Contacts of the helix formed by residues 470 - 476 (chain D) in PDB entry 2HVI
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 GLN 470 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400D LEU* 3.0 35.0 + - + +
401D LEU* 3.7 10.6 - - - +
465D LEU* 2.7 23.3 + - + +
468D ASN* 3.1 39.0 + - + +
469D GLU* 1.3 76.9 - - - +
471D ASP* 1.3 62.1 + - - +
472D ARG 3.3 2.9 - - - -
473D LEU* 3.1 15.3 + - + +
474D LEU* 3.0 22.3 + - - +
768D HIS 3.1 28.9 + - - +
769D ARG* 4.0 3.2 - - - +
770D ARG* 3.6 20.1 - - - +
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Residues in contact with ASP 471 (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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467A ARG* 3.7 30.5 - - + +
468A ASN* 4.8 4.0 - - - +
462D LEU* 4.6 10.3 - - + +
465D LEU* 3.3 14.2 + - + -
466D ARG* 3.8 33.7 - - + +
469D GLU* 4.1 9.2 - - - +
470D GLN* 1.3 77.6 + - - +
472D ARG* 1.3 76.3 + - - +
474D LEU* 3.3 5.8 + - - +
475D VAL* 3.1 28.5 + - + +
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Residues in contact with ARG 472 (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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464A GLU* 5.7 2.0 - - - -
468A ASN* 4.9 11.2 - - - +
760A LYS 4.7 7.1 + - - -
762A TYR* 3.7 16.8 + - - -
770A ARG* 3.7 20.4 - - - +
772A TYR* 4.2 22.6 + - - -
469D GLU* 4.2 8.4 + - - +
470D GLN 3.3 0.4 - - - -
471D ASP* 1.3 89.5 + - - +
473D LEU* 1.3 61.3 + - - +
475D VAL* 4.4 2.5 - - - +
476D GLU* 2.7 72.2 + - + +
477D LEU* 3.5 0.9 + - - +
768D HIS* 6.3 0.8 - - - -
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Residues in contact with LEU 473 (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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400D LEU* 3.7 29.2 - - + -
469D GLU 4.9 1.0 + - - +
470D GLN* 3.1 20.9 + - + +
472D ARG* 1.3 79.4 - - - +
474D LEU* 1.3 56.3 + - - +
477D LEU* 3.2 41.3 - - + +
478D GLU* 3.0 26.3 + - - +
767D LEU* 3.6 38.4 - - + +
768D HIS 3.9 4.7 - - - +
769D ARG* 3.8 32.3 - - + +
802D ASP* 4.7 0.4 - - - +
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Residues in contact with LEU 474 (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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392D PHE* 4.0 19.3 - - + -
393D ASP 4.3 0.9 - - - +
396D LEU* 3.7 30.5 - - + -
397D ALA* 3.8 12.8 - - + +
400D LEU* 3.7 15.4 - - + +
462D LEU* 4.1 10.1 - - + -
465D LEU* 3.4 27.8 - - + -
470D GLN 3.0 9.2 + - - +
471D ASP 3.6 6.5 - - - +
472D ARG 3.1 0.2 - - - -
473D LEU* 1.3 79.5 - - - +
475D VAL* 1.3 64.2 + - + +
478D GLU* 3.5 3.0 + - + -
479D GLN* 2.9 58.5 + - + +
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Residues in contact with VAL 475 (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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467A ARG* 3.5 45.8 - - - +
391D SER 4.7 1.8 - - - +
462D LEU* 5.0 1.6 - - + -
471D ASP* 3.1 15.9 + - + +
472D ARG* 4.5 1.3 - - - +
474D LEU* 1.3 93.1 - - + +
476D GLU* 1.3 68.7 + - + +
479D GLN* 4.0 21.1 + - - +
480D PRO* 3.3 17.1 - - - +
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Residues in contact with GLU 476 (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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464A GLU* 4.7 11.4 - - - +
472D ARG* 2.7 58.7 + - + +
475D VAL* 1.3 84.7 - - + +
477D LEU* 1.3 58.5 + - - +
480D PRO* 3.6 14.7 - - - +
809D ILE* 3.6 12.5 - - - +
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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