Contacts of the strand formed by residues 92 - 97 (chain G) in PDB entry 6A3V
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 PHE 92 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88G ARG 4.5 0.4 - - - -
89G GLN* 3.1 32.3 - - + -
91G MET* 1.3 73.9 - - - +
93G ALA* 1.3 66.5 - - - +
119G SER* 3.2 26.0 - - - -
121G THR* 3.1 42.0 + - + +
124G LEU* 3.4 10.2 - - - +
237G LEU 3.2 15.0 - - - +
238G PHE* 3.5 16.8 - - + +
140I VAL* 3.6 30.5 - - + -
203I LEU* 4.5 8.3 - - + -
240I VAL* 3.7 16.4 - - + -
241I THR* 3.6 25.8 - - + -
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Residues in contact with ALA 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G PHE* 1.3 79.7 - - - +
94G GLN* 1.3 61.8 + - - +
95G LEU* 5.1 1.6 - - + -
119G SER* 3.2 14.6 - - - +
120G LEU* 3.7 17.3 - - + -
124G LEU* 3.6 16.8 - - + +
133G LEU* 4.7 13.7 - - + -
235G LEU 4.8 0.4 - - - -
236G GLY* 4.4 0.2 - - - -
237G LEU* 2.7 38.5 + - + +
203I LEU* 3.2 9.4 - - - +
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Residues in contact with GLN 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93G ALA* 1.3 75.8 - - - +
95G LEU* 1.3 71.3 + - - +
117G GLY* 2.7 29.0 + - - +
118G VAL* 3.3 5.1 - - - +
119G SER* 2.6 41.7 + - - +
144G PHE* 3.9 4.7 - - - -
234G VAL* 3.5 30.4 - - + +
235G LEU 3.7 4.7 - - - +
236G GLY* 4.1 0.2 - - - -
202I ARG* 3.4 24.8 - - - +
203I LEU* 2.9 52.1 + - + +
204I LEU* 5.3 0.2 - - - +
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Residues in contact with LEU 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93G ALA* 5.1 0.7 - - + -
94G GLN* 1.3 87.9 - - - +
96G VAL* 1.3 62.8 + - - +
109G TRP* 3.3 38.6 - - + -
110G TYR 3.7 16.8 - - - +
111G SER* 4.5 9.6 - - - -
118G VAL* 5.3 0.2 - - + -
119G SER 4.7 0.4 - - - +
120G LEU* 4.4 23.1 - - + -
126G TYR* 4.0 12.3 - - + -
133G LEU* 4.0 40.6 - - + -
234G VAL* 3.3 7.0 - - - +
235G LEU* 2.9 41.3 + - + +
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Residues in contact with VAL 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G LEU* 1.3 72.6 - - - +
97G ALA* 1.3 74.3 + - - +
109G TRP* 3.4 2.5 - - - -
110G TYR* 2.9 33.1 + - + -
117G GLY* 4.0 20.2 - - - +
118G VAL* 3.6 28.2 - - + +
231G GLY* 3.6 32.3 - - - +
233G THR 3.5 5.4 - - - +
234G VAL* 3.7 20.6 - - + -
64H ILE* 3.9 16.2 - - + -
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Residues in contact with ALA 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96G VAL* 1.3 81.5 - - - +
98G GLN* 1.3 64.0 + - - +
99G ASN 4.6 10.7 - - - +
107G LEU* 4.8 11.0 - - + -
108G SER 3.5 9.2 - - - +
109G TRP* 3.4 15.7 - - + -
110G TYR* 4.0 4.5 - - - -
228G LEU* 5.1 0.7 - - + -
230G GLN* 5.7 2.1 - - - -
231G GLY 5.1 3.3 + - - -
233G THR* 2.9 43.7 + - + +
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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