Contacts of the strand formed by residues 502 - 510 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499A PRO* 4.2 25.1 + - + +
501A GLY* 1.3 82.1 + - - +
503A LEU* 1.3 59.8 + - - +
504A GLU* 4.2 0.9 - - + -
519A ARG* 3.2 63.3 - - + +
520A PHE 3.7 7.2 - - - -
521A PRO* 3.5 39.3 - - + -
522A LEU* 4.2 4.2 - - - +
578A GLY* 3.8 3.0 - - - -
579A ASP* 2.8 42.2 + - - +
801A TRP* 3.7 39.9 - + - -
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Residues in contact with LEU 503 (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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502A TRP* 1.3 74.3 - - - +
504A GLU* 1.3 82.9 + - - +
505A LEU* 4.8 1.6 - - + +
519A ARG* 3.3 1.5 - - - -
520A PHE* 2.7 52.4 + - + +
522A LEU* 4.1 20.2 - - + +
544A LEU* 4.5 22.0 - - + -
548A LEU* 4.6 18.2 - - + -
576A LEU* 4.3 18.2 - - + -
577A GLY 3.5 10.5 - - - +
579A ASP 4.7 2.0 - - - +
580A LEU* 4.6 12.6 - - + -
583A ILE* 5.3 7.9 - - + -
754A VAL* 5.5 3.1 - - + -
787A ILE* 5.3 6.3 - - + -
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Residues in contact with GLU 504 (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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502A TRP* 5.1 0.9 - - + +
503A LEU* 1.3 83.1 - - - +
505A LEU* 1.3 59.5 + - - +
506A ASN* 3.1 28.7 + - - +
518A VAL 3.3 9.4 - - - +
519A ARG* 3.7 32.9 + - + +
576A LEU* 3.4 5.4 - - - -
577A GLY* 3.0 35.4 + - - +
578A GLY* 3.9 17.2 + - - -
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Residues in contact with LEU 505 (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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503A LEU* 4.0 2.5 + - + +
504A GLU* 1.3 72.5 - - - +
506A ASN* 1.3 59.2 + - - +
508A VAL* 3.6 25.6 - - + -
516A LEU 4.0 1.6 - - - +
517A ASP* 3.8 1.0 - - - -
518A VAL* 2.8 41.6 + - + +
520A PHE* 4.3 9.1 - - + -
539A LEU* 3.9 31.6 - - + +
543A ALA* 4.1 10.1 - - + +
544A LEU* 4.2 17.7 - - + +
547A ALA* 3.8 22.4 - - + -
574A ALA* 3.5 28.9 - - + -
575A ARG 3.6 4.3 - - - +
576A LEU* 4.9 2.7 - - + +
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Residues in contact with ASN 506 (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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504A GLU* 3.1 40.2 + - - +
505A LEU* 1.3 76.1 - - - +
507A GLY* 1.3 68.3 + - - +
508A VAL 3.1 3.7 + - - -
517A ASP* 3.6 25.6 - - - +
518A VAL 4.1 2.3 + - - -
574A ALA* 3.8 2.1 - - - +
575A ARG* 2.8 57.8 + - + +
576A LEU 4.2 14.1 + - - -
577A GLY* 4.7 0.2 - - - -
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Residues in contact with GLY 507 (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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506A ASN* 1.3 71.3 - - - +
508A VAL* 1.3 64.0 + - - +
509A THR* 3.2 5.9 + - - -
515A ASN* 3.5 23.6 - - - +
516A LEU 3.0 6.5 + - - -
517A ASP* 2.7 24.3 + - - -
573A SER 4.5 4.2 - - - +
574A ALA* 4.3 7.4 - - - -
575A ARG* 4.3 12.1 + - - -
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Residues in contact with VAL 508 (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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505A LEU* 3.6 33.4 - - + +
506A ASN 3.1 2.3 + - - -
507A GLY* 1.3 70.8 - - - +
509A THR* 1.3 59.7 + - - +
510A ARG* 4.3 7.6 - - + +
513A LEU* 3.5 35.3 - - + +
514A ASP 3.8 1.4 - - - -
515A ASN 3.1 2.6 + - - -
516A LEU* 3.0 38.2 + - + +
518A VAL* 5.4 0.7 - - + -
539A LEU* 4.5 6.7 - - + -
543A ALA* 3.9 23.8 - - + -
572A GLY 5.3 2.9 - - - +
574A ALA* 4.5 9.4 - - + +
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Residues in contact with THR 509 (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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507A GLY 3.2 7.4 + - - -
508A VAL* 1.3 69.7 - - - +
510A ARG* 1.3 67.3 + - - +
511A ASN 5.8 0.2 - - - +
513A LEU 3.8 5.2 - - - +
514A ASP* 3.2 15.2 + - - +
515A ASN* 2.6 30.2 + - - +
572A GLY* 3.4 21.5 + - - +
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Residues in contact with ARG 510 (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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508A VAL* 3.9 8.1 - - + -
509A THR* 1.3 77.2 - - - +
511A ASN* 1.3 80.0 + - - +
513A LEU* 3.0 24.8 + - - +
538A THR* 3.7 36.8 - - - +
542A GLN* 3.9 27.3 + - - +
543A ALA* 4.1 6.3 - - - +
546A ASP* 4.1 16.0 + - - -
572A GLY* 3.5 32.5 - - - +
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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