Contacts of the strand formed by residues 492 - 497 (chain B) in PDB entry 6T8B
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 492 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438B THR 4.1 4.5 - - - +
439B VAL* 4.2 6.1 - - + -
483B ILE* 4.1 19.1 - - + -
487B SER* 3.7 22.4 - - - +
488B THR 3.5 3.2 + - - +
489B PRO 4.3 0.3 - - - +
491B GLU* 1.3 82.1 - - - +
493B ARG* 1.3 64.7 + - - +
494B LEU* 5.1 2.2 - - + +
512B HIS* 3.1 26.5 - - - +
588B PRO* 3.9 1.6 - - - +
589B THR 3.4 14.6 - - - +
591B VAL* 5.5 1.3 - - + -
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Residues in contact with ARG 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489B PRO* 3.4 33.7 + - - +
492B ALA* 1.3 72.2 - - - +
494B LEU* 1.3 62.7 + - - +
511B PRO 3.7 10.9 + - - -
512B HIS 3.3 14.4 - - - +
513B LEU 3.3 16.8 + - - -
514B LEU* 3.5 26.9 - - + +
588B PRO* 3.7 24.4 - - + +
589B THR 3.3 6.7 + - - -
590B ILE* 3.3 41.6 - - + +
591B VAL 3.3 3.0 + - - -
715B ASP* 2.7 37.6 + - - +
717B ILE* 4.8 6.2 - - - +
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Residues in contact with LEU 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480B LEU* 3.9 19.1 - - + -
483B ILE* 4.3 19.1 - - + -
484B LEU* 4.5 22.2 - - + -
492B ALA 5.1 1.3 - - - +
493B ARG* 1.3 77.3 - - - +
495B ILE* 1.3 68.4 + - - +
496B MET* 3.5 31.0 - - + -
510B ILE* 4.6 2.7 - - + -
512B HIS* 3.4 15.4 + - + -
513B LEU* 3.6 19.1 - - + +
514B LEU* 3.6 20.3 + - - +
515B CYS* 5.0 0.2 - - - -
591B VAL* 3.4 35.7 - - + +
593B VAL* 4.7 1.1 - - + -
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Residues in contact with ILE 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494B LEU* 1.3 78.1 - - - +
496B MET* 1.3 61.5 + - - +
497B ILE* 4.4 8.4 - - + +
514B LEU* 3.7 16.4 - - + -
515B CYS* 3.9 18.8 - - - -
527B ALA* 4.4 17.7 - - + +
530B TRP* 3.7 26.9 - - + -
531B SER* 3.3 24.2 - - - +
590B ILE* 3.8 21.1 - - + -
591B VAL 3.0 8.3 + - - -
592B VAL* 3.5 21.3 - - + +
593B VAL 3.1 23.0 + - - +
720B ILE* 5.8 0.4 - - + -
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Residues in contact with MET 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480B LEU* 3.5 17.0 - - + -
494B LEU* 3.5 34.2 - - + -
495B ILE* 1.3 75.4 - - - +
497B ILE* 1.3 63.9 + - - +
504B LEU* 4.0 27.4 - - + +
507B TYR* 3.5 49.4 - - + -
510B ILE* 4.6 1.8 - - + -
513B LEU* 3.9 19.4 - - + +
515B CYS* 5.2 1.6 + - - -
516B PRO 4.3 1.0 - - - +
517B VAL* 3.8 18.2 - - + -
518B VAL* 3.2 23.9 + - - +
593B VAL* 3.5 12.6 - - + -
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Residues in contact with ILE 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495B ILE* 4.4 11.4 - - + +
496B MET* 1.3 81.2 - - - +
498B ASP* 1.3 63.0 + - - +
499B PRO* 4.3 0.7 - - - -
504B LEU* 3.8 2.7 - - - +
518B VAL* 3.8 31.6 - - + +
521B MET* 4.7 5.4 - - - -
524B ALA* 4.1 8.5 - - + -
527B ALA* 4.5 10.5 - - + -
528B LEU* 4.1 32.1 - - + -
592B VAL* 4.6 1.1 - - + -
593B VAL 3.1 9.0 + - - +
594B VAL* 4.2 16.4 - - + -
595B ASP* 3.1 28.9 + - - +
600B MET* 3.4 28.3 - - + -
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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