Contacts of the helix formed by residues 703 - 708 (chain A) in PDB entry 2HWK
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 LEU 703 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637A VAL* 4.1 18.6 - - + -
663A LEU* 3.7 37.9 - - + +
666A GLY* 4.0 6.1 - - - -
667A ILE* 3.2 27.1 - - + +
679A VAL* 4.1 14.4 - - + -
681A VAL* 3.8 35.0 - - + -
699A LYS* 2.9 21.5 + - + +
702A MET* 1.3 89.4 - - + +
704A THR* 1.3 61.7 + - - +
705A LYS 3.4 1.1 - - - -
706A LYS 3.4 0.9 + - - -
707A ALA* 2.9 26.0 + - - +
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Residues in contact with THR 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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679A VAL* 3.8 15.7 - - - +
696A HIS* 5.8 0.2 + - - -
699A LYS 3.5 1.3 + - - -
700A LEU* 3.2 27.6 + - + +
703A LEU* 1.3 75.4 - - - +
705A LYS* 1.3 65.8 + - - +
707A ALA* 3.2 16.6 + - - +
708A CYS* 3.9 4.7 + - - -
717A CYS* 4.0 17.5 - - - -
719A SER* 2.9 38.8 + - - -
733A ILE* 5.7 0.9 - - + -
736A ILE* 3.6 20.6 - - + +
761A PHE* 4.5 7.0 - - + -
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Residues in contact with LYS 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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700A LEU 2.8 14.9 + - - +
701A SER* 3.4 25.4 - - - +
703A LEU 3.4 0.2 - - - -
704A THR* 1.3 74.0 - - - +
706A LYS* 1.3 62.4 + - + +
708A CYS* 3.2 21.4 + - - +
709A LEU* 4.7 1.7 + - - +
732A ILE* 4.2 21.4 - - + +
735A ALA* 4.5 20.3 - - + +
736A ILE* 3.8 17.4 - - + +
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Residues in contact with LYS 706 (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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665A LEU 4.5 4.7 - - - -
666A GLY* 4.4 4.5 - - - -
667A ILE* 3.7 31.0 - - + +
701A SER 3.9 6.7 + - - +
702A MET* 3.2 53.3 - - - +
703A LEU 3.4 3.1 + - - +
704A THR 3.3 0.2 - - - -
705A LYS* 1.3 72.9 - - + +
707A ALA* 1.3 65.1 + - - +
708A CYS 3.0 4.0 + - - -
709A LEU* 3.0 28.7 + - + +
710A HIS* 3.5 13.0 - - + +
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Residues in contact with ALA 707 (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 ILE* 3.7 10.1 - - + +
677A ILE* 3.5 42.6 - - + +
679A VAL* 5.0 1.1 - - + -
703A LEU 2.9 15.2 + - - +
704A THR* 3.3 15.9 - - - +
705A LYS 3.1 0.4 - - - -
706A LYS* 1.3 77.6 - - - +
708A CYS* 1.3 56.8 + - - +
710A HIS* 2.9 18.9 + - - -
711A LEU* 3.6 6.8 - - - +
717A CYS* 4.1 13.5 - - + -
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Residues in contact with CYS 708 (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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704A THR 4.3 5.4 - - - -
705A LYS* 3.2 17.0 + - - +
706A LYS 3.0 1.2 - - - -
707A ALA* 1.3 78.3 - - - +
709A LEU* 1.3 61.8 + - + +
710A HIS 3.1 1.3 + - - -
711A LEU* 3.7 11.2 + - - +
717A CYS* 5.5 2.2 - - - -
736A ILE* 3.9 22.7 - - - -
739A GLN* 5.2 6.1 - - + +
740A PHE* 3.8 30.5 - - - -
764A TYR* 3.3 40.9 + - + +
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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
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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