Contacts of the strand formed by residues 336 - 344 (chain B) in PDB entry 2COJ
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 336 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B LYS* 5.0 4.5 - - - +
101B PHE* 6.2 0.7 - - + -
290B THR* 3.1 22.6 - - + +
331B SER* 3.3 1.0 - - - -
332B GLY 2.5 30.3 + - - -
333B THR* 4.2 11.0 - - - +
334B ALA 3.6 2.2 - - - +
335B CYS* 1.3 80.4 - - - +
337B VAL* 1.3 66.4 + - + +
366B LEU* 4.0 30.1 - - + -
369B LEU* 3.5 38.8 - - + -
370B THR* 4.8 2.5 - - + -
373B GLN* 4.6 19.5 - - - +
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Residues in contact with VAL 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B PHE* 3.8 21.0 - - + -
294B ILE* 3.8 25.4 - - + -
329B PHE* 4.1 16.4 - - + -
330B GLY 3.1 11.4 - - - +
335B CYS* 2.9 16.5 + - - +
336B VAL* 1.3 90.0 - - + +
338B CYS* 1.3 63.5 + - - +
339B PRO* 4.3 1.1 - - - -
362B ALA* 3.8 13.7 - - + +
365B ILE* 3.8 14.1 - - + -
366B LEU* 3.7 31.2 - - + -
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Residues in contact with CYS 338 (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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194B PHE* 4.0 17.5 - - - -
200B ASN 4.6 3.8 - - - -
202B VAL* 3.7 34.5 - - - -
258B VAL* 5.2 1.2 - - - +
261B MET* 4.1 15.7 - - + -
329B PHE* 3.4 1.5 - - - -
330B GLY* 2.8 32.5 + - - +
335B CYS* 3.9 19.1 - - + -
337B VAL* 1.3 75.7 - - - +
339B PRO* 1.3 69.9 - - - +
340B VAL* 4.1 3.1 - - - +
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Residues in contact with PRO 339 (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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199B PHE* 3.6 46.9 - - + -
200B ASN 4.4 2.5 - - - +
201B PRO* 3.4 18.4 - - + +
202B VAL* 3.1 22.4 + - - +
328B MET 3.7 6.1 - - - +
329B PHE* 3.8 7.1 - - + -
337B VAL 4.3 0.4 - - - -
338B CYS* 1.3 94.0 - - - +
340B VAL* 1.3 59.9 + - - +
354B THR* 3.9 18.8 - - + -
355B MET* 4.1 11.9 - - - -
359B PRO* 4.8 5.6 - - + -
362B ALA* 5.2 2.2 - - + -
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Residues in contact with VAL 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B PRO* 4.8 0.4 - - - -
202B VAL* 3.5 13.5 - - + +
204B LEU* 3.7 33.7 - - + -
258B VAL* 4.0 17.7 - - + -
328B MET* 2.7 32.4 + - + +
329B PHE* 4.3 2.5 - - - -
338B CYS 4.1 5.6 - - - +
339B PRO* 1.3 78.7 - - - +
341B SER* 1.3 62.7 + - - +
342B ASP 3.8 13.9 - - - +
352B ILE* 3.9 18.8 - - + +
354B THR* 2.5 32.6 + - - -
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Residues in contact with SER 341 (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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201B PRO* 3.8 25.1 - - - +
202B VAL 3.0 13.5 + - - +
340B VAL* 1.3 75.1 - - - +
342B ASP* 1.3 87.2 + - - +
351B HIS* 3.3 11.7 - - - -
352B ILE* 2.8 35.4 + - - +
355B MET* 4.6 9.4 - - - -
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Residues in contact with ASP 342 (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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202B VAL 3.7 1.6 + - - -
203B SER* 3.3 19.4 - - - -
204B LEU 2.8 23.1 + - - -
340B VAL* 3.8 5.7 - - - +
341B SER* 1.3 106.7 + - - +
343B ILE* 1.3 69.6 + - - +
344B LEU* 4.8 1.1 - - + -
349B THR* 4.2 19.2 - - + +
350B ILE 3.3 8.7 - - - +
351B HIS* 3.0 30.0 + - - +
352B ILE* 4.4 0.9 - - - +
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Residues in contact with ILE 343 (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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204B LEU* 3.3 18.6 - - + +
206B ALA* 4.0 24.9 - - + -
246B LEU* 3.7 20.6 - - + -
313B MET* 4.2 12.8 - - + -
316B LEU* 3.7 22.9 - - + -
328B MET* 4.1 8.1 - - - -
340B VAL* 4.5 0.2 - - + -
342B ASP* 1.3 82.1 - - - +
344B LEU* 1.3 67.8 + - - +
345B TYR* 3.5 3.4 + - + +
350B ILE* 2.7 45.6 + - + +
352B ILE* 3.4 27.1 - - + -
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Residues in contact with LEU 344 (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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203B SER* 4.5 11.0 - - - -
204B LEU 2.9 9.2 + - - +
205B TRP* 3.7 28.9 + - + +
206B ALA* 2.9 28.9 + - - +
240B ASN* 3.3 27.8 - - + +
241B GLY* 5.3 1.3 - - - -
242B CYS* 3.6 17.3 - - - -
342B ASP* 4.8 0.7 - - + -
343B ILE* 1.3 76.6 - - - +
345B TYR* 1.3 61.9 + - - +
347B GLY 6.4 0.2 - - - -
348B GLU 3.3 7.0 - - - +
349B THR* 4.2 27.1 - - + +
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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