Contacts of the helix formed by residues 175 - 184 (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 CYS 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A TYR* 4.9 0.4 - - - -
93A ILE* 3.6 24.1 - - + +
96A ILE* 4.2 15.7 - - - -
102A LEU* 3.5 32.8 - - + -
103A THR 5.7 0.2 - - - +
106A ASP* 3.0 19.4 + - - +
107A ILE 4.0 3.4 - - - -
108A VAL* 3.8 31.9 - - - -
173A PHE 3.5 1.6 + - - -
174A ARG* 1.3 70.2 - - - +
176A LYS* 1.3 62.7 + - - +
178A PHE 3.3 1.9 + - - -
179A MET* 3.1 27.2 + - - +
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Residues in contact with LYS 176 (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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102A LEU* 4.7 9.3 - - + +
103A THR 4.5 6.1 + - - +
104A PRO* 3.9 44.2 - - + +
106A ASP 4.8 0.8 + - - -
174A ARG* 3.3 0.8 - - - +
175A CYS* 1.3 77.7 - - - +
177A ASP* 1.3 62.6 + - - +
179A MET* 3.2 8.0 + - + +
180A ASP* 2.8 65.2 + - - +
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Residues in contact with ASP 177 (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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104A PRO 5.0 1.9 - - - +
134A ASP* 4.5 9.7 - - - +
174A ARG* 3.2 43.0 + - + +
176A LYS* 1.3 82.0 - - - +
178A PHE* 1.3 61.9 + - - +
180A ASP* 3.5 3.6 + - - +
181A LEU* 3.1 29.1 + - - +
200A PHE* 3.8 19.4 - - + -
1236A 1PE 3.7 41.0 - - - +
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Residues in contact with PHE 178 (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* 3.6 39.9 - - - -
89A ILE* 3.7 18.8 - - + -
90A LYS* 3.8 16.2 - - + -
93A ILE* 3.5 15.9 - - + -
173A PHE* 3.6 37.9 - + + -
174A ARG 3.1 6.7 + - - -
175A CYS 3.7 6.3 - - - +
177A ASP* 1.3 75.7 - - - +
179A MET* 1.3 62.7 + - - +
181A LEU* 4.1 1.3 - - + +
182A TYR* 2.9 60.7 + + + +
196A ALA* 4.0 9.9 - - + -
199A ILE* 4.4 11.2 - - + -
200A PHE* 3.7 19.5 - + + -
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Residues in contact with MET 179 (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* 4.0 33.9 - - + -
93A ILE* 3.6 32.5 - - + -
94A GLU* 4.1 20.9 - - + +
102A LEU* 5.2 3.4 - - + -
175A CYS 3.1 16.6 + - - +
176A LYS* 3.2 9.4 + - - +
178A PHE* 1.3 78.7 - - - +
180A ASP* 1.3 61.2 + - - +
182A TYR* 4.1 3.4 - - - +
183A GLY* 2.9 28.6 + - - -
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Residues in contact with ASP 180 (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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176A LYS* 2.8 56.6 + - - +
177A ASP* 3.9 5.8 + - - +
179A MET* 1.3 77.6 - - - +
181A LEU* 1.3 61.4 + - - +
183A GLY* 3.9 1.2 - - - -
184A SER* 3.4 19.9 + - - -
1236A 1PE 4.4 22.0 - - - +
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Residues in contact with LEU 181 (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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177A ASP 3.1 14.2 + - - +
178A PHE* 4.1 2.7 - - - +
180A ASP* 1.3 72.6 - - - +
182A TYR* 1.3 65.9 + - - +
184A SER* 2.7 24.6 + - - +
185A LEU* 3.6 9.4 - - - +
199A ILE* 3.8 15.3 - - + +
200A PHE* 3.8 52.0 - - + +
203A LYS* 3.8 25.4 - - + -
205A LYS* 4.1 11.2 - - + -
1236A 1PE 3.3 41.3 - - - +
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Residues in contact with TYR 182 (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* 4.4 1.6 + - - -
86A ASN* 3.5 25.2 - - + +
87A THR* 3.3 25.8 + - - +
90A LYS* 4.1 32.3 - - + -
178A PHE* 2.9 44.1 + + + +
179A MET* 4.1 3.6 - - - +
181A LEU* 1.3 76.6 - - - +
183A GLY* 1.3 63.8 + - - +
184A SER 3.2 1.4 + - - -
185A LEU* 3.2 17.1 + - + +
190A LYS* 3.2 66.5 + - + +
199A ILE* 3.9 21.4 - - + +
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Residues in contact with GLY 183 (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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179A MET 2.9 18.8 + - - -
180A ASP* 3.9 2.5 - - - -
181A LEU 3.2 0.2 - - - -
182A TYR* 1.3 79.9 - - - +
184A SER* 1.3 58.4 + - - +
185A LEU 3.2 6.6 + - - +
190A LYS* 5.1 4.7 + - - -
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Residues in contact with SER 184 (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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180A ASP 3.4 11.2 + - - -
181A LEU* 2.7 21.3 + - - +
182A TYR 3.1 0.4 - - - -
183A GLY* 1.3 75.9 - - - +
185A LEU* 1.3 59.8 + - - +
186A SER 4.1 0.5 + - - -
189A GLU* 4.1 4.7 - - - +
203A LYS* 3.1 30.6 + - - -
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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