Contacts of the strand formed by residues 256 - 261 (chain B) in PDB entry 2AVD
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 LEU 256 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90B GLN* 3.7 21.8 - - + +
93B LEU* 4.0 26.7 - - + -
94B LEU* 4.7 8.5 - - + -
209B ALA* 4.2 11.0 - - + -
210B VAL 3.6 14.1 - - - +
211B LEU* 4.0 24.0 - - + -
213B VAL* 3.8 1.9 - - - +
248B SER 3.7 1.0 - - - +
249B LEU* 3.4 2.1 - - - +
250B LEU* 2.7 49.3 + - + +
252B LEU* 3.8 16.4 + - + +
255B GLY* 1.3 73.7 - - - -
257B THR* 1.3 68.1 + - - +
258B LEU* 4.0 14.5 + - + -
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Residues in contact with THR 257 (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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208B LEU 3.6 0.7 - - - +
209B ALA* 3.2 6.6 - - - -
210B VAL* 2.9 43.9 + - + +
213B VAL* 3.6 16.9 - - - +
236B ASN* 4.5 3.3 + - - -
239B ILE* 4.2 33.5 - - + +
247B ILE* 4.9 4.5 - - + -
248B SER 3.5 7.2 - - - +
249B LEU* 3.5 24.1 - - + +
256B LEU* 1.3 74.6 - - - +
258B LEU* 1.3 73.4 + - - +
259B ALA* 4.3 4.5 - - + +
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Residues in contact with LEU 258 (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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93A LEU* 4.7 9.9 - - + -
97A LEU* 5.7 0.2 - - + -
93B LEU* 4.4 4.9 - - + -
94B LEU* 3.7 29.2 - - + -
97B LEU* 3.8 24.9 - - + -
207B ILE* 4.6 6.1 - - + -
208B LEU 3.7 1.6 - - - -
209B ALA* 4.1 7.2 - - + -
246B TYR 4.0 0.7 - - - +
247B ILE* 3.3 5.2 - - - +
248B SER* 2.8 39.6 + - - +
250B LEU* 4.0 23.8 - - + -
256B LEU* 4.2 13.2 - - + -
257B THR* 1.3 79.7 - - - +
259B ALA* 1.3 60.7 + - - +
260B PHE* 3.7 26.7 - - + -
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Residues in contact with ALA 259 (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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195B TYR* 4.5 12.3 - - + -
202B LEU* 5.2 0.2 - - - +
206B GLY 4.0 0.2 - - - +
207B ILE* 3.8 0.5 - - - -
208B LEU* 2.8 53.6 + - + +
210B VAL* 6.1 0.2 - - + -
239B ILE* 4.9 0.7 - - + -
245B VAL* 4.1 17.6 - - + +
246B TYR 3.7 4.3 - - - -
247B ILE* 3.9 16.6 - - + -
257B THR* 4.0 8.0 - - + -
258B LEU* 1.3 73.1 - - - +
260B PHE* 1.3 62.6 + - - +
261B LYS* 3.9 1.0 + - - +
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Residues in contact with PHE 260 (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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93A LEU* 5.0 1.8 - - + -
96A ASN* 3.8 23.3 - - + -
97A LEU* 4.0 16.4 - - + -
100A LEU* 3.8 35.2 - - + -
97B LEU* 4.9 2.0 - - + -
206B GLY 3.6 3.8 - - - +
207B ILE* 4.0 20.9 - - + -
245B VAL* 3.1 6.8 - - - -
246B TYR* 2.8 87.3 + + + +
248B SER* 4.7 4.3 - - - -
258B LEU* 3.7 43.3 - - + -
259B ALA* 1.3 74.5 - - - +
261B LYS* 1.3 62.6 + - - +
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Residues in contact with LYS 261 (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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177B GLY* 5.0 1.8 - - - -
199B LEU* 2.9 46.3 + - + +
200B GLN* 3.9 9.9 + - - +
202B LEU* 2.8 33.5 + - + +
203B ARG 3.5 13.2 - - - +
204B PRO* 4.3 11.4 - - - +
205B GLY* 2.8 29.8 + - - -
206B GLY 2.9 18.3 + - - +
244B ARG* 3.9 8.3 - - + +
245B VAL* 4.2 2.5 - - - -
246B TYR* 4.5 5.6 + - - -
259B ALA 3.9 1.2 + - - -
260B PHE* 1.3 72.0 - - - +
262B ILE* 1.3 73.5 + - - +
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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