Contacts of the helix formed by residues 680 - 690 (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 ASP 680 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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656D GLN* 3.4 12.6 - - - +
678D ASP 3.8 2.0 + - - +
679D LEU* 1.3 77.1 - - - +
681D ILE* 1.3 56.6 + - - +
682D HIS 3.4 8.5 + - - -
683D THR* 2.4 31.7 + - - -
684D LYS* 2.9 27.3 + - - +
702D ARG* 2.7 37.0 + - - -
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Residues in contact with ILE 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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656D GLN* 2.8 11.2 + - - +
659D LEU* 4.4 12.8 - - + -
671D LEU* 4.6 11.9 - - + -
674D ALA* 3.6 26.5 - - + -
675D PHE* 3.7 29.2 - - + -
679D LEU* 4.2 9.0 - - + +
680D ASP* 1.3 68.9 - - - +
682D HIS* 1.3 60.1 + - - +
684D LYS* 3.7 19.1 - - + -
685D THR* 2.9 33.1 + - - +
709D ASN* 3.2 17.9 + - - +
739D TYR* 4.5 6.3 - - + +
743D PHE* 4.9 12.3 - - + -
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Residues in contact with HIS 682 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D DCT 2.9 36.9 + - - -
656D GLN* 3.8 13.4 - - + +
659D LEU* 3.7 19.5 - - + -
680D ASP* 3.2 6.5 + - - +
681D ILE* 1.3 77.7 - - - +
683D THR* 1.3 59.6 + - - +
686D ALA* 3.0 22.9 + - - +
702D ARG* 3.5 38.1 - - + +
705D ALA* 3.0 13.8 - - - +
706D LYS* 3.5 25.0 - - + +
709D ASN* 3.1 18.1 + - + +
710D TYR* 3.5 24.5 - + - -
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Residues in contact with THR 683 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680D ASP* 2.4 34.4 + - + -
682D HIS* 1.3 76.3 - - - +
684D LYS* 1.3 65.4 + - - +
686D ALA* 3.1 8.0 + - - +
687D MET* 2.9 25.5 + - - +
694D GLU* 4.0 25.6 - - + +
697D VAL* 3.9 23.9 - - + +
702D ARG* 3.4 15.6 - - - -
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Residues in contact with LYS 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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679D LEU* 4.7 25.4 - - + -
680D ASP 2.9 16.3 + - - +
681D ILE* 3.8 24.9 - - + +
682D HIS 3.3 0.2 - - - -
683D THR* 1.3 77.1 - - - +
685D THR* 1.3 63.0 + - - +
687D MET* 3.3 17.6 + - - +
688D ASP* 3.3 19.4 + - - +
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Residues in contact with THR 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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681D ILE* 2.9 23.4 + - - +
682D HIS 3.7 2.2 - - - -
684D LYS* 1.3 74.6 - - - +
686D ALA* 1.3 60.6 + - - +
688D ASP* 3.2 6.1 + - - +
689D ILE* 2.8 44.2 + - + +
705D ALA* 3.8 16.6 - - + +
708D VAL* 4.3 10.3 - - + -
709D ASN* 2.7 31.1 + - - +
735D PHE* 4.4 9.5 - - + -
739D TYR* 4.4 6.4 - - + -
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Residues in contact with ALA 686 (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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682D HIS 3.0 15.2 + - - +
683D THR 3.1 8.5 + - - +
685D THR* 1.3 76.7 - - - +
687D MET* 1.3 57.6 + - - +
689D ILE* 4.4 0.9 - - - -
690D PHE* 2.9 46.8 + - + +
692D VAL* 4.3 2.3 - - - +
697D VAL* 3.6 25.8 - - + -
701D MET 3.8 9.9 - - - +
702D ARG* 4.4 0.4 - - - -
705D ALA* 3.4 15.7 - - + +
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Residues in contact with MET 687 (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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683D THR* 2.9 20.0 + - - +
684D LYS* 3.4 17.9 - - - +
685D THR 3.2 0.2 - - - -
686D ALA* 1.3 77.8 - - - +
688D ASP* 1.3 57.3 + - - +
691D GLN* 2.9 29.8 + - - +
692D VAL* 3.0 25.9 + - - +
693D SER* 4.8 0.9 - - - -
694D GLU* 3.8 42.6 - - + +
697D VAL* 3.8 16.8 - - + -
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Residues in contact with ASP 688 (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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684D LYS 3.3 9.0 + - - +
685D THR* 3.2 9.9 + - - +
687D MET* 1.3 77.5 - - - +
689D ILE* 1.3 65.2 + - - +
691D GLN* 2.9 29.0 + - - +
735D PHE* 3.7 18.0 - - + -
738D ARG* 2.7 39.9 + - - -
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Residues in contact with ILE 689 (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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685D THR* 2.8 37.0 + - + +
686D ALA* 4.0 5.8 - - - +
688D ASP* 1.3 74.1 - - - +
690D PHE* 1.3 84.7 + - + +
691D GLN* 3.3 3.9 - - - +
705D ALA* 5.4 1.3 - - + -
708D VAL* 4.5 7.0 - - + -
725D LEU* 3.8 37.9 - - + -
735D PHE* 3.3 41.5 - - + -
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Residues in contact with PHE 690 (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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686D ALA* 2.9 32.4 + - + +
689D ILE* 1.3 92.1 - - + +
691D GLN* 1.3 71.7 + - - +
692D VAL* 3.1 11.5 - - + +
701D MET* 3.2 66.2 - - + -
704D GLN* 3.5 43.5 - - + -
705D ALA 4.8 1.3 - - - -
725D LEU* 4.9 3.1 - - + -
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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
------------------------------------------------------------
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