Contacts of the helix formed by residues 89 - 95 (chain B) in PDB entry 3DVA
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 VAL 89 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59B GLU* 3.5 31.4 - - + +
60B SER* 4.1 5.8 - - - +
63B GLY* 3.9 9.9 - - - -
80B ILE* 3.8 29.4 - - + -
85B PHE 4.2 4.0 - - - +
86B VAL* 3.1 14.6 + - - +
88B GLU* 1.3 80.2 - - - +
90B MET* 1.3 61.9 + - - +
91B ASP 3.3 2.9 - - - -
92B SER* 3.5 23.5 + - - +
93B ILE* 3.2 26.7 + - + +
114B ILE* 6.1 0.4 - - + -
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Residues in contact with MET 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 VAL* 3.1 35.2 + - - +
87B TYR* 4.0 13.6 + - + +
88B GLU 3.7 1.8 - - - -
89B VAL* 1.3 77.8 - - - +
91B ASP* 1.3 54.8 + - - +
93B ILE* 4.6 2.5 - - - +
94B CYS* 2.7 66.7 + - - +
135B LEU* 4.8 13.7 - - + -
136B VAL* 4.9 6.3 - - - -
87D TYR* 3.9 38.8 + - + +
90D MET* 4.0 31.6 - - + -
135D LEU* 4.3 8.5 - - + -
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Residues in contact with ASP 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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143A ILE* 3.5 25.8 - - - +
146A ALA* 3.8 6.4 - - - +
180A ASP* 4.8 6.6 - - - +
60B SER* 6.0 2.0 - - - +
89B VAL 3.3 0.8 - - - -
90B MET* 1.3 77.4 - - - +
92B SER* 1.3 61.5 + - - +
95B GLY* 2.7 27.7 + - - +
96B GLN* 2.8 40.3 + - - +
87D TYR* 3.6 29.7 + - + +
88D GLU* 3.2 26.7 - - - +
127D LEU* 4.8 0.2 - - - +
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Residues in contact with SER 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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149A ILE* 3.7 17.8 - - - +
150A GLN* 5.8 0.2 + - - -
60B SER* 3.7 5.1 + - - -
63B GLY* 3.8 15.7 - - - -
64B GLY 3.5 15.1 + - - -
67B ILE* 3.7 7.1 - - - +
89B VAL* 3.5 23.5 + - - +
90B MET 3.4 0.4 - - - -
91B ASP* 1.3 79.7 + - - +
93B ILE* 1.3 57.4 + - - +
96B GLN* 3.4 11.4 - - - +
97B MET* 2.9 36.1 + - - +
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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
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80B ILE* 4.0 7.4 - - + -
83B PHE* 5.2 2.0 - - + -
86B VAL* 3.9 19.3 - - + -
89B VAL* 3.2 39.7 + - + +
90B MET* 3.9 3.1 - - - +
91B ASP 3.1 0.2 - - - -
92B SER* 1.3 79.6 - - - +
94B CYS* 1.3 66.0 + - - +
97B MET* 3.5 7.5 - - + +
98B ALA* 3.2 30.0 + - - +
114B ILE* 3.8 30.5 - - + -
136B VAL* 4.3 3.4 - - + -
142B LEU* 3.9 12.9 - - + +
168B ILE* 3.8 29.6 - - + -
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Residues in contact with CYS 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 MET* 2.7 42.5 + - - +
93B ILE* 1.3 86.1 - - - +
95B GLY* 1.3 58.7 + - - +
96B GLN 3.3 2.0 - - - -
98B ALA* 4.2 0.3 - - - +
99B ARG* 2.8 25.2 + - - +
135B LEU 5.2 1.6 - - - -
136B VAL* 4.3 8.7 - - - -
139B GLN* 3.3 37.6 + - - +
142B LEU* 4.1 3.8 - - - -
87D TYR* 3.7 24.2 - - + +
135D LEU* 6.1 0.9 - - - -
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Residues in contact with GLY 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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90B MET 3.7 0.6 + - - -
91B ASP* 2.7 24.0 + - - -
94B CYS* 1.3 74.7 - - - +
96B GLN* 1.3 59.3 + - - +
99B ARG* 3.7 14.2 - - - -
103B ARG* 2.7 31.9 + - - -
87D TYR* 3.9 16.2 - - - -
127D LEU* 3.9 7.2 - - - +
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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