Contacts of the helix formed by residues 83 - 95 (chain B) in PDB entry 3W7F
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 83 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A TYR 5.3 0.5 - - - +
10B TYR* 2.6 34.2 + - - -
46B LYS* 3.8 12.4 + - + -
59B PHE* 5.2 4.9 - - + -
80B PHE* 4.8 1.6 - - - -
82B SER* 1.3 84.9 + - - +
84B ARG* 1.3 65.7 + - - +
85B ARG* 2.9 18.5 + - - -
86B ILE* 3.3 29.5 + - + +
87B MET* 3.2 26.8 + - + +
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Residues in contact with ARG 84 (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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3B MET* 6.3 0.4 - - - -
7B ASN* 4.9 11.1 + - - +
77B TYR* 2.3 47.1 + - - -
78B HIS 5.5 1.1 + - - +
80B PHE* 4.2 24.8 + - + +
82B SER 4.2 0.8 - - - -
83B ASP* 1.3 73.0 + - - +
85B ARG* 1.3 69.2 + - + +
87B MET* 4.1 0.2 - - - -
88B MET* 2.7 53.1 + - + +
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Residues in contact with ARG 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLY* 5.5 6.5 - - - -
6B MET* 4.7 6.2 + - - +
7B ASN* 3.4 38.1 - - - +
10B TYR* 2.7 81.8 + - + +
83B ASP* 2.9 10.8 + - - -
84B ARG* 1.3 80.6 - - + +
86B ILE* 1.3 58.7 + - - +
88B MET* 3.2 2.4 + - - +
89B ALA* 2.8 27.2 + - - +
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Residues in contact with ILE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B TYR* 3.8 9.9 - - + -
11B CYS* 4.0 10.8 - - - -
14B ILE* 3.8 10.1 - - + -
39B ALA* 4.3 1.7 - - - +
42B ALA* 3.9 15.7 - - + -
43B VAL* 3.2 42.0 - - + +
46B LYS* 3.3 37.7 - - + -
83B ASP* 3.3 28.8 + - + +
85B ARG* 1.3 74.7 - - - +
87B MET* 1.3 58.2 + - + +
89B ALA* 3.2 2.6 + - - +
90B LEU* 2.7 33.4 + - - +
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Residues in contact with MET 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 4.4 9.0 - - + -
46B LYS* 6.3 1.8 - - + -
63B ILE* 4.0 23.1 - - + -
66B ASP* 3.7 31.2 - - + +
67B ILE* 4.2 11.0 - - - -
70B ILE* 3.5 16.0 - - + +
80B PHE* 3.2 34.1 - - + -
82B SER* 3.5 15.9 - - - +
83B ASP* 3.2 15.7 + - + +
86B ILE* 1.3 88.4 - - + +
88B MET* 1.3 55.8 + - - +
90B LEU* 4.2 7.4 - - - -
91B GLN* 2.6 35.7 + - - +
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Residues in contact with MET 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B MET* 4.0 13.7 - - + +
7B ASN* 3.5 20.2 - - - +
77B TYR* 4.3 17.9 - - + -
78B HIS 5.2 2.0 - - - +
80B PHE* 3.5 15.5 - - + -
84B ARG* 2.7 61.0 + - + +
85B ARG 3.4 3.8 - - - +
87B MET* 1.3 76.5 - - - +
89B ALA* 1.3 57.3 + - - +
91B GLN* 3.3 28.6 - - - +
92B HIS* 2.8 30.8 + - - +
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Residues in contact with ALA 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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4B MET* 4.3 3.2 - - - -
7B ASN* 4.5 5.1 - - + +
8B PHE* 3.6 35.3 - - + -
11B CYS* 3.8 22.7 - - - -
39B ALA* 3.9 5.2 - - + -
85B ARG 2.8 16.6 + - - +
86B ILE 3.6 6.5 - - - +
88B MET* 1.3 72.5 - - - +
90B LEU* 1.3 62.8 + - - +
92B HIS* 3.1 4.2 + - - +
93B VAL* 2.9 25.6 + - - +
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Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ALA* 4.2 8.8 - - + +
40B ILE* 4.6 13.0 - - + -
43B VAL* 4.1 23.3 - - + -
67B ILE* 4.5 15.7 - - + -
70B ILE* 4.1 16.4 - - + -
86B ILE 2.7 20.6 + - - +
87B MET* 3.8 7.2 - - - +
89B ALA* 1.3 73.0 - - - +
91B GLN* 1.3 52.3 - - - +
93B VAL* 3.1 6.0 + - + +
94B ALA* 2.8 32.7 + - + +
99B ILE* 3.8 19.5 - - + -
101B PHE* 4.7 13.0 - - + -
104B PHE* 4.3 28.3 - - + -
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Residues in contact with GLN 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE* 4.0 24.8 - - + +
73B TYR 3.7 0.4 + - - -
74B PRO* 2.6 34.5 + - - +
76B GLU 3.3 27.2 + - - +
77B TYR* 5.3 0.2 - - - -
78B HIS* 3.7 8.1 + - - -
80B PHE* 3.5 12.6 - - - -
87B MET 2.6 22.5 + - - +
88B MET* 3.3 28.9 - - + +
90B LEU* 1.3 70.6 - - - +
92B HIS* 1.3 67.8 + - - +
94B ALA* 3.2 1.9 + - - +
95B GLN* 3.2 37.5 + - + +
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Residues in contact with HIS 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B MET* 3.8 29.4 - - + +
8B PHE* 3.3 31.9 - + + -
35B LYS* 4.8 5.1 + - - -
88B MET 2.8 17.9 + - - +
89B ALA 3.5 3.6 - - - +
91B GLN* 1.3 77.2 - - - +
93B VAL* 1.3 61.7 + - + +
95B GLN* 3.5 18.0 + - - +
96B HIS* 3.0 53.9 + + - -
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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
----------------------------------------------------------
8B PHE* 3.9 15.3 - - + -
36B ALA* 3.8 40.2 - - + -
39B ALA* 4.1 7.0 - - + -
40B ILE* 5.0 5.4 - - + -
89B ALA 2.9 17.8 + - - +
90B LEU* 3.5 9.9 - - + +
92B HIS* 1.3 79.2 - - + +
94B ALA* 1.3 66.1 + - - +
96B HIS* 2.9 17.2 + - - +
97B LYS* 3.0 16.3 + - + +
99B ILE* 3.9 15.0 - - + -
144B ILE* 4.0 16.6 - - + -
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Residues in contact with ALA 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE* 4.0 23.6 - - + +
74B PRO* 5.7 6.0 - - + +
90B LEU 2.8 18.8 + - - +
91B GLN 3.2 5.6 + - - +
93B VAL* 1.3 74.3 - - - +
95B GLN* 1.3 57.5 + - + +
96B HIS 3.2 1.6 + - - -
97B LYS 2.9 19.4 - - - +
99B ILE* 3.5 20.4 - - + +
101B PHE* 4.1 12.3 - - + -
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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
----------------------------------------------------------
74B PRO* 2.9 31.8 + - + +
75B TYR* 3.6 49.4 + - + +
91B GLN* 3.2 25.4 + - - +
92B HIS* 3.7 22.4 + - - +
93B VAL 3.0 1.2 - - - -
94B ALA* 1.3 75.1 - - + +
96B HIS* 1.3 73.5 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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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