Contacts of the helix formed by residues 643 - 647 (chain C) in PDB entry 6V3O
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 GLY 643 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601C TYR* 3.4 31.2 - - - -
640C GLY 3.6 4.8 + - - -
641C ARG 3.4 4.8 - - - -
642C GLY* 1.3 81.1 - - - +
644C THR* 1.3 68.2 + - - +
645C VAL* 3.1 6.1 - - - -
646C GLY* 3.1 16.8 + - - +
647C ARG* 4.1 7.3 + - - +
673C GLN* 4.5 2.6 + - - +
828C LEU* 4.7 1.8 - - - +
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Residues in contact with THR 644 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601C TYR* 4.2 15.0 + - + -
610C ARG* 4.8 1.3 - - - +
642C GLY 3.7 1.4 + - - -
643C GLY* 1.3 71.4 - - - -
645C VAL* 1.3 66.1 + - - +
646C GLY 3.2 1.2 + - - -
647C ARG* 3.4 24.2 + - - +
651C PRO 4.5 0.3 - - - +
652C THR* 4.2 2.3 - - - +
655C ALA* 3.5 25.7 - - - +
658C SER* 5.4 0.3 + - - -
659C GLN* 4.6 6.2 + - - -
824C VAL* 3.7 38.8 - - + +
825C THR* 4.6 6.3 - - - +
828C LEU* 4.2 19.9 - - + +
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Residues in contact with VAL 645 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601C TYR* 4.6 3.4 - - - +
639C HIS* 3.6 40.8 - - + +
640C GLY 5.7 0.4 - - - +
643C GLY* 4.6 4.9 - - - -
644C THR* 1.3 76.9 - - - +
646C GLY* 1.3 59.4 + - - +
647C ARG 3.3 1.1 - - - -
652C THR* 3.0 21.4 - - - +
655C ALA* 4.0 16.6 - - + +
656C ILE* 3.9 25.4 - - + -
659C GLN* 4.0 25.4 - - + +
668C ILE* 5.4 1.6 - - + -
670C VAL* 3.5 25.0 - - + +
694C PHE* 3.9 4.9 - - - -
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Residues in contact with GLY 646 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643C GLY* 3.1 14.8 + - - -
645C VAL* 1.3 79.0 - - - +
647C ARG* 1.3 56.1 + - - +
648C GLY 3.0 12.4 + - - -
670C VAL* 4.3 11.0 - - - -
671C THR 4.4 9.6 - - - +
672C VAL* 5.9 0.2 - - - -
673C GLN* 4.8 15.0 + - - +
676C VAL* 4.3 20.4 - - - +
694C PHE* 5.7 1.3 - - - -
968C ASN* 4.9 1.9 + - - +
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Residues in contact with ARG 647 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643C GLY 4.3 6.1 - - - +
644C THR* 3.6 18.8 - - - +
645C VAL 3.3 3.6 - - - -
646C GLY* 1.3 74.9 - - - +
648C GLY* 1.3 50.7 + - - +
649C GLY 2.6 19.9 + - - -
650C GLY 3.3 8.5 + - - -
651C PRO* 3.6 28.2 - - + +
652C THR* 3.1 12.1 + - + +
824C VAL* 4.7 4.0 + - - +
827C ASP* 4.0 12.7 + - - +
828C LEU* 3.8 42.4 - - + +
831C MET* 3.5 30.9 - - - +
887C LEU* 4.4 5.3 - - - +
968C ASN* 3.6 16.6 - - - +
1003C FLC 2.6 54.8 + - - +
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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
------------------------------------------------------------
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