Contacts of the helix formed by residues 656 - 664 (chain A) in PDB entry 6T8G
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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654A VAL* 3.7 4.7 - - - +
655A SER* 1.3 81.8 - - - +
657A LYS* 1.3 59.9 + - - +
658A ILE* 3.4 16.7 - - - +
659A ASP* 2.7 43.5 + - - +
660A SER* 2.8 25.8 + - - -
670A GLU* 3.2 11.4 - - - -
643F LYS* 5.4 11.2 - - - -
644F ALA* 6.0 0.7 - - - -
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Residues in contact with LYS 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656A SER* 1.3 69.8 - - - +
658A ILE* 1.3 62.7 + - + +
660A SER* 3.6 10.8 - - - +
661A ARG* 2.9 42.2 + - + +
667A GLY* 5.4 2.1 - - - -
668A GLY* 4.5 20.2 - - - +
670A GLU* 2.6 27.4 + - + +
671A GLN* 4.6 19.8 - - - +
11H A 5.0 14.1 - - - +
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Residues in contact with ILE 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656A SER* 3.4 14.4 - - - +
657A LYS* 1.3 78.8 - - + +
659A ASP* 1.3 61.5 + - - +
661A ARG* 3.5 5.3 + - - +
662A THR* 2.3 38.2 + - - +
9G A 4.8 2.5 - - - +
10G T 3.7 57.0 - - - +
11G A 4.5 2.9 - - - +
10H T 6.3 3.4 - - - -
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Residues in contact with ASP 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A ARG* 6.1 0.2 - - - +
633A PRO* 3.8 26.4 - - + +
634A SER* 4.1 20.1 - - - -
654A VAL* 4.9 10.9 - - + +
655A SER* 5.3 0.9 + - - -
656A SER* 2.7 28.2 + - - +
658A ILE* 1.3 78.7 - - - +
660A SER* 1.3 64.6 + - - +
662A THR* 3.3 8.9 + - - -
663A ILE* 3.0 28.8 + - - +
640F GLY 5.4 0.5 - - - +
644F ALA* 3.7 24.6 - - - +
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Residues in contact with SER 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654A VAL* 4.5 4.2 - - - +
656A SER 2.8 18.4 + - - -
657A LYS* 3.6 12.6 - - - -
658A ILE 3.2 0.2 - - - -
659A ASP* 1.3 77.0 - - - +
661A ARG* 1.3 51.0 + - - +
663A ILE* 4.5 1.7 - - - +
664A LEU* 2.6 43.0 + - - +
667A GLY* 3.3 2.4 - - - -
668A GLY 2.9 13.9 + - - -
669A ALA* 2.8 43.0 + - - +
670A GLU 4.2 3.8 - - - -
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Residues in contact with ARG 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657A LYS* 2.9 29.3 + - + +
658A ILE* 3.9 4.3 - - - +
660A SER* 1.3 72.9 + - - +
662A THR* 1.3 59.0 + - - +
664A LEU 3.3 7.9 - - - -
665A ASP* 2.9 43.8 + - - +
666A GLN 4.5 8.3 + - - -
667A GLY* 4.3 12.6 - - - -
10H T 3.9 30.7 + - - -
11H A 4.1 25.7 + - - -
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Residues in contact with THR 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633A PRO 3.3 24.5 - - - +
634A SER* 4.1 6.0 - - - -
635A VAL* 3.8 26.9 - - + -
638A ILE* 5.4 4.0 - - + +
643A LYS* 4.1 13.7 + - - +
649A ARG* 5.3 0.3 + - - -
658A ILE* 2.3 28.6 + - - +
659A ASP* 3.3 15.1 + - - -
660A SER 3.1 0.4 - - - -
661A ARG* 1.3 77.8 - - - +
663A ILE* 1.3 57.9 + - - +
665A ASP* 3.9 7.1 - - - +
657B LYS* 5.3 4.4 + - - +
11G A 3.8 12.7 + - - +
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Residues in contact with ILE 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463A LEU* 3.9 24.0 - - + -
464A VAL 4.8 2.0 - - - +
465A ALA* 3.7 28.5 - - + +
630A THR* 5.0 0.2 - - + -
633A PRO* 4.0 13.2 - - + +
638A ILE* 3.8 28.9 - - + -
649A ARG* 3.2 40.9 - - + +
650A ILE 5.0 1.7 - - - +
651A ALA* 3.8 27.6 - - + +
654A VAL* 5.6 2.0 - - + -
659A ASP 3.0 16.2 + - - +
660A SER* 4.5 1.6 - - - +
662A THR* 1.3 76.5 - - - +
664A LEU* 1.3 61.0 + - - +
665A ASP* 4.2 1.6 - - - -
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Residues in contact with LEU 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649A ARG* 4.9 7.4 - - + +
651A ALA* 4.8 11.7 - - + +
660A SER* 2.6 28.4 + - - +
661A ARG* 3.3 2.4 - - - -
662A THR 3.5 0.2 - - - -
663A ILE* 1.3 78.7 - - - +
665A ASP* 1.3 55.6 + - - +
666A GLN* 3.1 18.4 - - + -
667A GLY* 2.7 44.9 + - - +
668A GLY 5.3 0.7 - - - +
669A ALA* 5.1 3.6 - - + -
679A LEU* 4.2 26.7 - - + -
681A LEU* 3.7 38.8 - - + +
688A PRO* 4.0 18.6 - - + -
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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