Contacts of the helix formed by residues 464 - 471 (chain A) in PDB entry 2XCV
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 464 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A LEU* 4.1 17.3 - - - -
59A VAL* 6.6 0.4 - - - -
369A PHE* 3.8 0.2 - - - -
371A VAL* 4.3 10.1 - - - -
462A ALA* 3.1 18.9 - - - +
463A ALA* 1.3 81.7 - - - +
465A PHE* 1.3 70.4 + - - +
466A ILE* 3.1 30.5 + - - +
467A ASN* 3.4 15.0 + - - +
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Residues in contact with PHE 465 (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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51A PHE* 3.6 19.1 - + + -
56A THR* 3.3 32.3 - - + -
57A LEU* 3.7 17.3 - - + -
232A LEU* 3.7 34.8 - - + -
235A LEU* 3.5 23.9 - - + +
349A ILE* 3.5 27.1 - - + -
369A PHE* 3.9 12.6 - - + -
371A VAL* 3.6 8.3 - - + +
464A SER* 1.3 74.0 + - - +
466A ILE* 1.3 82.0 + - + +
467A ASN 3.0 4.2 + - - -
468A LEU* 3.1 26.1 + - + +
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Residues in contact with ILE 466 (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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12A ALA* 6.3 3.1 - - + -
33A HIS* 6.4 0.2 - - + -
229A ASP* 3.8 20.4 - - - +
231A LYS* 3.5 49.8 - - + +
232A LEU* 3.6 11.0 - - + +
235A LEU* 4.0 16.4 - - + -
464A SER* 3.1 19.4 + - - +
465A PHE* 1.3 92.2 - - + +
467A ASN* 1.3 66.2 + - - +
469A LEU* 2.8 40.7 + - + +
470A TYR* 4.2 13.3 - - + +
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Residues in contact with ASN 467 (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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32A TYR 3.0 23.9 + - - +
33A HIS* 3.4 27.5 - - - +
34A ARG 3.1 17.6 + - - +
35A VAL* 3.7 17.7 - - + -
462A ALA* 3.8 9.7 - - + +
463A ALA 4.2 2.0 - - - +
464A SER* 3.6 21.6 + - - +
465A PHE 3.0 0.8 - - - -
466A ILE* 1.3 87.2 - - - +
468A LEU* 1.3 60.4 + - - +
469A LEU 3.1 0.9 + - - -
470A TYR* 3.2 23.8 + - - -
471A TYR* 3.3 14.2 - - - -
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Residues in contact with LEU 468 (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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35A VAL* 3.9 5.1 - - + +
43A MET* 4.8 14.8 - - + -
235A LEU* 4.1 13.3 - - + +
239A MET* 3.7 24.7 - - + -
347A LEU* 4.5 7.2 - - + -
349A ILE* 4.2 14.1 - - + -
369A PHE* 3.7 35.2 - - + -
460A LEU* 4.8 3.4 - - + -
465A PHE* 3.1 17.9 + - + +
467A ASN* 1.3 77.3 - - - +
469A LEU* 1.3 61.7 + - - +
470A TYR 3.2 0.9 + - - -
471A TYR* 3.2 22.7 + - + +
477A PHE* 4.1 28.5 - - + -
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Residues in contact with LEU 469 (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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17A ALA* 4.1 13.2 - - + -
19A MET* 3.8 34.2 - - + +
24A LEU* 4.1 5.0 - - - +
231A LYS* 4.0 33.9 - - + +
234A LEU* 3.9 12.1 - - + -
235A LEU* 3.8 25.8 - - + +
238A ARG* 3.8 22.8 + - - +
466A ILE* 2.8 24.4 + - + +
468A LEU* 1.3 72.2 - - - +
470A TYR* 1.3 77.5 + - + +
471A TYR 3.3 7.6 + - - +
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Residues in contact with TYR 470 (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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17A ALA* 5.8 2.7 - - + -
18A ASN 6.3 0.2 - - - -
24A LEU* 3.7 37.6 - - + +
27A TYR* 3.6 42.8 - + - -
28A ARG* 2.8 43.4 + - + +
33A HIS* 3.7 19.9 - + + -
231A LYS* 3.5 28.1 - - + +
466A ILE* 4.2 11.1 - - + +
467A ASN* 3.2 36.7 + - - +
468A LEU 3.1 1.6 - - - -
469A LEU* 1.3 98.4 - - + +
471A TYR* 1.3 59.1 + - - +
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Residues in contact with TYR 471 (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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24A LEU* 6.1 2.0 - - - -
28A ARG* 3.5 39.9 + - + +
33A HIS 4.2 1.3 - - - -
34A ARG* 3.5 14.9 + - - +
35A VAL* 3.1 53.6 + - + -
43A MET* 6.2 0.4 - - + -
238A ARG* 5.1 4.7 + - - -
467A ASN 3.3 18.8 - - - -
468A LEU* 3.2 16.5 + - + +
469A LEU 3.3 5.6 - - - +
470A TYR* 1.3 78.7 - - - +
472A PRO* 1.4 72.1 - - + +
475A TYR* 3.7 36.8 - + + -
477A PHE* 3.8 24.0 - + + -
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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