Contacts of the strand formed by residues 382 - 388 (chain A) in PDB entry 2WNW
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 ARG 382 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A ALA* 3.9 21.7 - - + +
42A LEU 3.0 24.9 + - - +
43A GLN* 3.3 6.1 - - - +
44A GLN* 3.5 47.0 + - + +
380A GLY 4.3 2.7 - - - +
381A ALA* 1.3 76.5 - - - +
383A VAL* 1.3 68.8 + - - +
398A PHE* 3.2 5.8 - - - -
399A VAL* 2.8 37.5 + - + +
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Residues in contact with VAL 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ALA* 3.6 1.9 - - - -
42A LEU* 2.6 46.4 + - + -
43A GLN* 3.0 43.5 + - - +
45A ILE* 4.1 6.2 - - + +
321A PHE* 3.7 17.9 - - + +
322A LYS* 5.1 4.3 - - - -
382A ARG* 1.3 73.3 - - - +
384A MET* 1.3 69.2 + - - +
396A VAL* 4.2 9.4 - - + -
397A GLY 3.3 12.6 - - - +
398A PHE* 3.7 27.8 - - + -
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Residues in contact with MET 384 (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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36A VAL* 4.0 18.2 - - + -
38A PRO* 3.8 33.2 - - + +
40A HIS 3.6 8.5 - - - +
41A ALA* 4.5 1.6 - - - +
42A LEU* 4.1 3.4 - - - +
322A LYS* 5.4 2.6 - - - -
382A ARG 3.6 0.6 + - - -
383A VAL* 1.3 86.4 - - - +
385A LEU* 1.3 67.6 + - - +
386A SER* 3.5 8.2 + - - -
397A GLY* 2.9 23.3 + - - +
398A PHE 3.2 31.9 - - - +
399A VAL* 4.0 17.0 - - + -
405A ARG* 4.1 16.4 - - + -
406A VAL 3.8 13.5 - - - +
407A LEU* 5.3 0.4 - - + -
442A TRP* 4.3 9.4 - - + -
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Residues in contact with LEU 385 (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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37A LEU* 2.9 57.7 + - + +
40A HIS* 3.0 26.5 + - + +
42A LEU* 4.2 14.3 - - + +
322A LYS* 5.9 0.2 - - - +
384A MET* 1.3 75.7 - - - +
386A SER* 1.3 75.4 + - - +
246B VAL* 4.0 9.4 - - + -
276B SER* 4.1 14.6 - - - +
277B GLN* 5.0 3.6 - - + +
280B TYR* 3.6 54.3 - - + -
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Residues in contact with SER 386 (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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35A SER 3.0 15.5 - - - -
36A VAL* 4.1 13.9 - - - -
37A LEU* 4.7 2.2 - - - +
322A LYS* 2.9 29.5 + - - +
384A MET* 3.5 8.4 + - - -
385A LEU* 1.3 82.1 - - - +
387A SER* 1.3 61.6 + - - +
395A GLU* 2.6 29.4 + - - -
397A GLY 4.2 7.3 + - - -
407A LEU* 4.9 1.6 - - - -
276B SER* 3.1 12.3 - - - -
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Residues in contact with SER 387 (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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34A ILE* 3.1 4.9 - - - +
35A SER* 2.8 36.4 + - - -
386A SER* 1.3 76.3 - - - +
388A SER* 1.3 60.5 + - - +
395A GLU* 3.8 7.4 - - - -
274B HIS* 2.7 39.2 + - - -
276B SER* 4.0 11.4 - - - -
277B GLN* 3.0 32.3 + - - -
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Residues in contact with SER 388 (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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33A LEU 3.8 3.6 - - - -
34A ILE* 4.0 8.2 - - - +
387A SER* 1.3 75.1 - - - +
389A TYR* 1.3 64.3 + - - +
390A ASP 2.9 26.2 + - - -
391A ASN* 4.7 5.3 - - - +
393A LEU* 3.2 24.4 + - - +
395A GLU* 3.8 17.5 + - - -
273B ASP* 3.6 4.0 - - - +
274B HIS* 2.8 26.3 + - - +
275B PHE 4.7 0.3 + - - -
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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