Contacts of the helix formed by residues 463 - 471 (chain A) in PDB entry 3C5R
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 THR 463 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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433A HIS* 4.0 2.9 - - - -
454A PRO 4.4 6.5 - - - -
455A ASN* 5.5 2.7 - - - +
456A VAL 3.3 13.7 - - - +
457A LYS* 3.8 15.7 - - + -
461A GLY 4.1 1.1 - - - +
462A TRP* 1.3 77.6 - - - +
464A PRO* 1.3 73.6 - - - +
465A LEU* 3.3 10.9 + - - +
466A HIS* 2.8 53.1 + - + +
467A GLU* 3.1 12.6 + - - +
489A THR* 4.1 17.1 - - + -
497A PRO* 5.3 0.2 - - - +
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Residues in contact with PRO 464 (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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432A LEU* 3.9 28.9 - - + -
433A HIS* 3.6 23.1 - - + +
436A SER* 3.4 31.1 - - - +
454A PRO 3.6 11.2 - - - +
456A VAL* 3.3 24.9 - - + +
463A THR* 1.3 86.9 - - - +
465A LEU* 1.3 56.0 - - - +
467A GLU* 3.3 2.9 + - + -
468A ALA 3.0 23.2 + - - -
480A LEU* 3.5 14.4 - - + +
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Residues in contact with LEU 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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454A PRO 5.0 1.9 + - - +
463A THR* 3.1 9.4 + - - +
464A PRO* 1.3 77.0 - - - +
466A HIS* 1.3 65.6 + - - +
468A ALA* 3.3 0.9 + - - -
469A CYS* 3.0 33.2 + - - -
477A VAL* 3.8 42.8 - - + +
480A LEU* 3.6 15.1 - - + +
481A LEU* 4.1 14.4 - - + -
485A ALA* 4.4 13.5 - - + -
486A LEU 3.7 19.5 - - - +
487A VAL* 4.1 10.5 - - - -
497A PRO* 3.6 29.2 - - + -
513A LEU* 4.5 2.7 - - + -
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Residues in contact with HIS 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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462A TRP* 3.7 22.2 - + + -
463A THR* 2.8 50.7 + - + +
465A LEU* 1.3 74.9 - - - +
467A GLU* 1.3 57.4 + - - +
469A CYS* 3.4 5.0 + - - +
470A ASN* 3.0 30.0 + - - +
489A THR* 3.0 23.6 + - - -
491A GLY* 3.3 19.5 + - - -
492A TYR 5.4 0.7 - - - -
495A ASP* 2.8 29.0 + - + -
497A PRO* 3.5 20.7 - - + +
500A ASP* 3.3 23.4 - - - +
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Residues in contact with GLU 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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429A GLU* 5.2 2.4 - - - +
433A HIS* 4.7 8.0 - - + +
436A SER* 4.4 3.8 - - - -
437A ILE* 3.5 40.7 - - + +
458A ASP* 4.4 5.5 - - - +
462A TRP* 3.5 38.3 - - + +
463A THR 3.1 13.1 + - - +
464A PRO* 3.5 9.9 - - + +
465A LEU 3.2 0.2 - - - -
466A HIS* 1.3 77.2 - - - +
468A ALA* 1.3 56.5 + - - +
470A ASN* 3.4 1.3 + - - +
471A HIS* 3.0 59.1 + - - +
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Residues in contact with ALA 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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436A SER 3.9 10.0 + - - +
464A PRO 3.0 14.5 + - - +
465A LEU 3.3 2.9 + - - +
467A GLU* 1.3 74.6 - - - +
469A CYS* 1.3 58.3 + - - +
471A HIS 3.7 0.2 - - - -
472A GLY* 3.0 8.5 + - - -
473A HIS* 2.9 31.3 + - + +
476A VAL* 3.5 33.2 - - + -
477A VAL* 3.6 20.8 - - + +
480A LEU* 4.0 4.0 - - + -
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Residues in contact with CYS 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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465A LEU* 3.0 31.5 + - - +
466A HIS 3.7 4.0 - - - +
468A ALA* 1.3 73.8 - - - +
470A ASN* 1.3 65.6 + - - +
472A GLY* 3.5 2.4 + - - -
477A VAL* 3.7 12.8 - - - -
497A PRO* 3.5 28.0 - - + +
500A ASP* 4.1 2.5 - - + -
501A ALA* 3.6 14.8 - - + +
506A HIS* 3.3 20.3 - - - -
509A ILE* 3.7 13.9 - - - +
513A LEU* 3.7 28.3 - - - -
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Residues in contact with ASN 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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462A TRP* 3.6 22.5 - - + -
466A HIS 3.0 17.1 + - - +
467A GLU 3.7 4.5 - - - +
469A CYS* 1.3 77.0 - - - +
471A HIS* 1.3 72.0 + - - +
472A GLY 3.3 0.2 - - - -
500A ASP* 2.7 28.6 + - - +
503A LYS* 5.0 4.9 - - - +
504A ASN* 3.2 41.2 + - - +
506A HIS* 3.4 9.4 + - - -
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Residues in contact with HIS 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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437A ILE* 3.6 33.0 + - + +
467A GLU* 3.0 47.6 + - - +
470A ASN* 1.3 90.1 + - - +
472A GLY* 1.3 61.9 + - - +
473A HIS* 3.4 33.0 - - + +
506A HIS* 3.9 4.8 + - - -
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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