Contacts of the strand formed by residues 505 - 512 (chain V) in PDB entry 5IY8
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 505 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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494V MET* 4.1 19.3 - - + -
503V ALA* 4.0 6.4 + - + -
504V LYS* 1.3 73.3 - - - +
506V GLN* 1.3 74.3 + - - +
507V CYS* 3.2 20.9 + - - -
640V LEU* 4.0 18.2 - - + -
644V LEU* 4.2 16.2 - - + -
654V GLU 5.4 0.2 - - - -
655V TYR* 4.3 1.6 - - - -
657V ALA* 3.5 19.5 - - + +
659V PHE* 3.9 20.0 - - + +
685V TYR* 4.2 15.8 - - + -
686V SER* 3.8 12.7 + - - +
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Residues in contact with GLN 506 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505V VAL* 1.3 69.5 - - - +
507V CYS* 1.3 84.7 + - - +
508V ALA* 5.1 3.0 - - + +
655V TYR* 3.7 42.6 - - + +
657V ALA 3.1 7.5 + - - +
658V PHE* 3.6 24.0 - - + -
659V PHE 3.1 23.4 + - - +
660V TYR* 5.9 0.4 - - + -
686V SER* 3.6 23.1 + - - -
687V PHE 4.2 0.6 - - - +
688V LYS* 3.1 42.7 + - + +
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Residues in contact with CYS 507 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505V VAL* 3.8 15.3 - - - -
506V GLN* 1.3 90.2 + - - +
508V ALA* 1.3 60.5 + - - +
640V LEU* 4.0 17.5 - - - -
659V PHE* 3.7 11.4 - - + -
680V LEU* 4.3 4.3 - - - -
685V TYR* 3.7 33.7 - - - -
686V SER 3.0 17.1 + - - +
687V PHE* 3.3 22.8 - - + -
688V LYS* 3.0 14.6 + - - +
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Residues in contact with ALA 508 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506V GLN* 5.1 4.0 - - + +
507V CYS* 1.3 76.4 - - - +
509V GLU* 1.3 60.0 + - - +
659V PHE* 2.9 16.9 + - - +
660V TYR* 3.4 15.9 - - + -
661V SER* 3.0 24.6 + - - -
687V PHE* 4.3 6.7 - - - -
688V LYS* 3.3 15.0 - - + +
690V ILE* 3.7 31.2 - - + -
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Residues in contact with GLU 509 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508V ALA* 1.3 74.0 - - - +
510V VAL* 1.3 63.9 + - - +
511V TRP* 3.3 19.9 + - + -
661V SER* 3.4 8.3 - - - +
663V VAL* 3.5 22.1 - - + +
673V SER* 2.5 36.2 + - - -
676V ARG* 2.7 35.4 + - - +
687V PHE* 3.9 19.3 - - + -
688V LYS 2.9 8.3 + - - +
689V VAL* 3.4 11.9 - - + +
690V ILE* 2.8 28.1 + - - +
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Residues in contact with VAL 510 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508V ALA 4.9 0.4 - - - +
509V GLU* 1.3 77.8 - - - +
511V TRP* 1.3 71.4 + - - +
512V CYS* 3.6 14.5 + - - -
543V ALA* 5.0 4.5 - - + -
547V LEU* 4.5 7.9 - - + -
660V TYR* 4.4 15.3 - - + -
661V SER 2.8 15.6 + - - +
662V LEU* 4.1 20.4 - - + -
663V VAL* 2.9 31.1 + - - +
690V ILE* 3.3 34.5 - - + +
691V THR 6.1 0.2 - - - -
692V LYS 6.4 0.4 - - - -
693V LEU* 4.9 16.2 - - + -
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Residues in contact with TRP 511 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3912 ILE* 5.2 10.1 - - + -
3952 GLU* 3.0 50.5 - - + -
3982 ARG* 6.5 1.1 - - - -
509V GLU* 3.3 25.9 + - + -
510V VAL* 1.3 78.1 - - - +
512V CYS* 1.3 61.6 + - - +
513V PRO* 4.5 1.0 - - - +
663V VAL* 3.6 17.2 - - + +
665V GLN* 3.9 26.6 - - + +
670V MET* 4.0 16.0 - - + +
673V SER* 4.7 6.6 + - - -
689V VAL* 3.7 27.3 - - + +
690V ILE 2.9 15.6 + - - +
691V THR* 3.5 41.5 - - + +
692V LYS* 5.4 0.2 - - - -
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Residues in contact with CYS 512 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510V VAL* 3.7 25.8 - - - -
511V TRP* 1.3 77.2 - - - +
513V PRO* 1.3 71.6 - - + +
537V ASN* 4.5 0.7 - - - +
539V ASN 4.7 1.8 - - - +
540V LYS* 3.9 43.5 - - + +
543V ALA* 4.2 11.9 - - - -
662V LEU* 4.8 3.4 - - - -
663V VAL 2.9 14.3 + - - +
664V SER* 3.6 1.2 - - - -
665V GLN* 2.8 34.0 + - - +
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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