Contacts of the strand formed by residues 492 - 497 (chain A) in PDB entry 6T8G
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438A THR* 4.5 1.6 - - - +
439A VAL* 4.4 15.7 - - + -
483A ILE* 4.8 13.6 - - + +
487A SER* 4.0 22.0 - - - +
488A THR 3.7 3.4 + - - -
489A PRO 4.0 1.2 + - - -
491A GLU* 1.3 82.5 - - + +
493A ARG* 1.3 65.7 + - - +
494A LEU* 5.1 1.6 - - - +
512A HIS* 3.6 21.1 - - - +
589A THR* 3.3 17.7 - - + +
591A VAL* 5.7 1.8 - - + -
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Residues in contact with ARG 493 (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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489A PRO* 3.3 25.8 + - - +
492A ALA* 1.3 75.2 - - - +
494A LEU* 1.3 62.2 + - - +
511A PRO 4.7 1.6 - - - -
512A HIS* 2.8 29.8 + - - +
513A LEU 3.9 5.5 - - - +
514A LEU* 3.4 42.9 - - + +
588A PRO* 4.3 17.0 - - + -
589A THR 2.6 17.6 + - - +
590A ILE* 3.7 20.6 - - + -
591A VAL* 3.1 18.4 + - - +
715A ASP* 3.5 49.1 + - - +
716A TYR* 4.3 3.0 - - - +
717A ILE* 4.8 8.1 - - - +
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Residues in contact with LEU 494 (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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480A LEU* 3.8 30.1 - - + -
483A ILE* 5.9 9.6 - - + -
484A LEU* 5.5 6.1 - - + -
492A ALA 5.1 1.3 - - - +
493A ARG* 1.3 78.5 - - - +
495A ILE* 1.3 65.4 + - - +
496A MET* 4.1 21.5 - - + -
507A TYR* 5.8 1.3 - - + -
510A ILE* 3.7 14.6 - - + -
512A HIS* 3.0 41.3 + - + +
513A LEU* 3.4 11.8 - - + +
514A LEU 3.0 24.6 + - - -
590A ILE* 5.3 0.2 - - - +
591A VAL* 3.3 20.0 - - + +
593A VAL* 4.1 3.1 - - + -
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Residues in contact with ILE 495 (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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494A LEU* 1.3 79.4 - - - +
496A MET* 1.3 67.4 + - - +
497A ILE* 4.6 13.2 - - + -
513A LEU* 5.6 0.2 - - - -
514A LEU* 3.7 32.8 - - + -
515A CYS* 3.7 22.0 - - - +
527A ALA* 5.1 8.7 - - + +
530A TRP* 4.2 11.0 - - + -
531A SER* 3.8 22.7 - - - +
590A ILE* 4.4 12.8 - - + -
591A VAL 2.9 8.8 + - - +
592A VAL* 3.6 12.5 - - + +
593A VAL* 2.9 26.8 + - - +
720A ILE* 4.3 8.1 - - + -
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Residues in contact with MET 496 (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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480A LEU* 3.9 12.8 - - + -
494A LEU* 4.1 7.9 - - + -
495A ILE* 1.3 75.8 - - - +
497A ILE* 1.3 67.5 + - - +
504A LEU* 3.6 39.0 - - + +
507A TYR* 3.6 34.8 - - + -
513A LEU* 3.6 30.3 - - + +
515A CYS* 4.2 7.6 - - - -
517A VAL* 3.8 25.4 - - + +
518A VAL* 3.8 20.9 + - - +
593A VAL* 3.3 17.5 - - + -
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Residues in contact with ILE 497 (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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495A ILE* 4.6 13.0 - - + -
496A MET* 1.3 80.8 - - - +
498A ASP* 1.3 61.2 + - - +
499A PRO* 4.2 3.4 - - + -
504A LEU* 4.9 2.0 - - - +
518A VAL* 3.7 15.3 - - + -
520A ASP 5.7 0.4 - - - +
521A MET* 5.7 1.1 - - - -
524A ALA* 3.9 32.8 - - + +
527A ALA* 5.9 1.8 - - + -
528A LEU* 4.6 17.9 - - + +
592A VAL* 4.8 7.2 - - + -
593A VAL 2.9 12.2 + - - +
594A VAL* 4.0 19.2 - - + +
595A ASP* 2.6 34.8 + - - +
600A MET* 3.6 29.8 - - + -
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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