Contacts of the helix formed by residues 656 - 664 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654C VAL* 3.8 8.1 - - - +
655C SER* 1.3 80.9 - - - +
657C LYS* 1.3 62.5 + - - +
658C ILE* 3.2 19.1 + - - +
659C ASP* 2.8 36.1 + - - +
660C SER* 3.2 16.6 + - - -
670C GLU* 4.1 6.2 - - - +
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Residues in contact with LYS 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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383C ASN* 5.9 3.2 - - - +
656C SER* 1.3 71.7 - - - +
658C ILE* 1.3 64.2 + - + +
659C ASP 3.3 0.2 - - - -
660C SER* 3.2 10.8 + - - -
661C ARG* 2.9 62.8 + - - +
667C GLY* 5.1 7.2 - - - -
670C GLU* 3.3 33.8 - - + +
671C GLN* 5.8 0.2 - - - +
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Residues in contact with ILE 658 (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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656C SER* 3.2 16.1 - - - +
657C LYS* 1.3 83.8 - - + +
659C ASP* 1.3 55.9 + - - +
661C ARG* 3.3 13.0 + - - +
662C THR* 2.6 39.7 + - - +
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Residues in contact with ASP 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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633C PRO* 3.3 39.0 - - + +
634C SER* 5.1 0.5 - - - -
654C VAL* 4.4 12.7 - - + +
655C SER* 4.2 10.2 + - - -
656C SER* 2.8 34.4 + - - +
658C ILE* 1.3 80.0 - - - +
660C SER* 1.3 60.9 + - - +
662C THR* 3.3 10.3 + - - -
663C ILE* 3.0 33.8 + - - +
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Residues in contact with SER 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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654C VAL* 4.3 0.8 - - - +
656C SER 3.2 12.1 + - - -
657C LYS 3.2 10.9 + - - -
659C ASP* 1.3 77.5 - - - +
661C ARG* 1.3 56.6 + - - +
663C ILE* 4.5 1.8 - - - -
664C LEU* 2.9 28.2 + - - +
665C ASP 3.2 1.0 + - - -
666C GLN 2.4 33.8 + - - +
667C GLY* 4.0 2.7 - - - -
668C GLY 3.2 1.9 + - - -
669C ALA* 3.0 43.7 + - - +
670C GLU* 4.0 7.2 - - - -
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Residues in contact with ARG 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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643C LYS* 4.6 2.1 + - - -
657C LYS* 2.9 58.2 + - - +
658C ILE* 3.5 11.3 - - + +
660C SER* 1.3 73.5 - - - +
662C THR* 1.3 61.0 + - - +
665C ASP* 3.3 21.7 - - - +
666C GLN* 3.6 25.2 - - - +
667C GLY* 4.2 13.6 - - - +
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Residues in contact with THR 662 (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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633C PRO* 4.4 2.7 - - + -
634C SER* 3.5 40.0 - - - +
635C VAL* 5.3 5.6 - - + +
638C ILE* 4.2 15.1 - - + +
643C LYS* 3.3 32.9 + - - +
658C ILE* 2.6 24.8 + - - +
659C ASP* 3.1 18.4 + - - -
661C ARG* 1.3 78.9 - - - +
663C ILE* 1.3 61.4 + - - +
665C ASP* 3.6 0.7 - - - +
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Residues in contact with ILE 663 (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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463C LEU* 4.4 11.9 - - + +
464C VAL 4.7 0.9 - - - -
465C ALA* 3.7 26.0 - - + +
633C PRO* 5.2 2.7 - - + -
638C ILE* 4.4 19.5 - - + -
643C LYS* 4.8 0.4 - - - +
649C ARG* 2.8 48.1 + - + +
650C ILE 3.4 27.1 - - - +
651C ALA* 4.1 19.7 - - + -
654C VAL* 5.0 8.7 - - + -
659C ASP 3.0 17.7 + - - +
660C SER* 4.2 4.5 - - - +
662C THR* 1.3 77.9 - - - +
664C LEU* 1.3 64.0 + - + +
665C ASP* 3.2 4.9 + - - +
669C ALA* 5.3 0.2 - - + -
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Residues in contact with LEU 664 (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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649C ARG* 4.0 15.5 - - + +
651C ALA* 3.8 26.0 - - + -
660C SER* 2.9 14.2 + - - +
663C ILE* 1.3 72.2 - - + +
665C ASP* 1.3 65.7 + - - +
666C GLN* 3.1 25.3 + - + +
667C GLY 6.0 0.4 - - - +
669C ALA* 3.8 11.7 - - + +
679C LEU* 3.8 43.1 - - + +
681C LEU* 3.8 44.4 - - + +
688C PRO* 4.9 7.0 - - + -
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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