Contacts of the strand formed by residues 336 - 345 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A LYS* 5.0 4.0 - - - +
101A PHE* 6.4 0.7 - - + -
290A THR* 3.3 20.8 - - + +
331A SER* 3.5 8.8 - - - -
332A GLY 2.8 20.9 + - - -
333A THR 4.0 12.1 - - - +
334A ALA 4.6 2.7 - - - +
335A CYS* 1.3 81.8 - - - +
337A VAL* 1.3 68.9 + - + +
366A LEU* 4.0 20.6 - - + -
369A LEU* 3.5 37.9 - - + -
370A THR* 5.0 3.4 - - - +
373A GLN* 4.8 19.5 - - - +
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Residues in contact with VAL 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A PHE* 3.6 28.2 - - + -
294A ILE* 4.6 7.6 - - + -
329A PHE* 3.7 25.1 - - + -
330A GLY 3.4 4.9 - - - -
335A CYS* 2.5 20.4 + - - +
336A VAL* 1.3 87.0 - - + +
338A CYS* 1.3 66.2 + - - +
339A PRO* 4.3 0.2 - - - -
362A ALA* 4.0 27.6 - - + +
365A ILE* 3.6 32.5 - - + -
366A LEU* 4.4 6.7 - - + +
369A LEU* 4.8 0.2 - - + -
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Residues in contact with CYS 338 (chain A).
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* 4.3 15.5 - - - -
200A ASN 4.7 3.1 - - - -
202A VAL* 3.7 38.8 - - - -
258A VAL* 5.9 1.5 - - - +
261A MET* 4.0 15.7 - - - -
329A PHE* 3.2 5.1 - - - -
330A GLY* 2.9 39.4 + - - +
335A CYS* 4.0 15.9 - - + -
337A VAL* 1.3 75.7 - - - +
339A PRO* 1.3 70.9 - - - +
340A VAL* 4.1 1.9 - - - +
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Residues in contact with PRO 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A PHE* 3.4 53.6 - - + -
200A ASN 4.7 5.4 - - - +
201A PRO* 3.2 7.5 - - + +
202A VAL* 2.9 26.9 + - - +
328A MET 3.8 7.2 - - - +
329A PHE* 4.0 2.9 - - + -
337A VAL 4.3 0.2 - - - -
338A CYS* 1.3 89.2 - - + +
340A VAL* 1.3 59.8 + - - +
354A THR* 3.9 9.6 - - + -
355A MET* 3.9 23.8 - - - -
359A PRO* 4.6 4.5 - - + -
362A ALA* 4.9 4.0 - - + -
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Residues in contact with VAL 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A PRO* 4.8 0.2 - - - -
202A VAL* 3.6 8.7 - - + +
204A LEU* 3.4 37.0 - - + -
258A VAL* 4.2 15.7 - - + -
328A MET* 3.0 37.8 + - + +
329A PHE* 4.1 7.0 - - - -
338A CYS 4.1 7.2 - - - +
339A PRO* 1.3 76.3 - - - +
341A SER* 1.3 62.4 + - - +
342A ASP 3.8 15.3 - - - +
343A ILE* 4.4 3.4 - - + -
352A ILE* 3.6 6.3 - - + +
354A THR* 2.8 30.0 + - - -
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Residues in contact with SER 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A PRO* 3.5 25.5 - - - +
202A VAL 3.0 14.2 + - - -
203A SER* 5.3 0.3 - - - -
339A PRO 4.1 0.4 - - - -
340A VAL* 1.3 75.0 - - - +
342A ASP* 1.3 78.2 + - - +
351A HIS* 3.1 11.7 - - - -
352A ILE* 2.6 39.0 + - - -
355A MET* 4.6 9.4 - - - -
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Residues in contact with ASP 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A VAL 3.7 1.6 + - - -
203A SER* 3.5 21.3 - - - +
204A LEU 2.8 28.0 + - - -
340A VAL* 3.8 6.4 - - - +
341A SER* 1.3 107.4 + - - +
343A ILE* 1.3 64.7 + - - +
344A LEU* 4.9 0.2 - - + -
349A THR* 4.4 17.2 - - + +
350A ILE 3.3 7.2 - - - +
351A HIS* 2.9 31.1 + - - +
352A ILE* 4.2 0.9 - - - -
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Residues in contact with ILE 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A LEU* 3.4 19.5 - - + +
206A ALA* 3.8 16.8 - - + -
246A LEU* 3.8 26.7 - - + -
313A MET* 4.2 11.7 - - + -
316A LEU* 3.5 32.1 - - + -
328A MET* 3.9 20.6 - - + -
340A VAL* 4.4 0.7 - - + -
342A ASP* 1.3 81.1 - - - +
344A LEU* 1.3 67.0 + - - +
345A TYR* 3.4 2.9 + - + -
350A ILE* 2.9 38.9 + - + +
352A ILE* 4.1 11.4 - - + -
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Residues in contact with LEU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A SER* 3.7 22.2 - - - +
204A LEU 2.7 12.6 + - - +
205A TRP* 3.6 33.8 - - + -
206A ALA* 2.9 30.8 + - - +
240A ASN* 3.6 26.7 - - + +
242A CYS* 3.9 3.8 - - - -
343A ILE* 1.3 73.7 - - - +
345A TYR* 1.3 59.0 + - - +
347A GLY 5.5 1.1 - - - -
348A GLU 3.6 5.2 - - - +
349A THR* 3.9 32.8 - - + +
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Residues in contact with TYR 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ALA* 3.6 24.7 - - + -
208A PRO* 4.7 8.5 - - + -
248A LEU* 4.0 18.2 - - + -
253A HIS* 3.2 25.8 + + - -
313A MET* 3.4 46.4 - - + +
314A ASP* 5.1 4.3 + - - -
317A THR* 5.3 5.6 - - + -
343A ILE* 3.4 2.0 + - + -
344A LEU* 1.3 75.7 - - - +
346A LYS* 1.3 119.9 + - + +
347A GLY 3.4 1.3 - - - -
348A GLU* 2.9 26.6 + - - +
350A ILE* 4.0 18.5 - - + +
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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