Contacts of the helix formed by residues 91 - 102 (chain A) in PDB entry 2VWK
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 GLN 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A TYR* 3.5 19.6 + - - +
9A THR* 4.7 2.3 + - - +
58A ARG* 3.6 35.7 + - - +
89A HIS* 2.8 33.6 + - - +
90A PRO* 1.3 73.3 - - - +
92A ASP* 1.3 59.9 + - - +
93A GLN 3.2 1.8 - - - -
94A PRO* 3.2 20.2 - - - +
95A ALA* 4.5 3.5 + - - +
1777A SO4 4.2 6.7 + - - +
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Residues in contact with ASP 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ARG* 2.8 35.1 + - - +
63A VAL* 3.4 32.2 - - + +
64A ARG 5.3 2.8 + - - +
87A PHE* 4.6 13.8 - - + +
88A THR* 3.9 11.8 + - - -
89A HIS* 2.8 35.8 + - - +
91A GLN* 1.3 77.4 - - - +
93A GLN* 1.3 62.5 + - - +
94A PRO 3.5 0.2 - - - -
95A ALA* 3.5 4.5 + - - +
96A ILE* 3.2 26.2 + - - +
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Residues in contact with GLN 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PRO* 3.4 24.3 - - - +
37A TYR 3.8 10.0 + - - +
38A ILE* 3.6 22.9 - - + +
87A PHE* 4.1 19.7 - - + -
89A HIS 4.5 1.1 - - - +
90A PRO* 3.4 22.3 + - + +
91A GLN 3.2 0.2 - - - -
92A ASP* 1.3 76.1 - - - +
94A PRO* 1.3 61.7 - - + +
96A ILE* 3.5 7.2 - - - +
97A ARG* 2.7 33.7 + - - +
111A GLU 4.5 1.0 + - - -
112A TYR* 2.7 42.5 + - + +
114A ILE 5.3 5.2 + - - +
116A PHE* 5.7 0.5 - - - -
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Residues in contact with PRO 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A PRO 3.9 3.8 - - - +
91A GLN* 3.2 22.4 - - - +
93A GLN* 1.3 93.0 - - + +
95A ALA* 1.3 61.9 + - - +
97A ARG* 3.2 20.2 + - + +
98A ASP* 3.5 13.7 + - - +
112A TYR 5.8 2.7 - - - +
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Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ALA* 3.6 20.7 - - + +
57A GLU 4.6 12.6 - - - +
58A ARG* 4.9 9.6 - - + -
63A VAL* 4.7 6.7 - - + -
91A GLN 4.5 4.9 + - - +
92A ASP 3.5 9.4 + - - +
93A GLN 3.3 0.6 - - - -
94A PRO* 1.3 81.3 - - - +
96A ILE* 1.3 59.5 + - - +
98A ASP* 4.3 8.2 + - - +
99A LYS* 4.4 7.6 + - - +
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Residues in contact with ILE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ILE* 5.9 0.4 - - + -
54A ILE* 3.8 28.3 - - + +
55A THR* 4.3 1.8 - - - -
56A ALA* 4.2 11.2 - - + +
63A VAL* 3.5 29.4 - - + +
64A ARG 4.1 2.9 - - - -
65A VAL* 4.0 21.5 - - + +
87A PHE* 3.3 29.6 - - + -
92A ASP* 3.2 17.7 + - + +
93A GLN* 3.5 4.7 - - - +
95A ALA* 1.3 77.2 - - - +
97A ARG* 1.3 67.9 + - - +
98A ASP 3.3 0.7 - - - -
99A LYS* 3.4 3.4 + - + +
100A ILE* 3.1 33.4 + - + +
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Residues in contact with ARG 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ILE* 5.3 5.2 - - + -
93A GLN 2.7 20.0 + - - +
94A PRO* 3.2 11.4 + - + +
96A ILE* 1.3 78.3 - - - +
98A ASP* 1.3 66.1 + - - +
99A LYS 3.4 0.3 + - - -
100A ILE* 3.5 5.8 + - - +
101A LYS* 3.0 26.5 + - - +
109A ILE* 3.8 24.9 - - + +
112A TYR* 5.3 10.1 - - + -
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Residues in contact with ASP 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A PRO 3.5 11.7 + - - +
95A ALA* 4.4 6.0 - - - +
97A ARG* 1.3 82.8 - - - +
99A LYS* 1.3 63.3 + - + +
101A LYS* 3.6 5.8 + - - +
102A GLU* 3.4 28.5 + - - +
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Residues in contact with LYS 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ILE* 3.9 18.2 - - + +
55A THR* 2.8 31.7 + - - +
56A ALA* 3.8 19.7 - - + +
57A GLU* 5.3 1.2 - - - +
95A ALA 4.4 5.4 + - - +
96A ILE* 3.4 10.1 + - - +
97A ARG 3.3 0.6 - - - -
98A ASP* 1.3 77.6 - - + +
100A ILE* 1.3 66.2 + - - +
102A GLU* 3.0 20.9 + - - +
103A HIS* 3.6 4.7 + - - +
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Residues in contact with ILE 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ILE* 4.7 5.6 - - + -
40A ALA* 4.9 1.8 - - + -
51A VAL* 4.4 14.8 - - + -
54A ILE* 3.9 28.3 - - + -
65A VAL* 4.2 12.3 - - + -
85A LEU* 4.0 24.9 - - + -
87A PHE* 4.6 3.8 - - + -
96A ILE* 3.1 37.8 + - + +
97A ARG* 4.0 3.1 - - - +
99A LYS* 1.3 74.2 - - - +
101A LYS* 1.3 62.5 + - - +
103A HIS* 3.2 19.1 + - - +
106A VAL* 3.4 22.2 - - + +
109A ILE* 4.3 17.3 - - + -
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Residues in contact with LYS 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ARG 3.0 18.9 + - - +
98A ASP* 3.8 7.2 - - - +
99A LYS 3.2 0.2 - - - -
100A ILE* 1.3 77.3 - - - +
102A GLU* 1.3 65.8 + - - +
103A HIS 3.3 5.9 + - - +
106A VAL* 4.3 16.2 - - - +
108A ASP* 6.3 1.3 - - - -
109A ILE* 4.9 16.3 - - + +
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Residues in contact with GLU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ASP* 3.4 18.4 + - - +
99A LYS* 3.0 11.3 + - - +
101A LYS* 1.3 80.0 - - - +
103A HIS* 1.3 63.2 + - - +
104A PRO* 3.3 8.7 - - - +
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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