Contacts of the strand formed by residues 277 - 285 (chain B) in PDB entry 4GJ0
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 277 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180B GLY 3.4 0.9 - - - +
181B THR* 3.2 3.9 - - - -
182B LYS* 2.8 31.8 + - - +
217B THR 4.3 12.3 - - - +
218B GLY 4.2 2.2 - - - +
219B SER 3.9 3.6 - - - +
220B TRP* 3.6 44.6 - - + +
261B MET* 3.4 41.7 - - + -
275B ARG* 3.6 36.1 + - - +
276B LYS* 1.3 78.7 - - - +
278B GLY* 1.3 63.3 + - - +
279B ALA 3.3 11.4 + - - +
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Residues in contact with GLY 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LYS* 3.4 13.7 - - - -
180B GLY 3.0 30.6 + - - -
181B THR* 4.2 9.9 - - - -
215B SER* 5.3 1.1 - - - -
217B THR* 4.9 12.0 + - - -
218B GLY 4.4 3.8 + - - -
277B LEU* 1.3 72.2 - - - +
279B ALA* 1.3 58.7 + - - +
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Residues in contact with ALA 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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178B GLY 3.3 12.8 - - - +
179B LYS* 4.2 3.6 - - + -
215B SER* 3.4 20.6 - - - +
218B GLY 3.4 10.6 + - - +
219B SER* 3.3 24.1 - - - +
220B TRP* 3.1 23.7 + - - -
277B LEU* 3.3 3.3 + - - +
278B GLY* 1.3 80.5 - - - +
280B TRP* 1.3 70.4 + - - +
281B VAL* 6.1 0.2 - - + -
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Residues in contact with TRP 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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176B TYR* 3.8 16.2 - + - -
177B PHE 3.8 0.2 - - - -
178B GLY* 2.8 47.0 + - - -
179B LYS 3.8 19.2 - - - -
180B GLY 3.2 24.8 + - - -
182B LYS* 3.3 38.5 - - + +
187B ALA* 3.7 23.3 - - + -
190B ALA* 3.9 20.2 - - + -
191B CYS* 4.1 4.5 - - - -
194B MET* 4.4 10.5 - - + -
198B LEU* 4.3 2.5 - - + -
219B SER* 4.1 1.7 - - - -
220B TRP* 3.6 15.5 - + + +
277B LEU 5.0 0.2 - - - -
279B ALA* 1.3 86.0 - - - +
281B VAL* 1.3 66.5 + - - +
282B CYS* 3.8 29.2 - - - -
301C GOL 4.5 4.9 - - - -
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Residues in contact with VAL 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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175B TYR* 4.7 1.6 - - + -
176B TYR 3.3 10.3 - - - +
177B PHE* 3.9 36.8 - - + -
191B CYS* 4.2 0.7 - - - -
198B LEU* 3.4 9.5 - - - +
199B VAL* 2.8 50.1 + - + +
210B LEU* 4.2 10.5 - - + -
214B ALA* 5.9 0.4 - - - -
219B SER* 4.1 20.6 - - - +
220B TRP 3.2 7.7 + - - +
221B ILE* 5.2 0.2 - - + -
262B MET* 4.4 12.1 - - + -
280B TRP* 1.3 81.3 - - - +
282B CYS* 1.3 65.8 + - - +
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Residues in contact with CYS 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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167B TRP* 3.8 21.1 - - + -
175B TYR* 3.2 7.3 - - - +
176B TYR* 2.8 38.7 + - + -
190B ALA 5.0 0.2 - - - -
191B CYS* 2.0 52.7 - - + -
194B MET* 5.2 2.2 - - - -
197B GLN 3.2 8.5 - - - +
199B VAL 4.4 0.9 - - - -
280B TRP* 3.8 20.6 - - - -
281B VAL* 1.3 76.8 - - - +
283B ASP* 1.3 62.4 + - - +
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Residues in contact with ASP 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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167B TRP* 3.8 2.9 - - - -
173B LYS* 2.9 39.3 + - - -
174B CYS 3.1 12.8 - - - +
175B TYR* 3.9 10.5 - - + -
196B GLY* 3.3 2.3 - - - -
197B GLN* 2.8 39.5 + - - +
198B LEU 4.2 1.4 - - - +
199B VAL* 3.4 9.9 - - + +
200B SER* 3.1 18.4 + - - -
236B ASP* 4.5 5.7 - - - +
282B CYS* 1.3 75.8 - - - +
284B ARG* 1.3 67.8 + - - +
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Residues in contact with ARG 284 (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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164B PRO* 3.7 30.0 - - - +
167B TRP* 3.5 37.5 - - + +
173B LYS* 3.4 7.9 - - - +
174B CYS* 2.8 33.0 + - + -
194B MET 3.2 23.0 + - - -
195B GLU* 3.5 32.8 + - - +
196B GLY* 4.3 0.4 - - - -
283B ASP* 1.3 77.9 - - - +
285B LEU* 1.3 68.8 + - - +
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Residues in contact with LEU 285 (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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172B ARG* 3.9 15.9 - - + +
173B LYS* 4.3 13.5 - - + -
174B CYS* 4.0 6.0 - - - -
284B ARG* 1.3 84.1 + - - +
286B ALA* 1.3 69.6 + - - +
287B THR* 3.8 4.7 + - - +
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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