Contacts of the strand formed by residues 278 - 283 (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 PHE 278 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A PHE* 3.9 20.0 - + - -
247A SER* 3.7 14.1 - - - -
248A ALA 3.1 28.0 - - - -
249A GLY* 4.7 0.2 - - - -
148B GLN* 5.0 6.5 - - + -
149B LEU 3.3 13.9 - - - +
150B ILE* 4.0 12.3 - - + -
168B TRP* 3.6 5.7 - - - -
196B TYR* 4.2 21.1 - + - -
197B GLY* 3.4 1.4 - - - -
198B GLN* 2.9 72.0 + - + +
246B TYR* 4.3 4.3 - + - -
261B LEU* 4.4 0.7 - - - +
274B GLY 3.8 10.8 - - - -
275B ASP 3.8 11.4 - - - -
276B VAL 4.0 0.7 - - - -
277B THR* 1.3 82.7 - - - +
279B PHE* 1.3 62.3 + - - +
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Residues in contact with PHE 279 (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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148B GLN* 3.6 0.8 - - - -
149B LEU* 2.7 54.8 + - + +
168B TRP* 3.7 29.8 - + + -
183B ASN 5.5 0.2 - - - -
184B LYS* 5.4 1.6 - - - -
185B ILE* 3.8 22.9 - - + -
195B ILE* 4.1 14.4 - - + -
196B TYR* 3.3 23.1 - - - -
197B GLY* 4.2 0.7 - - - -
212B ILE* 4.1 21.1 - - + -
259B LEU* 3.8 25.8 - - + -
260B GLN* 3.8 23.1 - - - -
261B LEU* 3.9 25.1 - - + -
278B PHE* 1.3 76.1 - - - +
280B GLY* 1.3 57.2 + - - +
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Residues in contact with GLY 280 (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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147B LEU 3.2 12.8 - - - -
148B GLN* 4.1 0.4 - - - -
185B ILE* 4.0 7.2 - - - -
195B ILE* 3.5 5.9 - - - +
196B TYR* 2.9 55.9 + - - +
279B PHE* 1.3 76.1 - - - +
281B ALA* 1.3 62.1 + - - +
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Residues in contact with ALA 281 (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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250A ILE* 4.8 0.2 - - - +
146B CYS* 3.3 4.5 - - - +
147B LEU 3.0 31.2 + - - +
178B LEU* 3.4 23.1 - - + +
185B ILE* 4.3 6.3 - - + +
193B PHE* 4.7 4.3 - - + -
194B PHE 3.3 10.1 - - - +
195B ILE* 4.2 15.9 - - + -
196B TYR* 3.8 4.0 - - - -
259B LEU* 4.2 14.8 - - + -
280B GLY* 1.3 73.7 - - - +
282B LEU* 1.3 60.9 + - - +
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Residues in contact with LEU 282 (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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194A PHE* 5.4 7.6 - - + -
250A ILE* 4.4 11.9 - - + -
282A LEU* 6.5 0.2 - - + -
284A LEU* 4.1 28.3 - - + -
144B GLN* 3.7 39.5 - - + +
145B ASP 3.6 3.6 - - - -
146B CYS* 3.8 18.6 - - + -
193B PHE* 3.3 6.6 - - - -
194B PHE* 2.8 57.4 + - + +
196B TYR* 5.1 0.2 - - + -
281B ALA* 1.3 76.2 - - - +
283B LYS* 1.3 65.3 + - - +
284B LEU* 3.5 5.2 + - + +
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Residues in contact with LYS 283 (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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144B GLN* 3.4 27.2 + - - +
145B ASP* 2.7 31.2 + - + +
177B ALA* 3.9 19.5 - - + -
178B LEU* 4.7 0.2 - - - +
189B GLU* 3.7 21.7 + - + +
190B THR 3.5 22.9 + - - -
191B GLY* 4.7 4.5 - - - -
192B TYR 3.8 4.7 - - - +
193B PHE* 3.5 32.4 - - + -
282B LEU* 1.3 71.5 - - - +
284B LEU* 1.3 79.8 + - - +
285B LEU* 5.6 1.6 - - - +
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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