHE* 3.5 27.2 - - - -
26B PHE* 2.9 16.2 - - - -
91B LEU 3.4 11.2 + - - +
92B PHE* 3.1 11.8 + - + +
94B ARG* 1.3 80.1 - - - +
96B LYS* 1.3 78.6 + - + +
97B TYR 3.2 0.4 - - - -
98B PHE* 3.8 1.8 - - - -
99B VAL* 3.0 47.9 + - + +
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Residues in contact with LYS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B PHE* 2.9 26.4 + - + +
93B VAL* 3.5 6.7 - - + +
95B GLN* 1.3 96.0 - - - +
97B TYR* 1.3 58.5 + - - +
99B VAL* 3.9 17.4 - - + +
100B GLY* 3.5 14.9 + - - -
109B THR* 5.3 0.9 + - - +
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Residues in contact with TYR 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ALA 4.0 7.6 - - - -
59B ASN* 2.8 37.5 + - + +
60B CYS* 3.5 29.6 - - - -
93B VAL* 2.7 23.7 + - + +
94B ARG* 4.2 1.8 - - - -
96B LYS* 1.3 72.7 - - - +
98B PHE* 1.3 61.9 + - - +
99B VAL 2.9 8.2 + - - -
100B GLY 3.5 0.3 + - - -
101B TYR* 3.1 38.2 + + - +
109B THR* 3.3 33.6 + - + -
111B GLY 3.1 24.1 + - - -
112B TYR 3.5 2.9 + - - -
113B ILE 4.8 1.6 - - - -
114B PHE* 3.8 42.8 - + + -
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Residues in contact with PHE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B PHE* 4.3 14.8 - + - -
26B PHE* 3.4 66.9 - + + -
29B LYS* 4.3 16.2 - - + -
53B VAL* 4.1 13.9 - - + -
56B ALA* 3.6 26.0 - - + +
57B ASN* 3.4 30.5 - - + -
60B CYS* 4.2 3.6 - - - -
94B ARG 2.9 19.7 + - - +
95B GLN* 4.1 3.4 - - - +
97B TYR* 1.3 79.3 - - - +
99B VAL* 1.3 60.8 + - + +
101B TYR* 4.1 12.3 + - - +
102B LEU* 4.6 1.2 + - - +
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PHE* 6.1 0.7 - - + -
95B GLN* 3.0 38.7 + - + +
96B LYS* 4.1 17.7 - - + +
97B TYR 2.9 0.4 - - - -
98B PHE* 1.3 78.1 - - + +
100B GLY* 1.3 63.3 + - - +
101B TYR 3.0 3.8 - - - -
102B LEU* 2.9 32.2 + - - +
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Residues in contact with GLY 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B LYS 3.5 8.5 + - - -
97B TYR 3.5 2.6 + - - -
99B VAL* 1.3 80.4 - - - +
101B TYR* 1.3 56.1 + - - +
102B LEU* 2.9 12.3 + - - +
103B GLY 4.1 3.5 + - - +
108B SER* 3.7 15.6 - - - -
109B THR* 3.2 14.9 + - - -
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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) + - + + + + + -
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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