Contacts of the helix formed by residues 643 - 647 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601F TYR* 3.4 32.1 - - - -
639F HIS* 5.9 0.4 - - - -
640F GLY 3.6 4.7 + - - -
641F ARG 3.4 4.4 - - - -
642F GLY* 1.3 81.4 - - - +
644F THR* 1.3 63.1 + - - -
645F VAL* 3.1 3.8 - - - -
646F GLY* 3.0 22.1 + - - +
647F ARG* 4.0 6.8 - - - +
673F GLN* 4.5 2.2 + - - +
828F LEU* 4.5 2.1 - - - +
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Residues in contact with THR 644 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601F TYR* 4.4 8.4 - - + -
610F ARG* 4.9 7.4 - - - +
642F GLY 3.8 0.4 + - - -
643F GLY* 1.3 73.8 - - - -
645F VAL* 1.3 66.8 + - - +
646F GLY 3.2 0.7 + - - -
647F ARG* 3.2 29.6 + - - +
651F PRO 4.6 0.3 - - - +
652F THR* 4.1 3.3 + - - -
655F ALA* 3.4 26.4 + - - +
659F GLN* 5.0 2.8 + - - -
824F VAL* 3.9 35.2 - - + +
825F THR* 4.7 6.1 - - + +
828F LEU* 3.7 20.9 - - + -
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Residues in contact with VAL 645 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601F TYR* 4.1 4.9 - - - +
639F HIS* 3.9 25.8 - - + +
643F GLY* 3.1 1.3 - - - -
644F THR* 1.3 82.0 + - - +
646F GLY* 1.3 57.2 + - - +
647F ARG 3.3 0.2 - - - -
652F THR* 2.9 24.4 + - - +
655F ALA* 4.0 13.5 - - + +
656F ILE* 3.7 23.8 - - + -
659F GLN* 3.7 27.6 - - + +
668F ILE* 4.7 2.9 - - + -
670F VAL* 3.6 37.6 - - + +
694F PHE* 4.2 2.6 - - - -
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Residues in contact with GLY 646 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643F GLY* 3.0 15.8 + - - -
645F VAL* 1.3 77.4 - - - +
647F ARG* 1.3 56.3 + - - +
648F GLY 3.0 11.6 + - - -
670F VAL* 4.3 4.0 - - - +
671F THR 4.2 19.6 - - - +
672F VAL* 5.7 1.0 - - - +
673F GLN* 4.8 14.5 + - - +
676F VAL* 4.6 14.6 - - - +
694F PHE* 5.8 1.1 - - - -
968F ASN* 5.2 1.2 + - - -
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Residues in contact with ARG 647 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643F GLY 4.0 5.2 - - - +
644F THR* 3.2 30.0 + - - +
645F VAL 3.3 3.2 - - - -
646F GLY* 1.3 73.5 - - - +
648F GLY* 1.3 52.2 + - - +
649F GLY 2.7 18.0 + - - -
650F GLY 3.3 3.5 + - - -
651F PRO* 3.7 24.5 - - + +
652F THR* 3.2 20.4 + - - -
676F VAL* 5.3 1.8 - - - -
824F VAL 5.1 1.0 + - - -
827F ASP* 3.7 11.1 + - - +
828F LEU* 3.5 39.1 - - + +
831F MET* 3.3 35.4 - - - +
887F LEU* 4.3 5.9 - - - +
968F ASN* 4.0 11.0 - - - +
1004F FLC 2.7 54.9 + - - +
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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
------------------------------------------------------------
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