Contacts of the helix formed by residues 696 - 705 (chain A) in PDB entry 3CWW
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 THR 696 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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684A TYR* 3.5 11.9 - - - -
688A LEU* 3.9 23.1 - - + -
694A ALA 4.7 3.4 - - - +
695A TRP* 1.3 76.3 - - - +
697A LYS* 1.3 58.7 + - - +
698A ASP* 3.3 11.2 + - - +
699A GLU* 2.9 40.0 + - - +
700A LEU* 2.9 29.2 + - - +
995A MET* 5.3 6.5 - - - -
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Residues in contact with LYS 697 (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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669A SER 5.8 1.8 + - - -
670A LEU* 4.1 33.4 - - + +
673A PHE* 3.7 48.0 - - + +
684A TYR* 2.9 41.4 + - + +
696A THR* 1.3 71.5 - - - +
698A ASP* 1.3 62.2 + - - +
700A LEU* 3.5 11.5 + - + +
701A LYS* 2.9 34.7 + - - +
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Residues in contact with ASP 698 (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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696A THR* 3.2 8.8 + - - +
697A LYS* 1.3 81.8 - - - +
699A GLU* 1.3 58.2 + - + +
701A LYS* 3.3 31.5 + - - +
702A GLU* 3.0 31.2 + - - +
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Residues in contact with GLU 699 (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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587A PRO* 3.8 17.6 - - + +
694A ALA 4.1 1.6 - - - +
695A TRP* 3.4 25.8 - - + -
696A THR* 2.9 44.8 + - - +
698A ASP* 1.3 77.1 - - + +
700A LEU* 1.3 63.0 + - - +
702A GLU* 3.4 15.4 + - - +
703A ALA* 3.0 24.9 + - - +
996A THR* 5.8 0.3 + - - -
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Residues in contact with LEU 700 (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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584A TYR* 6.3 1.1 - - + -
587A PRO* 3.6 27.8 - - + +
590A SER* 4.0 18.8 - - - +
591A ASN* 2.8 41.4 + - - +
666A TYR* 4.1 9.6 - - - +
670A LEU* 4.0 20.4 - - + -
695A TRP* 4.1 17.0 - - + +
696A THR 2.9 22.9 + - - +
697A LYS* 3.8 10.1 - - + +
699A GLU* 1.3 76.2 - - - +
701A LYS* 1.3 62.8 + - - +
703A ALA 3.2 0.7 + - - -
704A LEU* 3.0 8.1 + - - +
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Residues in contact with LYS 701 (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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667A MET* 3.7 23.3 - - - +
670A LEU* 3.8 26.3 + - + +
671A ASN* 3.1 39.1 + - - +
674A ARG* 6.3 0.6 - - - +
697A LYS* 2.9 18.0 + - - +
698A ASP* 3.3 33.3 + - - +
700A LEU* 1.3 78.3 - - - +
702A GLU* 1.3 64.8 + - - +
704A LEU* 3.3 16.9 + - - +
705A ALA* 4.0 1.7 + - - +
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Residues in contact with GLU 702 (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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698A ASP 3.0 16.9 + - - +
699A GLU* 3.5 17.2 - - - +
700A LEU 3.2 0.2 - - - -
701A LYS* 1.3 80.4 - - + +
703A ALA* 1.3 60.5 + - - +
704A LEU 3.4 0.2 + - - -
705A ALA* 3.8 12.3 + - - +
706A ASP* 4.4 6.3 - - - +
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Residues in contact with ALA 703 (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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587A PRO* 3.9 6.5 - - + -
588A LEU* 3.4 36.7 - - + +
591A ASN* 3.6 13.7 - - - +
699A GLU 3.0 16.9 + - - +
700A LEU 3.2 0.2 + - - -
702A GLU* 1.3 75.3 - - - +
704A LEU* 1.3 63.4 + - - +
705A ALA 3.3 0.7 - - - -
706A ASP* 3.1 27.8 + - - +
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Residues in contact with LEU 704 (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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591A ASN* 3.6 6.1 - - - +
595A LEU* 3.8 28.5 - - + -
663A LYS* 3.5 25.0 + - + +
666A TYR* 3.6 24.5 - - + -
667A MET* 3.6 50.5 - - + +
670A LEU* 4.4 3.4 - - + -
700A LEU 3.0 12.4 + - - +
701A LYS* 3.5 12.6 - - - +
702A GLU 3.2 1.2 - - - -
703A ALA* 1.3 77.0 - - - +
705A ALA* 1.3 63.4 + - - +
707A VAL* 3.0 21.9 + - + +
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Residues in contact with ALA 705 (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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663A LYS* 4.0 13.0 + - - +
667A MET* 4.6 8.1 - - + +
701A LYS 4.0 3.1 + - - +
702A GLU 3.8 10.3 + - - +
703A ALA 3.3 0.6 - - - -
704A LEU* 1.3 77.4 - - - +
706A ASP* 1.3 63.9 + - - +
707A VAL 3.2 1.8 + - - +
708A THR* 5.0 4.0 - - - +
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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