Contacts of the helix formed by residues 84 - 100 (chain B) in PDB entry 2VSH
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 84 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82B GLY 4.6 0.9 - - - -
83B ALA* 1.3 79.5 - - - +
85B ARG* 1.3 65.8 + - + +
86B ASN* 3.3 9.0 + - - +
87B THR* 2.6 43.0 + - - -
88B SER* 3.1 24.0 + - - -
182B TYR* 4.3 2.2 + - - -
190B LYS* 4.9 10.7 - - - +
191B GLU* 4.5 11.5 - - - +
194B THR 6.0 0.4 - - - +
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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
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7B LEU* 4.0 28.3 - - + +
84B ASP* 1.3 76.5 - - + +
86B ASN* 1.3 61.4 + - - +
88B SER* 3.5 8.4 + - - -
89B ILE* 3.0 38.7 + - + +
110B THR* 5.1 3.4 + - - -
112B ASP* 3.2 30.7 + - - -
169B THR* 3.7 18.1 - - - +
171B GLN* 4.5 9.7 + - - -
194B THR* 3.2 28.5 - - - +
195B ASP* 4.1 17.0 - - - +
218B LYS* 4.7 9.3 - - - +
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Residues in contact with ASN 86 (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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84B ASP* 3.2 8.5 + - - +
85B ARG* 1.3 78.6 - - - +
87B THR* 1.3 58.5 + - - +
89B ILE* 3.3 15.1 + - - +
90B LYS* 3.0 25.8 + - - +
178B PHE* 3.6 12.5 - - - -
182B TYR* 3.6 23.1 - - + -
190B LYS* 4.9 3.5 + - - +
193B LEU 2.9 28.5 + - - -
194B THR* 3.8 14.2 + - - +
195B ASP* 3.8 2.5 - - - -
196B ALA 3.6 17.5 + - - -
199B ILE* 3.3 22.1 - - - +
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Residues in contact with THR 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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82B GLY* 4.1 16.6 - - - -
83B ALA* 4.1 8.1 + - + +
84B ASP* 2.6 32.0 + - - -
86B ASN* 1.3 75.0 - - - +
88B SER* 1.3 59.2 + - - +
90B LYS* 3.2 14.5 + - + +
91B ASN* 2.8 43.2 + - - +
182B TYR* 3.4 15.4 + - - +
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Residues in contact with SER 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.7 17.7 - - - -
9B GLY 4.1 10.5 - - - -
52B GLY* 5.5 1.6 - - - -
81B GLY* 3.7 10.6 - - - -
82B GLY 2.7 30.8 + - - +
84B ASP 3.1 13.9 + - - -
85B ARG* 3.6 11.4 - - - -
87B THR* 1.3 73.9 - - - +
89B ILE* 1.3 60.4 + - - +
91B ASN* 3.3 2.4 + - - +
92B ILE* 2.9 35.8 + - - +
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Residues in contact with ILE 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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7B LEU* 4.0 17.3 - - + -
85B ARG* 3.0 29.6 + - + +
86B ASN* 3.6 25.1 - - - +
87B THR 3.3 0.2 - - - -
88B SER* 1.3 72.4 - - - +
90B LYS* 1.3 64.2 + - - +
92B ILE* 3.2 10.1 + - + +
93B ILE* 2.9 37.1 + - + +
108B VAL* 5.0 0.7 - - + -
110B THR* 4.1 25.6 - - + +
171B GLN* 5.6 0.7 - - - +
173B PHE* 4.0 12.8 - - + -
178B PHE* 3.8 20.9 - - + -
196B ALA* 4.2 18.8 - - + +
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Residues in contact with LYS 90 (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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86B ASN 3.0 14.0 + - - +
87B THR* 3.2 17.5 + - + +
89B ILE* 1.3 76.9 - - - +
91B ASN* 1.3 65.0 + - - +
93B ILE* 3.3 2.8 + - - +
94B GLU* 3.0 52.4 + - + +
178B PHE* 4.0 0.8 - - + -
179B MET* 3.7 33.8 - - + +
182B TYR* 4.1 20.6 - - + -
190B LYS* 6.1 0.7 - - - +
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Residues in contact with ASN 91 (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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79B THR* 4.3 5.5 + - + +
80B LYS* 3.0 31.6 + - - +
81B GLY* 3.3 20.3 + - - -
82B GLY* 3.7 5.3 - - - +
87B THR* 2.8 29.5 + - - +
88B SER* 3.7 6.3 - - - +
89B ILE 3.3 0.2 - - - -
90B LYS* 1.3 78.2 - - - +
92B ILE* 1.3 60.4 + - - +
94B GLU* 3.4 8.2 + - - +
95B ALA* 2.9 29.2 + - - +
