Contacts of the strand formed by residues 258 - 263 (chain B) in PDB entry 3V56
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 GLU 258 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181B LYS* 5.5 6.6 - - + +
184B LYS* 3.4 31.4 - - + +
185B ILE 3.2 9.2 - - - +
186B LEU* 3.8 24.3 - - + +
213B GLN 3.8 0.2 - - - +
214B ARG* 3.4 4.5 - - - +
215B LYS* 2.7 52.4 + - + +
256B GLY 4.3 4.5 - - - +
257B ASP* 1.3 79.0 - - - +
259B LEU* 1.3 63.6 + - - +
260B GLN* 5.7 0.2 - - - +
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Residues in contact with LEU 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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178B LEU* 5.4 0.4 - - + -
184B LYS* 3.4 9.8 - - - +
185B ILE* 2.7 49.8 + - + +
187B VAL* 4.8 4.5 - - + -
195B ILE* 3.8 26.7 - - + -
212B ILE* 5.0 3.6 - - + -
213B GLN 3.3 11.7 - - - +
214B ARG* 4.2 5.4 - - + -
229B LEU* 4.0 24.5 - - + -
253B LEU* 3.8 32.5 - - + -
257B ASP* 6.0 0.2 - - + -
258B GLU* 1.3 78.6 - - - +
260B GLN* 1.3 60.8 + - - +
279B PHE* 3.8 15.9 - - + -
281B ALA* 4.2 13.7 - - + -
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Residues in contact with GLN 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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165B PHE* 4.0 28.4 - - + -
183B ASN 5.2 2.7 - - - +
184B LYS* 4.2 23.1 - - + +
211B LEU 3.3 1.6 - - - +
212B ILE* 3.5 2.3 - - - -
213B GLN* 2.7 74.7 + - + +
215B LYS* 6.0 2.2 - - + +
226B LEU* 4.1 20.9 - - + +
258B GLU 5.7 0.4 - - - +
259B LEU* 1.3 75.8 - - - +
261B LEU* 1.3 60.1 + - - +
262B ALA* 4.3 0.2 - - - +
279B PHE* 3.8 10.0 - - - -
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Residues in contact with LEU 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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165B PHE* 3.4 22.3 - - - +
166B VAL* 4.4 18.0 + - + -
168B TRP* 4.1 27.6 + - + +
183B ASN 5.8 0.4 + - - -
197B GLY* 4.3 10.5 - - - -
199B VAL* 3.6 28.3 - - + -
210B HIS* 3.7 39.9 - - + +
211B LEU 3.3 4.7 - - - +
212B ILE* 4.6 2.7 - - + +
260B GLN* 1.3 72.4 - - - +
262B ALA* 1.3 60.1 + - - +
263B ILE* 4.4 4.9 - - + -
278B PHE 4.4 2.0 - - - +
279B PHE* 3.9 29.9 - - + -
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Residues in contact with ALA 262 (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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163B TYR* 4.0 15.5 - - + -
164B THR 4.1 0.7 - - - -
165B PHE* 3.5 27.6 - - + -
210B HIS* 3.4 2.2 - - - -
211B LEU* 2.8 38.3 + - + +
213B GLN* 3.6 24.2 - - - +
260B GLN* 4.0 0.9 - - - +
261B LEU* 1.3 74.0 - - - +
263B ILE* 1.3 61.4 + - - +
264B PRO* 3.5 4.4 - - - +
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Residues in contact with ILE 263 (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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163B TYR* 3.3 3.9 - - - -
164B THR* 2.9 49.6 + - + +
166B VAL* 4.1 23.8 - - + -
199B VAL* 4.1 9.2 - - + -
201B TYR* 4.0 14.6 - - + +
208B MET* 4.1 6.7 - - + -
209B GLY 3.5 12.8 - - - +
210B HIS* 4.0 6.7 - - + -
261B LEU* 4.4 3.1 - - + -
262B ALA* 1.3 73.6 - - - +
264B PRO* 1.4 54.2 - - - +
265B ARG* 2.7 29.0 + - + -
268B ALA* 3.7 24.2 - - + -
270B ILE* 4.0 26.9 - - + -
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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