Contacts of the strand formed by residues 342 - 347 (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 ARG 342 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ILE* 5.7 0.8 - - - +
107A GLU* 4.5 12.9 + - - +
110A TRP* 3.6 62.2 - - - +
111A ARG* 6.3 0.8 - - - +
338A PHE* 3.1 6.2 - - - +
339A ASP* 3.0 39.2 + - - +
340A ASN 3.6 0.8 - - - -
341A LYS* 1.3 112.7 + - - +
343A ILE* 1.3 65.9 + - - +
344A VAL* 4.8 0.7 - - + -
354A VAL* 3.7 19.7 - - + -
355A TRP 3.0 17.7 - - - +
356A ASP* 5.0 0.2 - - - -
357A LEU* 3.8 6.0 - - - +
372A LEU* 4.5 16.2 - - + +
387A PHE* 3.6 13.5 - - + -
388A ASP 5.5 0.6 + - - -
389A GLU* 4.5 8.3 + - - +
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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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304A VAL* 4.4 10.8 - - + -
312A ILE* 4.8 2.2 - - + -
314A LEU* 4.1 15.0 - - + -
326A LEU* 3.6 26.7 - - + -
336A ILE* 3.9 26.7 - - + -
337A ARG 3.4 12.8 - - - +
338A PHE* 4.0 7.2 - - + -
342A ARG* 1.3 76.0 - - - +
344A VAL* 1.3 66.0 + - - +
354A VAL* 3.4 2.8 - - - -
355A TRP* 2.8 51.8 + - + +
357A LEU* 3.9 31.6 - - + -
360A ALA* 4.8 1.1 - - + -
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Residues in contact with VAL 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A TRP* 4.6 11.7 - - + -
336A ILE* 3.4 2.5 - - - -
337A ARG 2.9 29.7 + - - -
342A ARG* 4.8 0.4 - - + -
343A ILE* 1.3 79.7 - - - +
345A SER* 1.3 58.6 + - - +
352A ILE* 3.7 21.1 - - + -
353A LYS 3.3 12.3 - - - +
354A VAL* 4.4 7.6 - - + -
385A LEU* 3.6 24.3 - - + +
387A PHE* 3.6 39.9 - - + -
392A ILE* 3.9 16.6 - - + -
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Residues in contact with SER 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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312A ILE* 3.5 19.9 - - - +
329A HIS* 2.7 28.9 + - - -
333A VAL* 4.1 4.3 - - - -
335A CYS 3.4 10.3 - - - -
336A ILE* 4.2 5.6 - - - +
343A ILE 4.2 0.4 - - - -
344A VAL* 1.3 73.2 - - - +
346A GLY* 1.3 59.0 + - - +
352A ILE* 3.2 7.4 - - - +
353A LYS 2.8 29.5 + - - -
355A TRP* 2.8 21.2 + - - -
385A LEU* 3.9 4.5 - - - -
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Residues in contact with GLY 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A HIS* 4.5 2.5 - - - -
333A VAL* 3.7 3.1 - - - +
334A ARG 2.9 22.7 + - - -
335A CYS* 2.9 32.4 + - - +
345A SER* 1.3 72.6 - - - +
347A ALA* 1.3 59.9 + - - -
351A LYS 3.6 7.6 - - - -
352A ILE* 4.1 6.3 - - - -
382A VAL* 4.0 12.3 - - - -
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Residues in contact with ALA 347 (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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329A HIS* 3.4 32.5 - - + +
331A GLU 4.3 4.3 - - - +
332A LEU 3.1 15.7 - - - +
334A ARG* 4.2 1.1 - - - +
346A GLY* 1.3 75.0 - - - +
348A TYR* 1.3 56.2 + - - +
349A ASP* 3.1 18.4 - - - +
350A GLY* 2.9 25.3 + - - -
351A LYS 3.0 7.2 + - - +
382A VAL* 3.4 16.8 + - - +
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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