Contacts of the helix formed by residues 668 - 677 (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 668 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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663D ALA 3.5 5.1 + - - +
666D ALA* 3.2 3.3 - - + -
667D GLU* 1.3 75.3 - - - +
669D ASP* 1.3 64.1 + - - +
670D ASN* 3.1 9.7 + - - +
671D LEU* 2.9 29.3 + - + -
672D MET* 2.9 24.9 + - - +
743D PHE* 2.9 30.8 - - - -
744D PRO* 4.5 2.3 - - - +
745D GLY* 2.8 32.3 + - - -
746D VAL* 3.0 20.8 + - + +
748D ARG* 5.5 0.7 - - - +
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Residues in contact with ASP 669 (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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667D GLU 3.4 5.3 + - - +
668D ASP* 1.3 72.4 + - - +
670D ASN* 1.3 62.6 + - - +
672D MET* 3.8 17.3 - - - +
673D GLU* 3.0 29.5 + - - +
676D ARG* 5.6 0.9 + - - -
748D ARG* 5.5 7.0 + - - +
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Residues in contact with ASN 670 (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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668D ASP* 3.1 4.2 + - - +
669D ASP* 1.3 79.9 - - - +
671D LEU* 1.3 58.1 + - - +
673D GLU* 3.3 7.3 + - - +
674D ALA* 2.9 28.2 + - - +
741D GLU 5.0 1.4 + - - -
742D SER* 2.7 34.0 + - - +
743D PHE* 4.0 10.2 - - + -
744D PRO* 4.7 6.1 - - - +
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Residues in contact with LEU 671 (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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659D LEU* 3.7 26.7 - - + +
662D LEU* 4.4 8.3 - - + -
663D ALA* 3.7 21.1 - - + +
668D ASP* 2.9 23.2 + - + +
670D ASN* 1.3 74.4 - - - +
672D MET* 1.3 63.7 + - - +
674D ALA* 3.4 2.4 + - - +
675D PHE* 3.2 49.2 + - + -
681D ILE* 4.6 13.7 - - + -
713D VAL* 6.2 1.3 - - + -
739D TYR* 5.9 1.3 - - - +
743D PHE* 3.7 30.4 - - + -
746D VAL* 4.1 20.4 - - + -
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Residues in contact with MET 672 (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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663D ALA* 3.5 22.9 - - - +
667D GLU* 3.4 38.6 - - + +
668D ASP 2.9 18.3 + - - +
669D ASP* 3.8 15.7 - - - +
671D LEU* 1.3 74.1 - - - +
673D GLU* 1.3 65.6 + - - +
675D PHE 3.3 1.2 + - - -
676D ARG* 2.9 49.5 + - - +
859D ARG* 3.9 29.6 - - - -
860D VAL* 3.6 22.1 - - + +
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Residues in contact with GLU 673 (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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669D ASP 3.0 18.6 + - - +
670D ASN* 3.6 10.1 - - - +
672D MET* 1.3 77.5 - - - +
674D ALA* 1.3 63.0 - - - +
676D ARG* 3.1 19.7 + - - +
677D ARG* 2.8 73.6 + - - +
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Residues in contact with ALA 674 (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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670D ASN 2.9 16.8 + - - +
671D LEU* 3.5 10.8 - - + +
672D MET 3.2 0.2 - - - -
673D GLU* 1.3 78.6 - - - +
675D PHE* 1.3 60.4 + - + +
677D ARG* 3.2 7.8 + - - +
679D LEU* 2.9 44.4 + - + +
681D ILE* 3.6 31.4 - - + -
743D PHE* 5.5 2.0 - - + -
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Residues in contact with PHE 675 (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* 3.2 34.3 - - + -
659D LEU* 3.5 43.5 - - + -
660D ARG* 3.6 48.6 + - + +
663D ALA* 4.1 6.7 - - + -
671D LEU* 3.2 35.0 + - + +
672D MET 4.1 2.0 - - - +
674D ALA* 1.3 73.5 - - - +
676D ARG* 1.3 60.9 + - - +
677D ARG 3.0 2.0 - - - -
678D ASP* 3.0 18.0 + - - +
679D LEU 3.8 8.7 - - - -
681D ILE* 3.7 20.9 - - + -
860D VAL* 4.2 13.7 - - + -
861D PRO* 3.7 10.3 - - - +
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Residues in contact with ARG 676 (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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779A ARG* 3.1 46.1 - - - +
669D ASP 5.6 0.8 + - - -
672D MET* 2.9 51.1 + - - +
673D GLU* 3.1 18.9 + - - +
675D PHE* 1.3 77.3 - - - +
677D ARG* 1.3 60.7 + - + +
678D ASP* 3.2 1.7 + - - +
859D ARG* 2.9 30.8 + - - +
860D VAL* 4.5 0.7 - - + -
861D PRO* 4.1 22.5 - - + +
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Residues in contact with ARG 677 (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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673D GLU* 2.8 54.8 + - - +
674D ALA 3.6 7.4 - - - +
675D PHE 3.0 0.2 - - - -
676D ARG* 1.3 77.5 - - - +
678D ASP* 1.3 69.7 + - - +
679D LEU* 3.2 28.2 + - + +
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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