Contacts of the helix formed by residues 588 - 595 (chain A) in PDB entry 2HVH
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 ILE 588 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500A LEU* 3.5 40.8 - - + +
501A GLU* 5.1 1.1 - - - -
503A MET* 4.2 7.0 - - + -
504A GLY* 3.9 21.3 - - - +
507A LEU* 4.1 11.7 - - + -
583A LEU 3.0 14.3 + - - +
584A GLN* 3.3 15.2 + - + +
587A TYR* 1.3 79.2 - - - +
589A GLU* 1.3 65.7 + - + +
591A LEU* 3.5 1.3 + - - +
592A LEU* 3.0 49.3 + - + +
636A ILE* 3.7 24.0 - - + -
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Residues in contact with GLU 589 (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 GLN* 2.8 40.0 + - + +
585A SER* 3.4 21.4 - - - +
588A ILE* 1.3 75.7 - - + +
590A GLY* 1.3 64.3 + - - +
592A LEU* 3.8 6.0 + - + +
593A LYS* 3.3 33.1 + - - +
10C A 4.5 6.9 + - - -
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Residues in contact with GLY 590 (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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585A SER 2.9 12.7 + - - -
586A THR 3.4 11.5 + - - -
589A GLU* 1.3 75.8 - - - +
591A LEU* 1.3 63.1 + - - +
593A LYS* 3.2 20.5 + - - +
594A VAL* 3.6 12.6 + - - +
621A PRO* 6.2 0.7 - - - -
9C C 3.5 23.5 + - - -
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Residues in contact with LEU 591 (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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495A VAL* 5.1 3.1 - - + -
500A LEU* 3.7 21.5 - - + -
586A THR 3.3 6.9 + - - +
587A TYR* 3.6 28.7 - - + +
588A ILE 3.5 2.4 + - - +
589A GLU 3.4 0.4 - - - -
590A GLY* 1.3 77.3 - - - +
592A LEU* 1.3 57.7 + - - +
594A VAL* 3.3 15.6 + - - +
595A VAL* 3.1 21.2 + - + +
602A VAL* 4.1 20.4 - - + -
621A PRO* 4.2 23.1 - - + -
623A LEU* 4.6 4.3 - - + -
626A ILE* 5.4 4.3 - - + -
636A ILE* 4.7 4.3 - - + -
640A PHE* 3.5 37.9 - - + -
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Residues in contact with LEU 592 (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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497A THR* 4.1 25.6 - - + -
500A LEU* 3.6 30.7 - - + -
501A GLU* 3.8 28.7 - - + +
588A ILE* 3.0 40.9 + - + +
589A GLU* 4.4 5.8 - - + +
591A LEU* 1.3 72.3 - - - +
593A LYS* 1.3 63.8 + - + +
594A VAL 3.2 0.4 + - - -
595A VAL* 3.7 18.7 + - + +
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Residues in contact with LYS 593 (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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589A GLU* 3.3 18.8 + - - +
590A GLY* 3.2 13.8 + - - +
592A LEU* 1.3 77.4 - - - +
594A VAL* 1.3 65.8 + - + +
595A VAL 3.6 3.4 - - - +
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Residues in contact with VAL 594 (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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590A GLY 3.8 10.8 - - - +
591A LEU* 3.4 13.7 - - - +
592A LEU 3.2 0.2 - - - -
593A LYS* 1.3 83.2 - - + +
595A VAL* 1.3 65.1 + - - +
596A ARG* 3.5 7.4 + - - +
601A LYS 4.2 3.3 - - - +
602A VAL* 4.3 8.3 - - + +
603A HIS 5.0 1.6 + - - -
620A GLU* 4.3 29.8 - - + +
621A PRO* 3.9 35.0 - - + -
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Residues in contact with VAL 595 (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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495A VAL* 4.7 10.1 - - + -
497A THR* 4.3 22.7 - - + -
591A LEU 3.1 18.8 + - - +
592A LEU* 3.7 22.3 - - + +
593A LYS 3.6 3.9 - - - +
594A VAL* 1.3 80.4 - - - +
596A ARG* 1.3 64.5 + - - +
597A PRO* 3.3 14.7 - - + +
600A LYS* 3.6 35.9 - - + +
601A LYS 3.5 7.9 - - - +
602A VAL* 3.9 11.4 - - + -
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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