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Residues in contact with ILE 92 (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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5B GLY* 4.0 23.6 - - - -
6B ILE 3.9 16.4 - - - +
7B LEU* 3.6 26.0 - - + -
50B VAL* 3.8 30.0 - - + +
52B GLY* 4.0 14.4 - - - +
79B THR* 4.3 4.9 - - + -
88B SER 2.9 20.9 + - - +
89B ILE* 3.2 8.9 + - + +
91B ASN* 1.3 76.6 - - + +
93B ILE* 1.3 59.0 + - + +
95B ALA* 3.1 5.2 + - - +
96B ILE* 2.8 42.1 + - + +
108B VAL* 4.4 6.7 - - + -
110B THR* 5.9 1.6 - - + -
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Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ILE* 2.9 27.1 + - + +
90B LYS 3.8 3.6 - - - +
92B ILE* 1.3 76.4 - - + +
94B GLU* 1.3 58.1 + - + +
96B ILE* 3.3 10.7 + - + +
97B ASP* 2.9 27.6 + - - +
102B LEU* 3.6 23.2 - - + +
108B VAL* 4.4 10.8 - - + -
175B CYS* 3.7 35.0 - - + +
178B PHE* 3.7 33.2 - - + -
179B MET* 3.6 25.1 - - + -
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Residues in contact with GLU 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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90B LYS* 3.0 44.6 + - + +
91B ASN* 3.8 7.9 - - - +
93B ILE* 1.3 76.4 - - - +
95B ALA* 1.3 57.6 + - - +
97B ASP* 3.5 13.4 + - - +
98B ALA* 3.0 28.1 + - - +
179B MET* 4.9 9.7 - - - +
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Residues in contact with ALA 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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50B VAL* 4.2 9.2 - - + -
77B ILE* 4.9 10.1 - - + +
79B THR* 3.8 30.3 - - + +
91B ASN 2.9 15.3 + - - +
92B ILE 3.1 9.4 + - - +
94B GLU* 1.3 73.0 - - - +
96B ILE* 1.3 65.5 + - - +
98B ALA* 3.4 7.3 + - - +
99B TYR* 3.1 22.9 + - - +
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Residues in contact with ILE 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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3B TYR* 3.6 58.1 - - + +
50B VAL* 3.8 19.5 - - + -
77B ILE* 5.9 0.7 - - - -
92B ILE* 2.8 34.4 + - + +
93B ILE* 3.4 12.8 - - - +
95B ALA* 1.3 76.1 - - - +
97B ASP* 1.3 57.8 + - - +
99B TYR* 3.0 10.6 + - - +
100B ARG* 2.8 29.8 + - - +
102B LEU* 3.7 20.2 - - + -
108B VAL* 4.2 9.2 - - + -
175B CYS* 4.3 7.9 - - - -
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Residues in contact with ASP 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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93B ILE 2.9 17.1 + - - +
94B GLU* 3.8 17.1 - - - +
96B ILE* 1.3 76.5 - - - +
98B ALA* 1.3 62.2 + - - +
99B TYR 3.5 0.2 + - - -
100B ARG 3.5 17.6 - - - -
101B PRO* 3.6 9.7 - - - +
102B LEU* 2.9 44.8 + - + +
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Residues in contact with ALA 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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94B GLU 3.0 17.4 + - - +
95B ALA* 3.6 8.7 - - - +
96B ILE 3.2 0.2 - - - -
97B ASP* 1.3 76.8 + - - +
99B TYR* 1.3 62.9 - - - +
101B PRO* 5.7 0.3 - - - +
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Residues in contact with TYR 99 (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 TYR* 3.6 28.7 - + - -
47B GLU* 2.4 28.4 + - + -
48B LYS* 3.3 41.1 + - + -
77B ILE* 4.0 22.0 - - + -
95B ALA 3.1 12.9 + - - +
96B ILE* 3.0 8.3 + - - +
98B ALA* 1.3 80.5 - - - +
100B ARG* 1.3 79.5 + - + +
101B PRO* 4.6 1.3 - - - +
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Residues in contact with ARG 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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1B MET* 3.5 37.2 - - - +
3B TYR* 3.5 18.9 + - - +
47B GLU* 4.6 5.9 + - - -
96B ILE* 2.8 21.4 + - - +
97B ASP* 3.5 5.7 - - - +
98B ALA 3.6 0.4 - - - -
99B TYR* 1.3 97.0 + - + +
101B PRO* 1.3 86.3 + - + +
102B LEU* 3.3 3.8 + - - +
103B THR* 6.2 2.2 - - - +
106B ASP* 5.2 2.6 + - - +
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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