Contacts of the helix formed by residues 84 - 100 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A GLY 3.2 1.1 - - - -
83A ALA* 1.3 81.4 - - - +
85A ARG* 1.3 66.9 + - + +
86A ASN* 3.4 8.2 + - - +
87A THR* 2.7 42.7 + - - -
88A SER* 3.1 21.5 + - - -
182A TYR* 4.4 2.0 + - - -
190A LYS* 5.2 10.0 - - - +
191A GLU* 6.1 0.7 - - - -
194A THR* 6.1 6.1 - - + -
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Residues in contact with ARG 85 (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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7A LEU* 3.4 32.0 - - + +
84A ASP* 1.3 74.5 - - + +
86A ASN* 1.3 58.8 + - - +
88A SER* 3.1 10.8 + - - -
89A ILE* 2.9 34.4 + - + +
110A THR* 5.5 0.4 + - - -
112A ASP* 3.0 30.1 + - - -
169A THR* 3.9 17.1 - - - +
171A GLN* 4.4 15.3 - - - +
194A THR* 3.4 30.3 - - - +
195A ASP* 4.9 6.3 + - - +
196A ALA 5.4 1.2 - - - +
218A LYS* 4.3 12.7 - - - +
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Residues in contact with ASN 86 (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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84A ASP* 3.3 8.2 + - - +
85A ARG* 1.3 74.7 - - - +
87A THR* 1.3 61.7 + - - +
89A ILE* 3.3 4.8 + - - +
90A LYS* 3.0 25.6 + - - +
178A PHE* 3.6 16.4 - - + -
182A TYR* 3.5 23.9 - - + -
190A LYS 5.1 2.0 + - - -
193A LEU 3.0 27.1 + - - -
194A THR* 3.2 19.4 + - - +
195A ASP 4.0 0.6 - - - +
196A ALA* 3.6 27.2 + - - +
199A ILE* 3.6 17.2 - - - +
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Residues in contact with THR 87 (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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82A GLY* 3.8 19.7 - - - -
83A ALA* 4.1 7.0 + - + +
84A ASP* 2.7 31.6 + - - -
86A ASN* 1.3 75.4 - - - +
88A SER* 1.3 57.9 + - - +
90A LYS* 3.5 22.1 + - - +
91A ASN* 3.0 32.3 + - - +
182A TYR* 3.3 16.2 + - - +
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Residues in contact with SER 88 (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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7A LEU* 3.5 19.7 - - - -
9A GLY* 5.0 9.0 + - - -
52A GLY* 5.4 3.6 - - - -
81A GLY* 3.6 7.9 - - - -
82A GLY 2.9 30.4 + - - +
84A ASP 3.1 11.2 + - - -
85A ARG* 3.1 12.1 + - - -
87A THR* 1.3 74.7 - - - +
89A ILE* 1.3 60.2 + - - +
91A ASN* 3.2 4.9 + - - +
92A ILE* 2.8 35.8 + - - +
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Residues in contact with ILE 89 (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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7A LEU* 3.7 27.1 - - + -
85A ARG* 2.9 21.8 + - + +
86A ASN* 3.7 26.0 - - - +
87A THR 3.3 0.2 - - - -
88A SER* 1.3 76.0 - - - +
90A LYS* 1.3 58.1 + - - +
92A ILE* 3.1 9.0 + - + +
93A ILE* 2.9 41.8 + - + +
108A VAL* 5.1 0.2 - - + -
110A THR* 4.2 21.3 - - + +
171A GLN* 5.3 1.1 - - - +
173A PHE* 4.0 12.3 - - + -
178A PHE* 3.7 21.1 - - + -
196A ALA* 3.8 18.8 - - + -
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Residues in contact with LYS 90 (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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86A ASN 3.0 16.2 + - - +
87A THR* 3.7 20.9 - - - +
89A ILE* 1.3 75.0 - - - +
91A ASN* 1.3 80.2 + - - +
93A ILE* 3.1 3.5 + - - +
94A GLU* 2.9 49.5 + - - +
178A PHE* 3.8 4.9 - - + -
179A MET* 4.0 32.1 - - + -
182A TYR* 4.1 24.7 - - + -
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Residues in contact with ASN 91 (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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79A THR* 4.2 6.4 + - + +
80A LYS* 2.8 31.3 + - - +
81A GLY* 3.1 21.2 + - - -
82A GLY* 3.7 4.2 - - - +
87A THR* 3.0 19.5 + - - +
88A SER* 3.4 7.0 - - - +
90A LYS* 1.3 101.4 + - - +
92A ILE* 1.3 57.5 + - + +
94A GLU* 3.3 13.2 + - - +
95A ALA* 3.0 27.9 + - - +
