Contacts of the strand formed by residues 455 - 463 (chain A) in PDB entry 2R92
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 MET 455 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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443A LEU* 3.4 27.8 - - + +
444A PHE 3.1 6.1 - - - -
445A ASN* 3.2 40.8 - - + +
449A SER* 4.5 0.9 - - - +
452A LYS 3.1 18.0 + - - +
453A MET 2.7 1.2 - - - -
454A SER* 1.3 79.9 - - - +
456A MET* 1.3 66.9 + - - +
490A HIS* 4.3 10.5 - - + -
505A CYS* 5.3 0.7 - - - +
1130B PHE* 4.1 11.0 - - + -
1134B GLU* 3.5 36.3 - - + +
1137B CYS* 4.2 16.4 - - + -
1138B MET* 3.9 15.7 - - - +
1141B HIS* 3.2 11.5 + - - +
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Residues in contact with MET 456 (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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443A LEU* 3.4 6.9 - - - +
444A PHE* 2.7 41.9 + - - +
453A MET* 3.1 25.1 - - + +
455A MET* 1.3 79.8 - - - +
457A ALA* 1.3 61.4 + - - +
474A VAL* 3.8 5.2 - - + -
477A PRO* 3.5 24.7 - - + -
478A TYR* 3.2 42.8 + - + +
505A CYS* 3.6 7.4 - - - +
507A VAL* 3.6 17.7 - - + -
510A GLN* 3.9 24.7 - - + -
521A MET* 3.7 22.0 - - - -
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Residues in contact with ALA 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ASP* 4.3 2.8 - - - +
441A PRO* 5.5 2.7 - - + -
442A VAL 3.1 12.1 - - - +
443A LEU* 4.4 0.4 - - - +
456A MET* 1.3 72.1 - - - +
458A HIS* 1.3 61.0 + - - +
501A LEU* 3.4 39.0 - - + +
502A SER* 4.5 2.0 - - - +
505A CYS* 2.7 22.0 + - + +
506A ALA* 3.5 6.1 - - + +
507A VAL* 3.1 25.6 + - - +
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Residues in contact with HIS 458 (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 4.4 3.4 - - - -
362A ASP* 2.9 12.9 + - - +
363A GLN 3.4 16.4 + - - -
364A VAL* 3.4 25.1 - - + +
441A PRO* 3.4 6.7 - - - +
442A VAL* 2.9 32.1 + - + +
444A PHE* 3.0 38.7 - + + +
456A MET 3.9 2.0 - - - -
457A ALA* 1.3 71.6 - - - +
459A ARG* 1.3 63.1 + - - +
470A LEU* 5.8 2.2 - - + +
474A VAL* 4.1 15.5 - - + -
478A TYR* 2.5 27.1 + + - -
507A VAL* 3.0 31.8 - - + +
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Residues in contact with ARG 459 (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 GLU* 3.5 18.8 - - - +
362A ASP* 2.6 53.9 + - + +
363A GLN* 3.4 32.4 - - + +
364A VAL* 3.0 21.0 + - - -
439A ASN* 3.6 44.7 + - - +
440A ASP 4.7 0.9 - - - -
441A PRO* 5.0 2.0 - - - -
458A HIS* 1.3 72.3 - - - +
460A VAL* 1.3 65.8 + - - +
461A LYS 3.4 0.5 + - - -
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Residues in contact with VAL 460 (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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364A VAL* 4.0 3.8 - - - -
366A VAL* 3.5 23.3 - - + -
436A ILE* 3.7 20.9 - - + -
437A MET 3.0 31.4 - - - +
438A ASP* 3.3 2.6 - - - +
439A ASN* 2.6 29.6 + - - +
440A ASP 3.5 19.9 + - - +
442A VAL* 3.3 28.9 - - + -
458A HIS 3.7 1.0 + - - -
459A ARG* 1.3 72.8 - - - +
461A LYS* 1.3 66.4 + - - +
462A VAL* 4.0 12.6 - - + +
489A LEU* 4.9 1.1 - - + -
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Residues in contact with LYS 461 (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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359A LEU* 4.8 14.3 - - + +
363A GLN* 3.4 34.3 - - + +
364A VAL 3.3 14.9 + - - +
365A GLY* 3.4 5.7 - - - -
366A VAL* 3.0 22.2 + - - +
438A ASP* 3.0 19.7 - - - +
439A ASN* 5.9 0.9 - - - +
459A ARG 4.2 2.5 - - - +
460A VAL* 1.3 77.1 - - - +
462A VAL* 1.3 77.0 + - - +
463A ILE* 3.4 11.1 + - + +
68K PHE* 5.6 11.3 - - - -
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Residues in contact with VAL 462 (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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366A VAL* 3.3 9.0 - - + +
368A LYS* 4.9 5.8 - - + -
371A ALA* 3.1 37.2 - - + -
399A HIS* 3.5 29.8 - - + +
436A ILE 4.4 4.9 - - - +
438A ASP* 2.8 30.4 + - - +
460A VAL* 4.0 10.5 - - + +
461A LYS* 1.3 80.0 - - - +
463A ILE* 1.3 64.2 + - - +
68K PHE* 5.3 3.6 - - - -
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Residues in contact with ILE 463 (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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359A LEU* 5.6 7.0 - - + -
365A GLY* 3.3 23.1 - - - +
366A VAL 2.7 24.7 + - - +
367A PRO* 3.1 4.6 - - - +
368A LYS* 2.9 28.8 + - - +
461A LYS* 3.7 16.8 - - + +
462A VAL* 1.3 80.9 - - - +
464A PRO* 1.3 81.5 - - + +
467A THR 4.0 3.4 - - - +
469A ARG* 3.3 42.4 - - + -
65K HIS* 6.1 3.8 - - + +
67K PHE* 4.6 7.2 - - + -
68K PHE* 4.9 8.1 - - + -
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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