Contacts of the strand formed by residues 358 - 364 (chain A) in PDB entry 4X61
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 358 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356A THR 3.8 5.5 + - - +
357A ASN* 1.3 79.8 + - - +
359A GLN* 1.3 63.5 + - - +
360A VAL* 3.8 2.9 + - - +
385A ARG* 3.3 53.4 - - - +
386A ILE 3.9 15.3 - - - +
387A LYS* 4.0 12.1 - - + +
430A ASP* 4.2 2.8 - - - +
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Residues in contact with GLN 359 (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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345A LEU* 4.2 12.3 - - + -
348A ARG* 3.2 28.2 + - - +
349A VAL* 4.0 25.1 - - + +
357A ASN* 3.5 27.0 + - - +
358A VAL* 1.3 72.3 - - - +
360A VAL* 1.3 54.7 + - - +
361A LEU* 3.8 8.5 - - + -
384A ARG* 6.1 0.7 - - + -
385A ARG 2.7 16.9 + - - +
386A ILE* 3.0 18.7 - - + +
387A LYS* 2.6 32.2 + - - -
430A ASP* 2.9 41.8 + - - +
431A ILE* 4.4 3.5 - - - +
458A LYS* 4.8 0.4 - - - +
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Residues in contact with VAL 360 (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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358A VAL 3.8 2.8 + - - +
359A GLN* 1.3 70.4 - - - +
361A LEU* 1.3 59.8 + - - +
362A MET* 4.2 4.7 - - + -
387A LYS* 3.4 10.5 - - + +
389A TYR* 3.9 31.2 - - + -
427A GLU* 4.1 17.3 - - - +
428A LYS 3.2 27.8 - - - +
429A ALA* 3.8 7.8 - - + -
430A ASP* 2.8 53.6 + - - +
431A ILE 3.3 3.3 + - - -
458A LYS* 4.2 5.4 - - - +
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Residues in contact with LEU 361 (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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341A ILE* 4.0 21.3 - - + -
345A LEU* 4.3 0.7 - - + -
359A GLN* 3.6 9.2 + - + +
360A VAL* 1.3 78.4 - - - +
362A MET* 1.3 62.5 + - - +
363A VAL 4.1 0.7 - - - -
375A SER* 4.0 26.9 - - - +
386A ILE* 4.0 34.3 - - + -
387A LYS 2.7 12.5 + - - +
388A LEU* 3.3 16.2 - - + +
389A TYR* 2.9 24.3 + - - -
431A ILE* 3.4 37.9 - - + +
433A VAL* 4.9 7.4 - - + -
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Residues in contact with MET 362 (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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360A VAL* 4.2 4.3 - - + -
361A LEU* 1.3 74.8 - - - +
363A VAL* 1.3 63.3 + - - +
364A LEU* 3.3 15.2 + - + +
389A TYR* 3.5 40.4 - - + +
423A TRP* 3.6 20.4 - - + -
425A ALA* 4.3 2.2 - - + -
427A GLU 3.3 26.7 - - - +
429A ALA* 3.6 21.8 - - + +
431A ILE 2.9 9.5 + - - -
432A ILE* 3.4 11.1 - - + -
433A VAL* 2.9 25.9 + - - +
456A PHE* 3.6 30.7 - - + -
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Residues in contact with VAL 363 (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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361A LEU 5.6 0.2 - - - -
362A MET* 1.3 70.2 - - - +
364A LEU* 1.3 63.0 + - - +
365A GLY 4.5 3.4 - - - +
366A ALA* 3.7 26.7 - - + +
371A LEU* 4.0 37.0 - - + +
372A VAL* 4.0 22.4 - - + -
375A SER* 4.3 4.7 - - - +
388A LEU* 4.2 15.3 - - + -
389A TYR 2.9 15.2 + - - +
390A ALA* 3.8 0.4 - - - -
391A VAL 2.9 30.5 + - - +
433A VAL* 3.3 16.2 - - + +
434A SER* 5.7 0.4 - - - -
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Residues in contact with LEU 364 (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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362A MET* 3.8 22.0 - - + +
363A VAL* 1.3 76.3 - - - +
365A GLY* 1.3 61.6 + - - +
391A VAL* 3.8 25.6 - - + -
420A MET* 3.5 26.5 - - + -
432A ILE* 3.9 23.6 - - + -
433A VAL 2.7 14.4 + - - +
434A SER* 3.6 16.5 - - - -
436A LEU* 3.5 18.2 - - - +
450A LEU* 4.5 6.5 - - + -
453A ALA* 3.8 29.4 - - + -
456A PHE* 4.0 13.5 - - + -
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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