Contacts of the strand formed by residues 501 - 510 (chain C) in PDB entry 2VF7
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 GLY 501 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499C PRO* 3.2 3.4 - - - +
500C ALA* 1.3 78.6 - - - +
502C TRP* 1.3 68.2 + - - -
521C PRO* 3.5 4.0 - - - +
522C LEU* 2.7 35.1 + - - +
579C ASP* 3.5 10.3 - - - -
582C GLN* 3.9 12.6 - - - +
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Residues in contact with TRP 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B GLU* 6.5 0.4 - - + -
341B ASN* 3.3 36.7 + - + +
499C PRO* 3.5 35.1 + - + +
501C GLY* 1.3 80.9 - - - -
503C LEU* 1.3 63.5 + - - +
504C GLU* 4.7 2.5 - - - +
519C ARG* 3.8 39.9 - - + +
520C PHE 3.4 5.6 - - - -
521C PRO* 3.6 35.4 - - + -
522C LEU* 4.6 0.4 - - - -
578C GLY* 3.6 5.7 - - - -
579C ASP* 2.7 37.5 + - - +
801C TRP* 3.5 42.8 - + - -
819C GLN* 5.0 1.8 - - - -
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Residues in contact with LEU 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502C TRP* 1.3 72.9 - - - +
504C GLU* 1.3 76.5 + - - +
505C LEU 4.0 2.7 - - - +
518C VAL 3.8 0.2 - - - +
519C ARG* 3.2 7.1 - - - +
520C PHE* 2.6 56.1 + - + +
522C LEU* 4.0 24.9 - - + +
544C LEU* 4.0 22.9 - - + -
548C LEU* 4.5 8.7 - - + -
576C LEU* 3.8 18.8 - - + -
577C GLY 4.0 4.0 - - - -
579C ASP 4.7 2.0 - - - +
580C LEU* 4.3 13.2 - - + -
583C ILE* 4.1 20.2 - - + -
754C VAL* 5.6 2.0 - - + -
787C ILE* 5.4 5.6 - - + -
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Residues in contact with GLU 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B LYS* 5.4 0.5 + - - -
502C TRP 4.7 2.1 - - - +
503C LEU* 1.3 83.9 - - - +
505C LEU* 1.3 58.3 + - - +
506C ASN* 3.2 30.0 + - - +
518C VAL 3.5 3.4 - - - -
519C ARG* 3.6 34.6 + - + +
575C ARG 3.6 0.9 - - - +
576C LEU* 3.4 6.1 - - - -
577C GLY* 2.7 41.7 + - - -
578C GLY* 4.2 19.7 + - - +
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Residues in contact with LEU 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503C LEU* 4.0 3.8 - - + +
504C GLU* 1.3 70.5 - - - +
506C ASN* 1.3 63.3 + - - +
508C VAL* 3.7 17.0 - - + +
516C LEU 3.6 6.9 - - - +
518C VAL* 3.0 33.9 + - + +
520C PHE* 4.4 12.5 - - + -
539C LEU* 4.1 15.5 - - + +
543C ALA 4.1 2.0 - - - +
544C LEU* 3.7 46.7 - - + +
547C ALA* 4.2 17.3 - - + -
574C ALA* 3.5 31.2 - - + -
575C ARG 4.2 4.9 - - - +
576C LEU* 4.3 6.3 - - + -
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Residues in contact with ASN 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504C GLU* 3.2 38.5 + - - +
505C LEU* 1.3 78.0 + - - +
507C GLY* 1.3 61.9 + - - +
508C VAL 3.4 1.2 + - - -
517C ASP* 3.2 24.2 - - - +
518C VAL 4.4 2.3 + - - +
519C ARG* 6.0 0.5 - - - +
574C ALA* 3.6 1.9 - - - +
575C ARG* 2.9 64.6 + - + +
576C LEU 5.5 0.4 + - - -
577C GLY* 5.1 4.4 - - - -
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Residues in contact with GLY 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506C ASN* 1.3 72.9 - - - +
508C VAL* 1.3 65.1 + - - +
509C THR* 3.3 13.5 + - - +
515C ASN* 3.6 19.7 - - - +
516C LEU 3.2 4.6 + - - -
517C ASP* 2.9 12.5 + - - -
573C SER* 3.3 9.6 + - - +
574C ALA* 4.1 1.9 - - - -
575C ARG* 3.4 22.8 + - - +
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Residues in contact with VAL 508 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505C LEU* 3.7 44.2 - - + +
507C GLY* 1.3 69.8 - - - -
509C THR* 1.3 59.7 + - - +
510C ARG* 4.2 4.3 - - - -
513C LEU* 3.7 24.6 - - + -
514C ASP* 3.7 3.6 + - - -
515C ASN 3.0 5.5 + - - -
516C LEU* 2.8 50.1 + - + +
518C VAL* 5.7 0.2 - - + -
539C LEU* 4.3 10.3 - - + -
543C ALA* 3.5 26.9 - - + -
573C SER 3.6 7.4 - - - +
574C ALA* 4.0 1.6 - - + -
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Residues in contact with THR 509 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507C GLY 3.4 13.2 - - - +
508C VAL* 1.3 76.3 - - - +
510C ARG* 1.3 62.8 + - - +
513C LEU 3.3 8.9 + - - -
514C ASP* 4.1 5.9 - - - +
515C ASN* 3.5 15.7 - - + +
572C GLY* 3.2 20.0 + - - -
573C SER* 3.3 29.1 + - - +
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Residues in contact with ARG 510 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508C VAL* 4.2 2.0 - - + -
509C THR* 1.3 75.4 - - - +
511C ASN* 1.3 75.4 + - - +
512C ASN 3.2 0.5 + - - -
513C LEU* 2.9 27.9 + - + +
538C THR* 3.1 33.7 - - + -
542C GLN* 4.0 26.6 + - - +
543C ALA* 4.0 21.4 - - - +
546C ASP* 4.0 20.1 + - - +
572C GLY* 3.5 42.7 + - - +
573C SER* 4.3 2.3 - - - +
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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