Contacts of the helix formed by residues 656 - 665 (chain F) in PDB entry 6T8O
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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654F VAL* 3.5 3.6 - - - +
655F SER* 1.3 82.6 - - - +
657F LYS* 1.3 61.0 + - - +
658F ILE* 3.7 20.7 + - - +
659F ASP* 3.2 15.8 + - - +
660F SER* 3.0 25.1 + - - -
670F GLU* 4.0 12.3 - - - -
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Residues in contact with LYS 657 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383F ASN* 5.5 8.5 - - - +
656F SER* 1.3 74.8 - - - +
658F ILE* 1.3 63.7 + - + +
660F SER* 3.6 2.1 - - - -
661F ARG* 2.9 79.5 + - - +
667F GLY* 4.9 10.4 - - - -
670F GLU* 3.3 34.5 + - + +
8H A 4.5 20.2 + - - +
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Residues in contact with ILE 658 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656F SER* 3.2 14.7 - - - +
657F LYS* 1.3 85.0 - - + +
659F ASP* 1.3 62.6 + - - +
661F ARG* 3.3 14.4 + - - +
662F THR* 2.8 33.5 + - - +
10G T 5.2 16.4 - - - +
11G A 3.8 22.7 - - - +
7H T 6.0 6.1 - - - -
8H A 5.9 2.2 - - - +
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Residues in contact with ASP 659 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633F PRO* 3.5 44.7 - - + +
634F SER* 5.2 1.6 - - - -
654F VAL* 3.9 14.1 - - + -
655F SER* 3.3 29.3 + - - -
656F SER* 3.2 15.4 + - - +
658F ILE* 1.3 79.2 - - - +
660F SER* 1.3 60.7 + - - +
662F THR* 3.2 2.9 + - - -
663F ILE* 3.0 30.9 + - - +
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Residues in contact with SER 660 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654F VAL* 3.9 3.9 - - - +
656F SER 3.0 8.1 + - - -
657F LYS 3.6 7.2 - - - -
658F ILE 3.3 0.2 - - - -
659F ASP* 1.3 78.0 - - - +
661F ARG* 1.3 56.2 + - - +
663F ILE* 3.4 9.0 - - - +
664F LEU* 2.9 26.7 + - - +
666F GLN 2.7 28.7 + - - +
667F GLY* 3.2 5.5 + - - -
669F ALA* 3.1 29.8 + - - +
670F GLU* 3.6 21.3 - - - -
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Residues in contact with ARG 661 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643F LYS* 5.0 0.7 + - - -
657F LYS* 2.9 70.3 + - - +
658F ILE* 3.7 13.4 - - - +
659F ASP 3.3 0.2 - - - -
660F SER* 1.3 73.5 - - - +
662F THR* 1.3 62.3 + - - +
665F ASP* 2.9 33.5 + - - +
666F GLN* 3.7 24.6 - - - +
667F GLY 4.4 4.4 - - - +
6H A 5.2 0.4 - - - -
7H T 2.6 50.1 + - - -
8H A 5.6 3.0 + - - -
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Residues in contact with THR 662 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633F PRO* 3.3 29.8 + - + +
634F SER* 3.9 20.5 - - - +
635F VAL* 4.3 9.8 - - + +
638F ILE* 4.3 17.8 - - + +
643F LYS* 3.4 32.1 - - - +
658F ILE* 2.8 27.4 + - - +
659F ASP 3.2 2.7 + - - -
661F ARG* 1.3 77.4 - - - +
663F ILE* 1.3 59.1 + - - +
665F ASP 4.8 0.3 + - - -
11G A 4.5 7.1 + - - -
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Residues in contact with ILE 663 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463F LEU* 5.4 5.1 - - + +
464F VAL 4.9 0.9 - - - +
465F ALA* 3.6 28.7 - - + +
633F PRO* 5.2 4.0 - - + -
638F ILE* 4.9 15.3 - - + -
649F ARG* 3.0 36.0 + - + +
650F ILE 3.3 26.9 - - - +
651F ALA* 3.7 19.3 - - + -
654F VAL* 4.8 8.5 - - + -
659F ASP 3.0 19.9 + - - +
660F SER* 3.4 12.8 - - - +
662F THR* 1.3 79.8 - - - +
664F LEU* 1.3 71.7 + - + +
665F ASP 3.8 0.4 - - - -
669F ALA* 4.8 2.5 - - + -
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Residues in contact with LEU 664 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649F ARG* 3.7 35.0 + - + +
651F ALA* 3.7 24.2 - - + -
660F SER* 2.9 12.4 + - - +
663F ILE* 1.3 85.3 - - + +
665F ASP* 1.3 69.1 + - - +
666F GLN* 3.1 27.3 + - + +
667F GLY 5.1 3.1 - - - +
669F ALA* 4.3 9.0 - - + -
679F LEU* 4.2 26.7 - - + +
681F LEU* 3.8 29.7 - - + +
688F PRO* 4.8 8.3 - - + -
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Residues in contact with ASP 665 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655A SER* 3.3 23.8 - - - +
656A SER* 6.0 1.3 - - - -
643F LYS* 4.0 19.9 + - - +
649F ARG* 4.4 16.8 + - - +
661F ARG* 2.9 26.4 + - - +
663F ILE 3.8 0.6 - - - -
664F LEU* 1.3 77.4 - - - +
666F GLN* 1.3 59.1 + - - +
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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