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Residues in contact with ILE 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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5A GLY* 3.9 25.1 - - - -
6A ILE 3.7 23.3 - - - +
7A LEU* 3.9 20.0 - - + -
50A VAL* 3.9 29.7 - - + +
52A GLY* 3.9 20.2 - - - +
79A THR* 4.4 4.0 - - + -
88A SER 2.8 16.8 + - - +
89A ILE* 3.4 11.0 - - + +
91A ASN* 1.3 73.0 - - - +
93A ILE* 1.3 60.6 + - + +
95A ALA* 3.2 4.5 + - - +
96A ILE* 2.9 38.5 + - + +
108A VAL* 4.4 6.1 - - + -
110A THR* 6.0 1.1 - - + -
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Residues in contact with ILE 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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89A ILE* 2.9 25.2 + - + +
90A LYS 3.6 6.3 - - - +
92A ILE* 1.3 76.2 - - + +
94A GLU* 1.3 58.1 - - - +
96A ILE* 3.3 10.7 - - + +
97A ASP* 2.8 27.4 - - - -
102A LEU* 3.7 21.3 - - + -
108A VAL* 4.5 9.6 - - + -
175A CYS* 3.6 36.1 - - + +
178A PHE* 3.5 35.9 - - + -
179A MET* 3.6 26.9 - - + -
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Residues in contact with GLU 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 LYS* 2.9 46.9 + - - +
91A ASN* 3.5 16.4 - - - +
93A ILE* 1.3 77.0 + - - +
95A ALA* 1.3 57.1 + - - +
97A ASP* 3.2 9.2 + - - +
98A ALA* 3.0 28.2 + - - +
179A MET* 4.1 17.1 - - + +
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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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50A VAL* 4.0 9.4 - - + -
77A ILE* 4.6 12.8 - - + +
79A THR* 3.9 29.8 - - + +
91A ASN 3.0 13.6 + - - +
92A ILE 3.5 8.1 - - - +
94A GLU* 1.3 71.8 - - - +
96A ILE* 1.3 65.7 + - - +
98A ALA* 3.3 8.6 + - - +
99A TYR* 3.0 22.0 + - - +
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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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3A TYR* 3.4 57.9 - - + +
50A VAL* 3.6 20.6 - - + -
77A ILE* 5.9 0.2 - - - -
92A ILE* 2.9 32.7 + - + +
93A ILE* 3.3 9.9 - - - +
95A ALA* 1.3 76.5 - - - +
97A ASP* 1.3 57.6 + - - +
99A TYR* 3.1 10.0 + - - +
100A ARG 3.0 27.1 + - - +
102A LEU* 3.7 19.5 - - + -
108A VAL* 4.1 10.8 - - + -
175A CYS* 4.2 9.9 - - - -
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Residues in contact with ASP 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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93A ILE* 2.8 19.8 - - + -
94A GLU* 3.2 9.2 + - - +
96A ILE* 1.3 73.4 - - - +
98A ALA* 1.3 60.6 + - - +
100A ARG 3.8 5.2 - - - -
101A PRO* 3.3 27.6 - - - +
102A LEU* 2.7 44.3 + - + +
1234A CA 2.5 30.9 - - - -
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Residues in contact with ALA 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 GLU 3.0 13.8 + - - +
95A ALA* 3.6 11.4 - - - +
96A ILE 3.2 0.2 - - - -
97A ASP* 1.3 75.7 - - - +
99A TYR* 1.3 64.7 + - - +
101A PRO* 5.4 0.2 - - - +
1237A PG4 4.7 6.4 + - - -
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Residues in contact with TYR 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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1A MET* 4.7 1.9 - - + +
3A TYR* 3.6 31.2 - + - -
47A GLU* 2.6 35.6 + - + -
48A LYS* 3.5 33.3 + - + -
77A ILE* 4.1 19.7 - - + -
95A ALA 3.0 13.2 + - - +
96A ILE* 3.1 8.5 + - - +
98A ALA* 1.3 79.7 - - - +
100A ARG* 1.3 73.4 + - + +
1237A PG4 4.3 11.6 + - - -
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Residues in contact with ARG 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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1A MET* 4.6 17.9 - - + +
3A TYR* 4.0 10.6 + - - +
96A ILE* 3.0 15.8 + - - +
97A ASP* 3.3 4.4 - - - +
99A TYR* 1.3 98.5 + - + +
101A PRO* 1.4 79.5 - - + +
102A LEU* 3.2 4.9 + - - +
106A ASP* 5.1 1.4 - - - +
1237A PG4 3.4 46.1 - - - -
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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