Contacts of the strand formed by residues 514 - 523 (chain C) in PDB entry 6VVT
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 514 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510C VAL* 3.9 3.1 - - - +
511C GLU 3.2 28.6 + - - +
512C ASN* 3.2 4.5 - - + +
513C GLY* 1.3 80.4 - - - +
515C VAL* 1.3 67.7 + - - +
516C THR* 3.3 4.3 + - - -
543C GLY* 5.3 5.6 - - - -
544C ARG* 4.8 8.5 - - - +
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Residues in contact with VAL 515 (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 ARG* 3.4 35.0 - - - +
510C VAL* 4.8 8.5 - - - +
513C GLY 4.3 0.8 + - - -
514C VAL* 1.3 72.2 - - - +
516C THR* 1.3 60.2 + - - +
517C ASP* 3.9 7.5 + - - +
543C GLY* 5.5 4.7 - - - -
544C ARG* 5.5 2.8 - - - +
570C MET* 5.0 5.2 - - + -
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Residues in contact with THR 516 (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 ARG* 3.3 24.3 + - - +
509C LYS* 2.9 26.9 + - - +
511C GLU* 5.2 6.3 - - - -
514C VAL 3.3 5.3 + - - -
515C VAL* 1.3 73.0 - - - +
517C ASP* 1.3 59.6 + - - +
518C GLN* 3.0 20.3 + - - +
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Residues in contact with ASP 517 (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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36C ARG* 5.0 9.0 + - - -
38C PRO* 5.4 3.1 - - - +
508C ARG* 4.3 18.8 + - - +
515C VAL 4.6 5.7 - - - +
516C THR* 1.3 70.4 - - - +
518C GLN* 1.3 56.6 + - - +
519C ILE* 3.1 12.5 + - - +
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Residues in contact with GLN 518 (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 TYR 3.7 0.3 - - - +
508C ARG* 3.4 17.1 - - - -
509C LYS* 3.5 12.5 + - + +
516C THR* 3.0 12.3 + - - +
517C ASP* 1.3 73.8 - - - +
519C ILE* 1.3 61.9 + - - +
520C ASP* 3.8 3.6 + - + +
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Residues in contact with ILE 519 (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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39C LEU* 5.1 15.7 - - + -
506C PRO* 5.4 1.8 - - + -
507C TYR 3.0 14.8 - - - +
508C ARG* 4.3 3.8 - - + +
517C ASP 3.1 9.1 + - - +
518C GLN* 1.3 71.2 - - - +
520C ASP* 1.3 59.8 + - - +
572C VAL* 4.7 11.9 - - + -
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Residues in contact with ASP 520 (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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496C ARG* 4.3 4.5 - - - -
505C THR 3.6 1.9 - - - +
506C PRO* 4.1 1.5 - - - +
507C TYR* 2.7 37.0 + - - +
509C LYS* 6.1 3.8 - - + +
518C GLN* 3.8 4.2 + - + +
519C ILE* 1.3 74.1 - - - +
521C TYR* 1.3 67.0 + - - +
522C LEU* 3.6 10.7 + - + -
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Residues in contact with TYR 521 (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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496C ARG* 3.0 41.8 - - - +
498C ASN* 4.4 7.6 - - - +
504C GLU* 3.9 9.2 - - + -
505C THR 4.1 1.8 - - - -
520C ASP* 1.3 73.3 - - - +
522C LEU* 1.3 69.8 + - - +
523C THR 4.1 1.4 + - - -
526C GLU* 5.2 0.3 - - - +
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Residues in contact with LEU 522 (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* 4.7 0.2 - - - -
505C THR* 3.6 25.6 + - - +
507C TYR* 3.3 46.8 - - + -
520C ASP* 4.4 9.9 - - + +
521C TYR* 1.3 82.6 - - - +
523C THR* 1.3 69.3 + - - +
526C GLU* 4.1 30.5 - - + +
527C GLU* 4.3 6.6 - - - +
530C HIS* 5.1 9.4 - - + +
532C VAL* 5.7 2.0 - - + -
569C TYR* 4.3 16.6 - - + -
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Residues in contact with THR 523 (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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365C GLY 5.7 0.5 + - - -
498C ASN* 5.9 4.3 - - - -
502C PHE* 4.2 17.1 - - - +
503C ILE 3.7 20.1 + - - -
504C GLU* 4.5 5.1 - - - +
521C TYR 4.1 1.6 + - - -
522C LEU* 1.3 79.6 - - - +
524C ALA* 1.3 75.7 + - - +
525C ASP* 3.8 9.3 + - + +
526C GLU* 3.4 25.6 - - + +
527C GLU* 3.0 17.8 + - - +
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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