Contacts of the strand formed by residues 456 - 462 (chain A) in PDB entry 1OGS
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 ALA 456 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A LEU* 4.3 10.8 - - + -
449A LEU 3.8 6.3 - - - +
450A MET* 4.8 1.6 - - + +
451A HIS* 5.3 1.6 - - - -
454A GLY 3.9 0.4 + - - -
455A SER* 1.3 75.9 - - - +
457A VAL* 1.3 62.0 + - - +
493A LEU* 3.3 8.6 - - - +
494A TRP* 2.9 70.9 + - + +
496A ARG* 4.1 13.4 - - - +
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Residues in contact with VAL 457 (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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426A PHE* 3.8 12.3 - - + +
427A ILE* 4.5 9.4 - - + -
447A VAL 4.1 0.2 - - - +
448A ALA* 3.4 2.6 - - - +
449A LEU* 2.9 62.2 + - + +
451A HIS* 3.9 20.9 - - + +
456A ALA* 1.3 75.5 - - - +
458A VAL* 1.3 68.5 + - - +
459A VAL* 4.7 4.9 - - + -
491A THR* 3.8 26.5 - - + -
492A TYR 3.2 6.1 - - - +
493A LEU* 3.8 14.4 - - + -
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Residues in contact with VAL 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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67A LEU* 5.2 0.9 - - + -
69A LEU* 4.7 5.6 - - + -
436A LEU* 4.0 21.8 - - + -
447A VAL 3.3 10.3 - - - +
448A ALA* 3.7 17.0 - - + -
456A ALA* 5.4 0.2 - - + -
457A VAL* 1.3 82.4 - - - +
459A VAL* 1.3 64.3 + - - +
460A VAL* 3.9 20.6 - - + -
472A ILE* 4.4 11.4 - - + -
491A THR* 3.4 0.9 - - - -
492A TYR* 2.8 41.7 + - + +
494A TRP* 3.6 32.5 - - + -
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Residues in contact with VAL 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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368A ILE* 4.7 3.7 - - + +
422A HIS* 3.7 20.2 - - + +
423A PHE* 3.5 43.7 - - + -
427A ILE* 4.8 5.2 - - + -
445A ASP 3.8 0.6 - - - +
446A ALA* 3.1 26.2 - - - +
447A VAL* 3.0 17.8 + - + +
449A LEU* 5.5 1.1 - - + -
457A VAL* 4.7 7.0 - - + -
458A VAL* 1.3 75.6 - - - +
460A VAL* 1.3 65.0 + - - +
489A ILE* 4.1 17.5 - - + -
490A HIS 3.2 11.4 - - - +
491A THR* 3.9 11.9 - - + +
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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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67A LEU* 4.5 3.8 - - + -
444A LEU* 3.8 30.5 - - + -
445A ASP 3.5 5.8 - - - +
446A ALA* 4.3 8.3 - - + -
458A VAL* 3.9 18.4 - - + -
459A VAL* 1.3 79.1 - - - +
461A LEU* 1.3 62.0 + - - +
462A ASN 4.2 0.3 + - - -
470A LEU* 4.1 20.6 - - + -
472A ILE* 4.6 0.9 - - + -
484A SER* 3.9 14.8 + - - +
488A SER* 5.4 0.2 + - - -
489A ILE* 3.4 4.8 - - - -
490A HIS* 2.8 45.8 + - + +
492A TYR* 4.3 14.6 - - + -
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Residues in contact with LEU 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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361A MET* 4.0 6.1 - - + +
364A SER* 3.4 30.1 - - - +
365A HIS* 3.6 25.8 - - + +
368A ILE* 3.9 9.2 - - + -
419A HIS* 4.1 14.6 - - + -
444A LEU* 3.5 7.6 - - - +
445A ASP* 2.7 50.3 + - + +
459A VAL 4.2 0.6 - - - -
460A VAL* 1.3 73.9 - - - +
462A ASN* 1.3 62.0 + - - +
463A ARG* 3.7 29.8 + - + -
488A SER 3.6 16.8 - - - +
489A ILE* 4.1 9.4 - - + +
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Residues in contact with ASN 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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361A MET* 4.6 1.0 - - - +
443A ASP 4.8 2.1 - - - +
444A LEU* 3.5 14.3 - - + +
460A VAL 4.2 0.6 + - - -
461A LEU* 1.3 72.0 - - - +
463A ARG* 1.3 59.7 + - - +
464A SER* 2.7 35.5 + - - -
466A LYS 2.9 20.4 + - - -
468A VAL* 3.8 7.3 - - - +
484A SER* 2.8 42.5 + - - +
485A PRO 3.1 15.0 + - - +
486A GLY* 3.6 0.2 - - - -
487A TYR* 3.2 19.8 + - - -
488A SER 3.0 18.7 + - - +
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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