Contacts of the strand formed by residues 333 - 338 (chain A) in PDB entry 6WNX
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 333 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294A ALA* 3.4 17.7 - - - +
295A CYS* 3.4 10.0 - - - -
306A GLY* 3.6 27.4 - - - +
307A SER 3.2 7.9 + - - +
310A ASN 3.8 22.0 - - - +
311A THR 3.8 13.0 - - - +
312A ILE* 3.9 14.8 - - + -
329A HIS* 3.6 24.2 - - + -
332A LEU* 1.3 71.2 - - - +
334A ARG* 1.3 59.9 + - - +
335A CYS 3.6 15.3 - - - +
336A ILE* 4.5 0.9 - - + -
345A SER* 4.1 9.6 - - - -
346A GLY 3.8 7.2 - - - +
347A ALA* 4.3 0.9 - - - +
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Residues in contact with ARG 334 (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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131A TYR* 3.9 11.7 + - - +
171A LEU 5.7 1.6 + - - -
294A ALA* 3.9 10.2 + - - +
295A CYS* 3.6 11.0 - - - +
332A LEU* 3.5 13.8 + - + +
333A VAL* 1.3 71.7 - - - +
335A CYS* 1.3 58.2 + - - +
346A GLY 2.9 8.1 + - - +
348A TYR* 3.9 19.1 - - + +
382A VAL 3.1 24.5 - - - +
383A PHE* 3.1 41.8 + - + +
32C ASP* 3.0 38.0 + - - -
34C GLY* 3.5 19.2 + - - -
35C ILE* 3.7 26.2 - - - +
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Residues in contact with CYS 335 (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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295A CYS* 3.5 11.9 - - - -
333A VAL* 4.0 0.9 - - - +
334A ARG* 1.3 77.7 - - - +
336A ILE* 1.3 65.2 + - - +
345A SER* 3.4 3.1 - - - -
346A GLY* 2.9 28.6 + - - +
382A VAL* 3.6 28.3 - - - -
383A PHE 3.7 13.9 - - - +
384A ARG* 3.7 22.9 - - - +
385A LEU* 3.6 27.8 - - - +
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Residues in contact with ILE 336 (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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295A CYS* 3.3 23.9 - - + +
296A LEU* 3.7 27.6 - - - +
297A GLN* 4.3 6.2 - - + +
304A VAL* 3.4 30.7 - - + +
305A SER 4.3 5.6 - - - +
306A GLY 4.5 0.7 - - - +
312A ILE* 3.6 39.7 - - + -
333A VAL* 4.5 1.8 - - + -
335A CYS* 1.3 77.8 - - - +
337A ARG* 1.3 81.3 + - - +
338A PHE* 6.0 0.2 - - + -
343A ILE* 3.9 14.4 - - + -
344A VAL 3.4 9.2 - - - +
345A SER* 4.2 2.9 - - - -
384A ARG* 5.9 0.3 + - - -
385A LEU* 4.9 0.8 - - - +
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Residues in contact with ARG 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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214A ARG* 6.1 1.4 - - - +
257A ASP* 4.8 4.8 + - - -
296A LEU 4.8 3.4 + - - -
297A GLN* 3.0 53.0 + - - +
336A ILE* 1.3 84.5 + - - +
338A PHE* 1.3 67.6 + - - +
343A ILE* 3.4 5.5 - - - +
344A VAL 2.9 28.6 + - - +
384A ARG* 4.4 23.5 - - - +
385A LEU* 3.3 35.2 - - + +
386A GLN* 4.5 8.1 - - - +
387A PHE* 3.7 20.0 - - + +
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Residues in contact with PHE 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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297A GLN* 2.7 66.1 + - + +
299A ARG* 3.9 52.1 + - + -
302A LEU* 3.9 28.9 - - + -
304A VAL* 3.8 27.4 - - + -
337A ARG* 1.3 78.1 + - - +
339A ASP* 1.3 73.4 + - - +
342A ARG 3.1 15.7 - - - +
343A ILE* 4.0 12.3 - - + -
357A LEU* 4.4 4.5 - - + -
387A PHE* 3.7 9.0 - - - -
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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