Contacts of the strand formed by residues 234 - 239 (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 VAL 234 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94G GLN* 3.5 32.1 - - + +
95G LEU 3.3 3.4 - - - +
96G VAL* 3.7 24.7 - - + -
109G TRP* 4.1 3.8 - - - -
144G PHE* 4.0 3.0 - - + +
145G PHE* 3.8 3.6 - - - -
146G GLN* 3.0 58.5 + - + +
231G GLY 3.9 6.7 - - - +
232G ALA 4.6 0.9 - - - -
233G THR* 1.3 79.9 - - - +
235G LEU* 1.3 60.4 + - - +
236G GLY 3.8 7.6 - - - +
202I ARG* 3.8 21.3 - - - +
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Residues in contact with LEU 235 (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 4.4 0.5 - - - +
94G GLN* 3.7 1.0 - - - -
95G LEU* 2.9 36.2 + - + +
109G TRP* 3.5 28.5 - - + +
133G LEU* 3.8 31.8 - - + +
143G VAL* 3.6 30.3 - - + -
144G PHE 3.6 10.5 - - - +
145G PHE* 4.6 11.9 - - + +
165G LEU* 3.8 15.0 - - + -
212G LEU* 5.0 1.8 - - + +
214G VAL* 3.6 22.2 - - + -
234G VAL* 1.3 73.0 - - - +
236G GLY* 1.3 59.8 + - - +
237G LEU* 6.0 0.9 - - + -
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Residues in contact with GLY 236 (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 3.4 9.4 - - - -
94G GLN* 4.1 5.2 - - - -
143G VAL* 3.7 8.8 - - - +
144G PHE* 3.4 56.3 + - - -
234G VAL* 3.8 2.1 - - - +
235G LEU* 1.3 76.7 - - - +
237G LEU* 1.3 63.3 + - - +
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Residues in contact with LEU 237 (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* 3.2 2.2 - - - -
93G ALA* 2.7 39.9 + - + +
124G LEU* 3.5 32.1 - - + -
133G LEU* 5.2 10.5 - - + -
135G VAL* 4.3 7.4 - - + -
141G TYR* 3.4 36.8 - - + -
142G TYR 3.5 8.1 - - - +
143G VAL* 3.7 23.8 - - + -
144G PHE* 4.0 0.4 - - - -
206G LEU* 4.1 14.6 - - + -
212G LEU* 4.2 10.8 - - + -
235G LEU* 6.0 1.3 - - + -
236G GLY* 1.3 76.1 - - - +
238G PHE* 1.3 68.8 + - - +
203I LEU* 3.3 6.0 - - - +
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Residues in contact with PHE 238 (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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91G MET 4.3 0.7 - - - +
92G PHE* 3.5 22.9 - - + +
141G TYR* 3.3 6.8 - - - -
142G TYR* 2.7 79.0 + + + -
144G PHE* 4.2 4.0 - + - -
237G LEU* 1.3 80.3 - - - +
239G ARG* 1.3 65.0 + - - +
240G VAL* 4.5 9.9 - - + -
142I TYR* 3.8 20.0 - + - -
203I LEU* 4.0 16.4 - - + -
238I PHE* 4.0 29.6 - + - -
240I VAL* 4.5 15.9 - - + -
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Residues in contact with ARG 239 (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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88G ARG* 3.4 43.2 + - + +
91G MET* 3.5 31.8 + - + +
137G LYS* 4.5 4.6 - - - +
138G ALA 3.0 25.5 + - - -
139G GLY* 4.0 5.1 - - - -
140G VAL 3.7 7.0 - - - +
141G TYR* 3.4 33.6 + - + -
238G PHE* 1.3 80.4 - - - +
240G VAL* 1.3 63.1 + - - +
241G THR* 3.0 44.6 + - - +
243G GLU* 3.4 34.1 + - - +
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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