Contacts of the helix formed by residues 656 - 661 (chain C) in PDB entry 7KHC
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 656 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C PRO 5.9 0.2 - - - -
20C GLN* 5.2 19.3 - - - -
21C VAL 5.6 0.4 - - - -
22C LEU 5.3 1.3 - - - -
578C TYR* 3.0 35.7 + - - -
619C ALA* 3.9 10.3 - - - +
654C ASP* 3.4 2.0 - - - +
655C VAL* 1.3 84.2 - - - +
657C THR* 1.3 67.4 + - - +
658C GLN* 3.1 11.2 + - - +
659C GLN* 3.3 18.7 + - - +
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Residues in contact with THR 657 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ARG* 5.8 7.4 - - + +
20C GLN* 6.0 4.7 - - - +
619C ALA* 3.8 19.9 - - - +
620C ASN* 5.9 1.1 - - - -
656C SER* 1.3 74.8 - - - +
658C GLN* 1.3 75.0 + - + +
659C GLN* 3.2 2.6 + - - +
660C VAL* 4.1 7.3 + - - +
1185C PRO* 5.2 4.9 - - + -
1187C PHE* 3.2 31.1 - - + +
1188C ASP* 4.0 28.4 + - + +
769D VAL* 4.1 20.7 - - - +
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Residues in contact with GLN 658 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C GLN* 5.6 5.5 - - - +
24C VAL* 4.7 5.7 - - - +
577C VAL* 3.9 8.9 - - + +
578C TYR* 4.7 5.1 + - - +
656C SER* 3.1 9.8 + - - +
657C THR* 1.3 81.0 - - + +
659C GLN* 1.3 57.8 + - - +
660C VAL* 2.8 13.0 + - - -
661C VAL* 3.2 25.1 + - + +
666C SER* 5.1 8.7 + - - -
702C THR* 4.0 15.6 + - - -
704C MET* 4.2 31.7 - - - +
1185C PRO* 3.9 23.0 - - + +
1186C VAL* 3.8 29.0 - - + +
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Residues in contact with GLN 659 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555C TYR* 3.9 16.5 - - + +
556C GLY* 3.5 21.3 - - - +
576C SER* 4.1 8.5 - - - -
577C VAL* 3.8 13.9 - - - +
578C TYR* 3.4 29.0 + - + -
589C THR* 3.5 19.6 + - - -
590C PRO* 3.6 10.7 - - - +
591C TYR* 3.7 16.8 + - - -
654C ASP* 3.5 28.8 + - + +
655C VAL* 4.1 9.3 - - - +
656C SER* 3.3 16.3 + - - +
657C THR 3.2 2.9 + - - +
658C GLN* 1.3 75.7 - - - +
660C VAL* 1.3 64.4 + - + +
661C VAL 3.3 0.8 + - - -
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Residues in contact with VAL 660 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555C TYR* 4.7 19.3 - - + +
556C GLY* 4.3 10.9 + - - +
558C VAL 4.2 0.7 - - - +
559C CYS* 3.9 4.2 - - - -
560C PRO* 3.3 36.4 - - + +
561C ILE* 5.3 0.7 - - + -
576C SER* 3.9 5.1 + - - -
657C THR 4.1 9.8 + - - +
658C GLN 2.8 4.5 + - - +
659C GLN* 1.3 82.6 - - - +
661C VAL* 1.3 72.4 + - + +
1187C PHE* 3.8 22.2 - - + -
769D VAL* 4.5 12.1 - - + +
773D PHE* 4.0 20.4 - - + +
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Residues in contact with VAL 661 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559C CYS* 3.7 5.2 - - - -
561C ILE* 3.5 26.7 - - + -
576C SER* 4.5 0.2 - - - -
577C VAL* 3.4 26.6 + - - +
658C GLN* 3.4 13.9 - - - +
660C VAL* 1.3 94.2 - - + +
662C SER* 1.3 72.3 + - - +
665C ALA* 4.1 8.5 - - + -
666C SER* 4.0 20.6 - - - -
671C LEU* 4.5 15.9 - - + -
1186C VAL* 4.8 13.0 - - + -
1187C PHE* 4.6 7.2 - - + -
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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