Contacts of the helix formed by residues 467 - 477 (chain B) in PDB entry 3VRY
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 SER 467 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427B LYS* 4.5 0.2 - - - -
465B GLY 3.6 2.2 + - - -
466B MET* 1.3 76.4 - - - +
468B ASN* 1.3 65.0 + - - +
469B PRO* 3.1 22.1 - - - +
470B GLU* 3.0 33.1 + - - +
471B VAL* 2.9 23.8 + - - +
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Residues in contact with ASN 468 (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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424B PHE* 3.8 41.7 + - + -
426B ILE* 3.4 34.5 + - + +
427B LYS* 4.0 21.9 - - - +
467B SER* 1.3 76.4 - - - +
469B PRO* 1.3 69.3 - - + +
471B VAL* 3.3 10.8 + - - +
472B ILE* 3.3 8.5 + - - +
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Residues in contact with PRO 469 (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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426B ILE* 5.1 0.2 - - + -
467B SER* 3.1 13.7 - - - +
468B ASN* 1.3 91.9 - - + +
470B GLU* 1.3 64.4 + - - +
472B ILE* 3.3 13.3 + - + +
473B ARG* 3.3 44.7 + - + +
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Residues in contact with GLU 470 (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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465B GLY 4.4 2.3 - - - +
466B MET* 3.7 19.6 - - + -
467B SER* 3.0 43.2 + - - +
469B PRO* 1.3 78.8 - - - +
471B VAL* 1.3 63.4 + - - +
473B ARG* 3.4 27.2 + - - +
474B ALA* 3.1 23.0 + - - +
477B ARG* 5.4 1.0 + - - -
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Residues in contact with VAL 471 (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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426B ILE* 4.8 11.9 - - + +
427B LYS* 3.9 13.5 - - + -
463B TYR* 3.6 51.5 - - + -
466B MET* 3.6 20.4 - - + -
467B SER 2.9 17.4 + - - +
468B ASN* 3.6 8.3 - - - +
470B GLU* 1.3 75.8 - - - +
472B ILE* 1.3 64.1 + - + +
474B ALA* 3.2 3.5 + - - +
475B LEU* 2.9 39.7 + - + +
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Residues in contact with ILE 472 (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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426B ILE* 3.7 23.3 - - + -
434B ILE* 3.9 35.0 - - + -
435B ASN* 5.3 6.1 - - - +
468B ASN 3.3 12.1 + - - +
469B PRO* 3.3 12.8 + - + +
470B GLU 3.2 0.8 - - - -
471B VAL* 1.3 77.2 - - + +
473B ARG* 1.3 63.6 + - + +
475B LEU* 2.9 30.2 + - + +
476B GLU* 3.5 5.9 + - - +
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Residues in contact with ARG 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B PRO* 3.3 37.4 + - + +
470B GLU* 4.0 30.8 + - - +
472B ILE* 1.3 78.7 - - + +
474B ALA* 1.3 61.2 + - - +
476B GLU* 3.5 5.9 + - - +
477B ARG* 3.2 40.1 + - - +
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Residues in contact with ALA 474 (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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466B MET* 4.1 16.8 - - + -
470B GLU 3.1 17.8 + - - +
471B VAL 3.5 5.2 - - - +
473B ARG* 1.3 78.0 - - - +
475B LEU* 1.3 57.7 + - - +
477B ARG* 3.4 25.6 - - - +
478B GLY 3.2 5.5 + - - -
479B TYR* 2.9 45.5 + - + +
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Residues in contact with LEU 475 (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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426B ILE 5.3 1.1 - - - +
429B THR 4.7 3.4 - - - +
431B PRO* 4.6 18.8 - - + +
434B ILE* 4.7 17.3 - - + -
446B TRP* 4.2 23.6 - - + -
463B TYR* 3.9 25.1 - - + +
471B VAL* 2.9 31.2 + - + +
472B ILE* 2.9 12.6 + - + +
474B ALA* 1.3 76.7 - - - +
476B GLU* 1.3 62.1 + - - +
478B GLY* 3.5 7.4 + - - -
479B TYR* 3.6 20.4 - - + +
480B ARG* 3.7 20.2 + - - +
501B ASN* 3.9 11.8 - - - +
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Residues in contact with GLU 476 (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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472B ILE 3.5 5.5 + - - +
473B ARG* 3.5 7.8 + - - +
475B LEU* 1.3 75.0 - - - +
477B ARG* 1.3 59.2 + - - +
478B GLY* 2.8 12.7 + - - -
501B ASN* 4.4 13.3 - - - +
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Residues in contact with ARG 477 (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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470B GLU 5.4 1.0 + - - -
473B ARG* 3.2 39.5 + - - +
474B ALA* 3.4 27.8 - - - +
476B GLU* 1.3 74.2 - - - +
478B GLY* 1.3 59.3 + - - +
479B TYR* 3.8 6.9 + - + +
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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