Contacts of the helix formed by residues 588 - 593 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500D LEU* 3.6 30.5 - - + +
501D GLU* 5.3 0.9 - - - -
503D MET* 4.2 8.3 - - + -
504D GLY* 3.8 26.7 - - - +
507D LEU* 4.3 9.0 - - + -
583D LEU 3.1 15.7 + - - +
584D GLN* 3.4 17.3 - - + +
587D TYR* 1.3 79.3 - - - +
589D GLU* 1.3 67.7 + - + +
590D GLY 3.3 0.2 - - - -
591D LEU* 3.3 1.9 + - - +
592D LEU* 2.9 48.4 + - + +
636D ILE* 3.5 24.0 - - + -
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Residues in contact with GLU 589 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584D GLN* 3.0 41.9 + - + +
585D SER* 3.6 20.4 - - - +
588D ILE* 1.3 80.9 - - + +
590D GLY* 1.3 63.5 + - - +
592D LEU* 3.3 7.3 + - + +
593D LYS* 3.0 43.3 + - - +
10F A 4.4 7.4 + - - -
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Residues in contact with GLY 590 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585D SER 3.4 10.0 + - - -
586D THR 3.3 12.9 + - - -
588D ILE 3.3 0.4 - - - -
589D GLU* 1.3 81.2 - - - +
591D LEU* 1.3 61.8 + - - +
593D LYS* 3.5 17.5 + - - +
594D VAL* 3.5 15.8 - - - +
621D PRO* 5.6 1.5 - - - +
9F C 3.8 22.0 + - - -
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Residues in contact with LEU 591 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495D VAL* 4.8 5.6 - - + -
500D LEU* 3.8 25.4 - - + -
586D THR 3.3 8.4 + - - +
587D TYR* 3.8 21.5 - - + +
588D ILE 3.3 6.0 + - - +
589D GLU 3.3 0.4 - - - -
590D GLY* 1.3 73.0 - - - +
592D LEU* 1.3 67.8 + - - +
594D VAL* 2.9 17.1 + - - +
595D VAL* 3.2 15.4 + - + +
602D VAL* 4.5 12.6 - - + -
621D PRO* 4.1 29.6 - - + -
623D LEU* 4.5 10.8 - - + -
626D ILE* 5.2 6.7 - - + -
636D ILE* 4.8 3.8 - - + -
640D PHE* 3.7 29.4 - - + -
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Residues in contact with LEU 592 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497D THR* 3.9 34.5 - - + +
500D LEU* 4.3 13.7 - - + -
501D GLU* 4.1 33.4 - - + +
588D ILE* 2.9 38.8 + - + +
589D GLU* 3.7 7.2 - - - +
591D LEU* 1.3 76.8 - - - +
593D LYS* 1.3 60.7 + - + +
594D VAL 3.4 0.7 + - - -
595D VAL* 3.7 18.0 + - - +
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Residues in contact with LYS 593 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589D GLU* 3.0 35.1 + - - +
590D GLY* 3.6 10.8 - - - +
591D LEU 3.1 0.4 - - - -
592D LEU* 1.3 77.9 - - + +
594D VAL* 1.3 63.1 + - + +
595D VAL 4.7 2.1 - - - +
9F C 5.9 1.6 - - - +
10F A 5.5 4.9 + - - -
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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