Contacts of the helix formed by residues 680 - 685 (chain D) in PDB entry 1HQR
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 680 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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516D ALA* 5.8 0.2 - - - -
678D GLU* 4.1 18.1 - - + +
679D GLY* 1.3 81.8 - - - +
681D ARG* 1.3 55.4 + - - +
682D SER* 2.7 18.8 + - - -
683D ASP* 2.6 40.5 + - - -
684D ILE* 2.8 14.9 + - - +
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Residues in contact with ARG 681 (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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515D TYR 3.2 12.4 + - - -
516D ALA* 3.0 37.1 + - - +
518D THR 3.0 27.5 + - - -
519D ILE* 4.1 5.2 - - - +
575D PHE* 3.2 56.1 - - - +
576D TYR* 3.7 13.0 - - - +
680D THR* 1.3 72.0 - - - +
682D SER* 1.3 55.9 + - - +
684D ILE* 4.5 4.5 - - - -
685D PHE* 2.9 45.3 + - + +
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Residues in contact with SER 682 (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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576D TYR* 3.8 25.8 + - - +
587D TYR* 3.5 14.1 + - - -
680D THR* 2.7 13.3 + - - -
681D ARG* 1.3 79.2 - - - +
683D ASP* 1.3 64.8 + - - -
686D ALA* 3.2 24.8 + - - +
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Residues in contact with ASP 683 (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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676D PRO* 3.2 37.3 - - + +
677D ASN* 3.5 21.9 + - + +
678D GLU* 3.5 9.2 - - - +
679D GLY* 3.1 8.9 + - - -
680D THR* 2.6 39.6 + - - +
682D SER* 1.3 73.6 + - - +
684D ILE* 1.3 66.1 + - - +
686D ALA* 3.3 14.8 + - - +
687D LYS* 4.4 2.4 + - - +
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Residues in contact with ILE 684 (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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512D ASP 3.8 8.5 - - - +
513D LEU* 3.6 22.7 - - + -
516D ALA* 3.5 25.1 - - + -
517D TYR* 3.7 17.9 - - + +
674D ASP 4.8 3.1 - - - +
675D SER* 4.2 9.6 - - - +
676D PRO* 4.5 15.9 - - + -
679D GLY* 3.9 20.4 - - - +
680D THR 2.8 13.0 + - - +
681D ARG* 4.5 0.2 - - - -
683D ASP* 1.3 77.1 - - - +
685D PHE* 1.3 81.9 + - + +
686D ALA 3.5 0.9 + - - -
687D LYS* 2.9 33.5 + - - +
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Residues in contact with PHE 685 (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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516D ALA* 3.5 28.9 - - + -
517D TYR* 3.3 43.5 - + - -
519D ILE* 4.2 5.6 - - + -
574D LEU* 3.5 35.0 - - + +
575D PHE 3.2 24.7 - - - +
576D TYR* 5.1 0.7 - - + -
587D TYR* 3.3 27.4 - - + +
681D ARG* 2.9 30.6 + - + +
682D SER 4.3 0.2 - - - -
684D ILE* 1.3 91.4 - - + +
686D ALA* 1.3 58.7 + - - +
687D LYS 3.4 2.2 - - - -
688D TYR* 3.5 23.9 - + + -
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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