Contacts of the helix formed by residues 504 - 509 (chain A) in PDB entry 6CNC
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 VAL 504 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389A ILE* 4.1 26.5 - - + -
390A ASP 5.4 0.4 - - - +
486A LEU* 5.4 4.9 - - + -
488A HIS* 4.8 14.4 - - + -
500A LEU* 4.0 17.3 - - + -
501A ASN* 3.0 22.9 + - + +
502A GLU 2.8 1.6 + - - -
503A CYS* 1.3 78.5 - - + +
505A CYS* 1.3 64.7 + - - +
506A THR 3.2 2.5 - - - -
507A PRO* 3.1 18.9 - - + +
508A TYR* 3.3 29.7 - - + -
537A VAL* 4.6 8.7 - - + -
551A ILE* 4.4 14.1 - - + -
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Residues in contact with CYS 505 (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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500A LEU* 4.6 4.0 - - - +
502A GLU* 2.7 38.2 + - - +
503A CYS 3.3 0.2 - - - -
504A VAL* 1.3 74.0 - - - +
506A THR* 1.3 61.1 + - + +
508A TYR* 3.5 4.3 + - - +
509A ASN* 2.8 27.1 + - - -
510A ALA* 3.3 16.4 + - - +
512A PHE* 3.3 36.8 - - - -
554A THR* 4.7 9.0 - - - +
767B ILE* 5.8 0.9 - - - -
768B GLU* 3.5 22.2 - - - +
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Residues in contact with THR 506 (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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481A HIS* 5.7 0.2 - - - -
503A CYS 4.1 5.6 + - - +
505A CYS* 1.3 78.3 - - + +
507A PRO* 1.3 67.4 - - - +
509A ASN* 2.9 19.2 + - - +
550A ILE* 2.6 35.1 + - - +
554A THR* 3.5 33.2 - - + +
671A ASP* 3.5 9.2 + - - +
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Residues in contact with PRO 507 (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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481A HIS* 3.6 16.1 - - + +
483A LEU* 3.6 38.9 - - + +
484A SER* 5.1 0.2 + - - -
486A LEU* 5.3 9.9 - - + -
504A VAL* 3.1 23.3 - - + +
506A THR* 1.3 97.4 - - - +
508A TYR* 1.3 65.5 + - + +
509A ASN* 4.9 2.9 + - - -
550A ILE* 3.8 20.4 - - + +
551A ILE* 3.5 23.6 - - + -
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Residues in contact with TYR 508 (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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474A PHE* 3.3 38.4 + + - -
475A ASN* 4.7 0.9 - - - -
476A ARG* 3.6 41.7 - - + +
477A GLN* 4.0 5.7 + - - +
484A SER* 2.8 39.2 + - - -
486A LEU* 3.5 18.5 - - + +
488A HIS* 3.4 13.4 + - - -
500A LEU* 4.5 3.1 - - + -
504A VAL* 3.3 38.8 - - + -
505A CYS* 3.5 2.4 + - - +
506A THR 3.3 0.2 - - - -
507A PRO* 1.3 77.9 - - + +
509A ASN* 1.3 75.8 + - - +
510A ALA* 2.9 16.0 + - + +
517A MET* 4.0 10.5 - - + -
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Residues in contact with ASN 509 (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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476A ARG* 4.5 7.8 + - - -
477A GLN* 3.9 14.0 + - - +
480A LEU* 4.3 22.4 - - - +
481A HIS* 6.0 1.2 - - - -
505A CYS 2.8 13.1 + - - -
506A THR* 2.9 15.2 + - - +
507A PRO 4.9 3.0 + - - -
508A TYR* 1.3 87.6 + - - +
510A ALA* 1.3 64.6 + - - +
511A ASP* 3.3 6.1 + - - +
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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