Contacts of the helix formed by residues 496 - 504 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466B HIS* 3.7 2.2 - - - -
487B VAL 5.1 1.3 - - - -
488B ASN* 4.6 13.9 - - - -
489B THR 3.6 7.9 - - - -
490B THR* 4.8 2.7 - - - +
494B ASN 3.5 3.4 + - - -
495B ASP* 1.3 75.3 - - - +
497B PRO* 1.4 74.6 - - - +
498B LEU* 3.5 11.7 + - - +
499B HIS* 2.9 48.1 + - - +
500B ASP* 3.4 7.8 + - - +
519B SER 5.0 0.6 + - - -
522B ALA* 4.2 16.9 - - - +
530B PRO* 4.5 0.3 - - - +
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Residues in contact with PRO 497 (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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463B THR* 5.2 0.2 - - - +
465B LEU* 3.7 25.6 - - + +
466B HIS* 3.5 22.9 - - + +
469B CYS* 3.5 26.7 - - + +
486B LEU 4.6 1.8 - - - +
487B VAL 3.5 26.0 - - - +
489B THR 3.2 15.9 - - - +
496B SER* 1.4 86.4 - - - +
498B LEU* 1.3 60.8 + - - +
500B ASP* 3.3 5.7 + - - +
501B ALA 3.1 18.7 + - - -
513B LEU* 3.5 13.4 - - + +
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Residues in contact with LEU 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B VAL 5.1 0.8 + - - +
496B SER* 3.1 11.5 + - - +
497B PRO* 1.3 77.8 - - - +
499B HIS* 1.3 66.0 + - - +
501B ALA 3.4 0.9 + - - -
502B ALA* 3.0 26.9 + - - +
510B VAL* 3.9 33.7 - - + +
513B LEU* 3.6 26.6 - - + +
514B LEU* 4.1 10.5 - - + -
518B ALA* 4.3 11.9 - - + +
519B SER 3.5 25.6 - - - +
520B ARG* 3.8 14.6 - - - -
530B PRO* 3.8 18.8 - - + -
543B LEU* 4.0 10.3 - - + -
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Residues in contact with HIS 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B ASN 4.9 0.4 - - - -
495B ASP* 3.4 29.2 - - - +
496B SER* 2.9 40.1 + - - +
498B LEU* 1.3 75.7 - - - +
500B ASP* 1.3 57.6 + - - +
502B ALA* 3.9 0.3 - - - +
503B LYS* 2.8 39.8 + - + +
522B ALA* 3.3 27.8 - - + -
523B VAL 4.1 1.3 - - - -
524B ASN* 3.8 11.2 + - + -
528B LEU 2.7 25.6 + - - -
529B ARG 3.7 2.7 - - - -
530B PRO* 3.4 31.0 - - + +
533B TYR* 3.8 16.9 - + + +
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Residues in contact with ASP 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B TRP* 3.7 12.1 - - - -
466B HIS* 3.4 40.1 - - - +
469B CYS* 4.1 2.9 - - + -
470B ASN* 2.7 46.1 + - - +
495B ASP* 4.2 12.1 - - - +
496B SER 3.4 5.5 + - - +
497B PRO* 3.3 9.9 + - + +
499B HIS* 1.3 79.2 - - - +
501B ALA* 1.3 60.6 + - - +
503B LYS* 3.6 13.9 + - - +
504B ASN* 3.4 24.4 + - - +
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Residues in contact with ALA 501 (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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469B CYS* 3.7 12.9 + - + +
497B PRO 3.1 15.4 + - - +
498B LEU 4.0 0.7 - - - +
500B ASP* 1.3 73.4 - - - +
502B ALA* 1.3 64.2 + - - +
504B ASN* 3.3 2.9 + - - -
505B GLY 3.2 3.8 + - - -
506B HIS* 2.9 31.4 + - + +
509B ILE* 3.8 28.5 - - + -
510B VAL* 3.6 19.5 - - + -
513B LEU* 3.9 5.4 - - + -
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Residues in contact with ALA 502 (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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498B LEU 3.0 17.5 + - - +
499B HIS 3.9 1.3 - - - +
501B ALA* 1.3 73.6 - - - +
503B LYS* 1.3 67.3 + - - +
505B GLY* 2.9 14.9 + - - -
510B VAL* 3.6 4.4 - - + +
530B PRO* 3.7 25.1 - - + +
533B TYR 4.2 5.5 - - - +
534B THR* 4.4 7.7 + - - -
539B MET* 3.8 19.7 - - + +
543B LEU* 4.0 20.9 - - + -
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Residues in contact with LYS 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B ASN* 5.1 5.6 - - - +
493B GLN* 5.0 5.7 + - - -
495B ASP* 3.0 29.7 + - - -
499B HIS* 2.8 26.4 + - - +
500B ASP* 3.6 16.6 + - - +
502B ALA* 1.3 73.2 - - - +
504B ASN* 1.3 68.4 + - - +
505B GLY 3.7 0.5 + - - -
533B TYR* 3.7 60.5 + - + +
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Residues in contact with ASN 504 (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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507A VAL* 6.3 1.0 - - - +
508A ASP* 4.4 16.3 - - - +
470B ASN* 2.7 46.9 + - - +
500B ASP 3.4 5.6 + - - +
501B ALA 3.3 2.2 + - - -
502B ALA 3.1 1.0 - - - -
503B LYS* 1.3 90.5 - - - +
505B GLY* 1.3 61.4 + - - +
506B HIS* 3.3 35.9 + - + +
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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