Contacts of the strand formed by residues 864 - 869 (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 VAL 864 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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652D ALA* 3.8 21.8 - - + -
653D ASP 3.4 6.3 - - - +
654D TYR* 3.5 32.8 - - + -
849D PRO* 4.3 19.4 - - + +
852D MET* 3.8 20.2 - - + -
853D GLU* 3.7 19.7 + - + +
863D LYS* 1.3 84.0 - - - +
865D ASP* 1.3 80.1 + - - +
866D TYR* 3.9 13.3 - - + -
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Residues in contact with ASP 865 (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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651D ALA 3.9 0.2 - - - +
652D ALA* 3.2 2.8 - - - -
653D ASP* 2.8 43.9 + - + +
655D SER* 4.4 19.3 - - - -
863D LYS* 4.7 13.0 + - - -
864D VAL* 1.3 77.0 - - - +
866D TYR* 1.3 62.5 + - - +
867D HIS* 4.5 16.3 + - + -
881D DCT 4.7 8.1 + - - -
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Residues in contact with TYR 866 (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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650D PHE* 3.6 29.6 - + + -
651D ALA 3.1 12.3 - - - +
652D ALA* 4.1 4.7 - - + -
845D CYS* 3.6 36.6 + - + +
849D PRO* 3.5 27.4 - - + -
864D VAL* 3.9 12.1 - - + -
865D ASP* 1.3 79.1 - - - +
867D HIS* 1.3 79.7 + - - +
868D TYR* 5.7 1.3 - + - -
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Residues in contact with HIS 867 (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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650D PHE* 3.7 3.3 - - - -
651D ALA* 2.8 30.9 + - - +
865D ASP* 4.5 12.0 - - + -
866D TYR* 1.3 94.5 + - - +
868D TYR* 1.3 67.8 + - - +
875D ALA* 2.7 25.4 + - - +
876D LYS* 3.1 50.7 + - + +
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Residues in contact with TYR 868 (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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648D LEU* 4.3 20.0 - - + -
649D ILE 3.2 14.1 - - - +
650D PHE* 4.1 7.2 - + + -
841D MET* 3.8 30.3 - - + -
845D CYS* 3.6 31.9 - - - -
866D TYR* 5.7 1.6 - + - -
867D HIS* 1.3 79.7 - - - +
869D GLY* 1.3 62.8 + - - +
874D ASP 3.6 8.3 - - - +
875D ALA* 4.0 6.3 - - - -
876D LYS* 5.2 2.1 + - - -
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Residues in contact with GLY 869 (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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648D LEU* 3.6 11.6 - - - +
649D ILE* 2.9 33.2 + - - +
868D TYR* 1.3 80.8 - - - +
870D SER* 1.3 62.1 + - - -
871D THR 3.2 4.3 + - - -
874D ASP* 4.2 16.2 - - - -
875D ALA* 4.1 2.0 - - - +
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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