Contacts of the strand formed by residues 502 - 511 (chain C) in PDB entry 2VZE
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 502 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316C ARG* 3.5 14.2 - - - +
339C GLU* 4.5 6.5 - - - -
342C LEU* 6.0 1.1 - - - -
497C PRO* 3.8 5.9 - - - +
498C ASP 2.9 32.4 + - - +
501C ARG* 1.3 76.2 - - - +
503C GLU* 1.3 61.0 + - - +
568C TRP* 5.0 2.9 - - - -
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Residues in contact with GLU 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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339C GLU* 4.9 4.6 + - - +
465C ILE 4.7 2.3 - - - +
466C ILE* 4.2 2.2 - - + -
467C ASN* 3.4 40.4 + - - +
468C SER* 3.4 22.8 + - - -
469C SER 4.2 2.6 + - - -
495C SER* 3.3 35.2 + - - -
496C SER 3.5 5.6 - - - +
498C ASP 4.3 0.6 - - - +
501C ARG* 3.6 5.4 + - - +
502C GLY* 1.3 77.8 - - - +
504C VAL* 1.3 64.8 + - - +
568C TRP* 3.8 25.1 - - + -
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Residues in contact with VAL 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466C ILE* 4.6 3.4 - - - -
468C SER* 4.5 5.6 - - - +
495C SER* 3.4 6.8 - - - -
496C SER* 2.9 40.7 + - - +
498C ASP* 3.7 22.4 - - + -
501C ARG* 4.1 15.7 - - + -
503C GLU* 1.3 78.5 - - - +
505C VAL* 1.3 69.1 + - - +
542C ARG* 3.9 31.2 - - + +
543C LYS* 4.1 35.2 - - + -
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Residues in contact with VAL 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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466C ILE* 3.9 16.6 - - + -
468C SER* 4.4 4.6 + - - +
473C ILE* 3.6 33.2 - - + -
478C VAL* 4.3 3.8 - - + -
493C VAL* 3.8 23.1 - - + -
494C ILE 3.7 2.9 - - - -
504C VAL* 1.3 76.7 - - - +
506C LYS* 1.3 62.6 + - - +
538C TYR 5.2 0.9 - - - +
539C LYS 4.0 16.6 - - - +
540C TYR 3.7 12.5 + - - +
541C PRO* 3.4 19.0 - - + +
542C ARG* 2.9 28.7 + - - +
543C LYS 3.3 5.4 + - - -
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Residues in contact with LYS 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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492C ALA 3.8 0.3 - - - +
493C VAL* 3.2 4.0 - - - +
494C ILE* 2.8 52.3 + - + +
496C SER* 4.0 14.1 - - - -
505C VAL* 1.3 78.1 - - - +
507C ALA* 1.3 65.5 + - - +
508C PHE* 3.6 16.8 - - + -
543C LYS* 3.2 24.6 - - + +
544C ILE 5.1 0.4 - - - -
545C GLU* 2.8 42.3 + - - +
567C GLU* 2.6 46.2 + - + +
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Residues in contact with ALA 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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482C LEU* 3.3 34.3 - - + -
491C THR* 3.9 4.7 - - - +
492C ALA 3.4 4.5 - - - -
493C VAL* 3.7 8.7 - - + -
506C LYS* 1.3 75.5 - - - +
508C PHE* 1.3 61.6 + - - +
509C VAL* 4.1 5.6 - - + -
541C PRO* 4.0 11.6 - - + +
543C LYS 3.1 7.5 + - - -
544C ILE* 3.4 9.8 - - + +
545C GLU 3.1 23.4 + - - +
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Residues in contact with PHE 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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491C THR* 2.6 26.2 + - - -
492C ALA 2.8 26.2 + - - +
494C ILE* 3.6 29.6 - - + -
506C LYS* 3.6 14.8 - - - -
507C ALA* 1.3 72.7 - - - +
509C VAL* 1.3 55.9 + - - +
545C GLU* 3.1 43.1 - - + +
547C VAL* 4.1 15.3 - - + -
550C LEU* 3.6 22.0 - - + +
563C LEU* 3.4 47.3 - - + -
567C GLU* 3.7 11.4 - - - -
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Residues in contact with VAL 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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482C LEU* 4.5 7.6 - - + -
488C VAL* 4.2 25.8 - - + -
490C GLU 3.7 2.5 - - - -
491C THR* 3.5 16.4 - - - +
507C ALA* 4.1 13.2 - - + -
508C PHE* 1.3 78.5 - - - +
510C VAL* 1.3 74.7 + - - +
511C LEU* 3.8 7.2 + - + +
527C LEU* 4.7 5.4 - - + -
544C ILE* 4.3 11.7 - - + -
545C GLU 2.9 9.6 + - - +
546C PHE* 3.3 32.1 - - + +
547C VAL* 3.0 23.3 + - - +
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Residues in contact with VAL 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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487C ALA 3.8 1.2 - - - +
488C VAL 3.9 0.3 - - - -
489C VAL* 3.0 50.7 + - + +
490C GLU* 3.0 30.4 + - + +
509C VAL* 1.3 73.0 - - - +
511C LEU* 1.3 63.9 + - - +
547C VAL* 3.3 21.5 - - + +
548C LEU* 3.6 26.7 - - - +
549C ASN* 4.1 12.6 - - - +
550C LEU* 4.3 5.4 - - + -
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Residues in contact with LEU 511 (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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487C ALA* 3.3 20.4 - - + +
489C VAL* 4.1 3.2 - - - +
509C VAL* 3.8 6.4 + - + +
510C VAL* 1.3 82.9 - - - +
512C ALA* 1.3 67.4 + - - +
513C SER* 4.0 0.5 + - - -
515C PHE* 4.4 7.4 - - + +
516C LEU* 4.2 25.6 - - + +
520C PRO* 5.9 3.8 - - + -
523C LEU* 3.4 34.3 - - + -
527C LEU* 4.8 1.3 - - + -
546C PHE* 3.5 48.7 - - + +
547C VAL 4.4 2.2 + - - -
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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