Contacts of the strand formed by residues 502 - 510 (chain B) in PDB entry 2VF8
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 TRP 502 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499B PRO* 3.7 21.9 - - + +
501B GLY* 1.3 87.0 + - - -
503B LEU* 1.3 61.1 + - - +
504B GLU* 4.3 0.7 - - + -
519B ARG* 3.1 59.2 - - + +
520B PHE 3.6 9.0 - - - -
521B PRO* 3.4 44.0 - - + -
522B LEU* 3.2 8.6 - - - +
578B GLY* 3.7 2.8 - - - -
579B ASP* 2.9 41.5 + - - +
801B TRP* 3.7 32.8 - + - -
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Residues in contact with LEU 503 (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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502B TRP* 1.3 76.1 - - - +
504B GLU* 1.3 72.9 + - - +
518B VAL 3.9 0.3 - - - +
519B ARG* 3.1 5.7 - - - -
520B PHE* 2.8 48.7 + - + +
522B LEU* 3.9 17.9 - - + -
544B LEU* 3.9 27.4 - - + -
548B LEU* 4.2 24.0 - - + -
576B LEU* 5.5 0.9 - - + -
577B GLY 4.3 1.8 - - - -
579B ASP 4.6 2.2 - - - +
580B LEU* 4.7 16.8 - - + +
583B ILE* 4.1 32.1 - - + -
754B VAL* 5.9 3.6 - - + -
787B ILE* 6.0 2.5 - - + -
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Residues in contact with GLU 504 (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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502B TRP 6.2 0.2 - - - -
503B LEU* 1.3 82.3 - - - +
505B LEU* 1.3 60.8 + - - +
506B ASN* 2.9 33.4 + - - +
518B VAL 3.5 3.1 - - - -
519B ARG* 3.3 40.4 + - + -
544B LEU* 5.7 0.2 - - - +
576B LEU* 3.4 8.8 - - - +
577B GLY* 2.6 48.7 + - - +
578B GLY* 4.5 6.2 + - - -
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Residues in contact with LEU 505 (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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503B LEU 4.1 0.2 + - - -
504B GLU* 1.3 74.1 - - - +
506B ASN* 1.3 61.4 + - - +
508B VAL* 3.7 22.4 - - + +
516B LEU 3.7 4.9 - - - +
518B VAL* 2.8 34.9 + - + +
520B PHE* 4.3 14.1 - - + -
539B LEU* 3.9 25.8 - - + +
543B ALA* 4.3 4.9 - - + -
544B LEU* 3.8 45.5 - - + +
547B ALA* 4.8 11.9 - - + -
574B ALA* 4.1 18.2 - - + -
575B ARG 4.1 3.1 - - - +
576B LEU* 4.5 2.7 - - + +
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Residues in contact with ASN 506 (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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504B GLU* 2.9 43.0 + - - +
505B LEU* 1.3 79.2 - - - +
507B GLY* 1.3 61.5 - - - +
508B VAL 3.3 3.4 + - - -
517B ASP* 3.0 25.4 - - - +
518B VAL 4.1 1.9 + - - -
519B ARG* 5.2 0.3 - - - +
574B ALA* 3.5 0.9 - - - +
575B ARG* 2.8 64.4 + - - +
576B LEU 5.2 1.6 - - - -
577B GLY 5.2 2.2 - - - +
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Residues in contact with GLY 507 (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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506B ASN* 1.3 72.9 - - - +
508B VAL* 1.3 67.0 + - - +
509B THR* 2.9 13.7 + - - -
515B ASN* 3.7 30.0 - - - +
516B LEU 3.1 2.2 + - - -
517B ASP* 2.5 17.0 + - - -
573B SER 3.9 1.7 - - - +
574B ALA* 3.4 7.1 - - - +
575B ARG* 4.3 10.5 + - - -
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Residues in contact with VAL 508 (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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505B LEU* 3.7 30.3 - - + +
506B ASN 3.3 1.4 - - - -
507B GLY* 1.3 69.6 - - - +
509B THR* 1.3 63.6 + - - +
510B ARG* 4.7 2.7 - - - -
513B LEU* 3.2 39.4 - - + +
515B ASN 3.0 15.4 + - - -
516B LEU* 3.0 33.6 + - + +
518B VAL* 5.3 0.4 - - + -
539B LEU* 3.9 16.2 - - + -
543B ALA* 3.7 19.7 - - + -
574B ALA* 3.1 10.5 - - + -
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Residues in contact with THR 509 (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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507B GLY 2.9 10.6 + - - -
508B VAL* 1.3 72.7 - - - +
510B ARG* 1.3 63.1 + - - +
513B LEU 2.9 8.1 - - - +
514B ASP* 3.9 17.6 - - - +
515B ASN* 2.9 24.3 + - - +
572B GLY* 3.0 33.1 + - - -
573B SER 3.5 9.4 + - - -
574B ALA* 4.1 0.2 - - - +
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Residues in contact with ARG 510 (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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508B VAL* 4.1 2.6 - - + -
509B THR* 1.3 77.8 - - - +
511B ASN* 1.3 72.2 + - - +
512B ASN 3.0 0.7 + - - -
513B LEU* 2.8 38.6 + - + +
538B THR* 4.3 9.6 - - - +
542B GLN* 3.9 18.4 + - - +
543B ALA* 3.7 38.6 + - - +
546B ASP* 3.8 24.2 + - - +
569B HIS* 6.1 0.4 - - - +
570B THR* 3.3 48.2 + - + +
571B ALA 4.5 2.0 + - - -
572B GLY* 2.7 29.4 + - - +
573B SER* 4.2 8.1 + - - +
574B ALA* 5.4 0.8 - - - +
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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