Contacts of the helix formed by residues 496 - 504 (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 SER 496 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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466A HIS* 3.8 2.2 - - - -
488A ASN* 4.6 13.7 - - - -
489A THR 3.6 5.8 - - - -
490A THR* 4.9 1.8 - - - +
494A ASN 3.5 3.1 + - - -
495A ASP* 1.3 75.1 - - - +
497A PRO* 1.4 72.7 - - - +
498A LEU* 3.4 11.7 + - - +
499A HIS* 2.8 54.6 + - - +
500A ASP* 3.3 8.5 + - - +
519A SER 5.1 0.6 + - - -
522A ALA* 4.3 15.5 - - - +
530A PRO* 4.5 0.5 - - - +
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Residues in contact with PRO 497 (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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463A THR* 5.3 0.2 - - - +
465A LEU* 3.6 24.9 - - + +
466A HIS* 3.5 21.7 - - + +
469A CYS* 3.5 23.9 - - + +
486A LEU 4.6 1.8 - - - +
487A VAL 3.3 27.4 - - - +
489A THR* 3.1 18.6 - - - +
496A SER* 1.4 85.2 - - - +
498A LEU* 1.3 60.2 + - - +
500A ASP* 3.3 6.4 + - - +
501A ALA 3.1 18.4 + - - -
513A LEU* 3.5 13.9 - - + +
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Residues in contact with LEU 498 (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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487A VAL 5.2 0.8 + - - +
496A SER* 3.1 10.4 + - - +
497A PRO* 1.3 75.4 - - - +
499A HIS* 1.3 60.4 + - - +
501A ALA* 3.4 0.5 + - - -
502A ALA* 2.8 33.8 + - - +
510A VAL* 4.0 30.5 - - + +
513A LEU* 3.6 31.2 - - + +
514A LEU* 4.1 10.5 - - + -
518A ALA* 4.3 10.7 - - + +
519A SER 3.5 26.0 - - - +
520A ARG* 3.8 15.5 - - - -
530A PRO* 3.8 17.9 - - + -
543A LEU* 3.9 10.1 - - + -
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Residues in contact with HIS 499 (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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494A ASN 4.8 0.2 - - - -
495A ASP* 3.4 28.7 - - - +
496A SER* 2.8 45.3 + - - +
498A LEU* 1.3 75.3 - - - +
500A ASP* 1.3 54.6 + - - +
502A ALA* 3.7 0.5 - - - +
503A LYS* 2.8 40.9 + - + +
522A ALA* 3.3 24.7 - - + -
523A VAL 4.0 1.1 - - - -
524A ASN* 3.8 17.4 + - - -
528A LEU 2.8 25.2 + - - -
529A ARG 3.7 5.2 - - - -
530A PRO* 3.4 30.3 - - + +
533A TYR* 4.0 9.5 - + + +
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Residues in contact with ASP 500 (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 12.0 - - - -
466A HIS* 3.3 41.3 - - - +
469A CYS* 4.0 2.2 - - + -
470A ASN* 2.7 43.9 + - - +
495A ASP* 4.3 10.3 - - - +
496A SER 3.3 5.6 + - - +
497A PRO 3.3 9.7 + - - +
499A HIS* 1.3 78.9 - - - +
501A ALA* 1.3 60.3 + - - +
503A LYS* 3.5 11.2 + - - +
504A ASN* 2.9 31.5 + - - +
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Residues in contact with ALA 501 (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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469A CYS* 3.6 14.3 + - + +
497A PRO 3.1 14.3 + - - +
498A LEU 4.1 0.9 - - - +
500A ASP* 1.3 73.2 - - - +
502A ALA* 1.3 64.6 + - - +
504A ASN 3.4 1.6 + - - -
505A GLY 3.2 3.8 + - - -
506A HIS* 3.0 29.7 + - + +
509A ILE* 3.6 33.4 - - + -
510A VAL* 3.9 17.0 - - + -
513A LEU* 4.0 4.9 - - + -
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Residues in contact with ALA 502 (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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498A LEU* 2.8 19.5 + - + +
499A HIS 3.7 1.1 - - - +
501A ALA* 1.3 76.3 - - - +
503A LYS* 1.3 62.3 + - - +
505A GLY* 3.2 13.3 + - - -
510A VAL* 3.8 4.6 - - + +
530A PRO* 3.6 33.7 - - + +
533A TYR 4.3 2.4 - - - +
534A THR* 4.3 13.3 - - + -
539A MET* 3.9 17.3 - - + +
543A LEU* 4.2 13.5 - - + -
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Residues in contact with LYS 503 (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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470A ASN* 5.0 2.5 - - - +
493A GLN* 5.4 3.4 + - - -
495A ASP* 3.0 29.9 + - - -
499A HIS* 2.8 23.9 + - + +
500A ASP* 3.5 19.0 + - - +
502A ALA* 1.3 73.2 - - - +
504A ASN* 1.3 66.7 + - - +
505A GLY 3.3 2.3 + - - -
524A ASN* 5.5 0.2 - - - +
533A TYR* 4.0 55.4 + - + +
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Residues in contact with ASN 504 (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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470A ASN* 3.2 40.7 + - - +
500A ASP 2.9 19.5 + - - +
501A ALA 3.4 0.2 + - - -
502A ALA 3.2 1.0 - - - -
503A LYS* 1.3 86.3 + - - +
505A GLY* 1.3 62.5 + - - +
506A HIS* 3.3 36.9 + - + +
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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