Contacts of the helix formed by residues 871 - 875 (chain D) in PDB entry 2HHW
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 871 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499D ARG* 4.5 11.7 - - - +
637D ARG 4.0 0.9 - - - -
638D GLN* 3.6 26.2 - - + +
640D PHE 3.5 12.6 - - - -
641D VAL* 4.0 9.9 - - + -
649D ILE* 3.9 9.9 - - - +
869D GLY 3.3 4.0 - - - +
870D SER* 1.3 86.2 - - - +
872D TRP* 1.3 67.0 + - - +
873D TYR* 3.3 20.6 + - - +
874D ASP* 2.8 31.8 + - - +
875D ALA 3.4 6.2 + - - -
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Residues in contact with TRP 872 (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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493D VAL* 5.8 0.9 - - + -
623D LEU* 3.6 23.1 - - + -
626D ILE* 3.7 28.7 - - + -
637D ARG* 3.2 49.9 + - + +
640D PHE* 3.0 49.1 + + + +
649D ILE* 3.9 21.5 - - + +
651D ALA* 5.0 1.0 - - + +
826D LEU* 3.6 24.5 - - + -
828D VAL* 4.6 8.3 - - + -
831D GLU* 5.3 1.1 + - - -
833D ILE* 3.8 31.2 - - + +
871D THR* 1.3 72.9 - - - +
873D TYR* 1.3 64.3 + - - +
875D ALA* 3.0 24.9 + - + +
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Residues in contact with TYR 873 (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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631D GLU* 2.6 34.1 + - - -
634D ARG* 3.2 53.8 + - + +
635D LYS* 4.0 3.7 + - - -
637D ARG* 3.3 12.7 + - - +
638D GLN* 3.4 48.0 - - + +
871D THR* 3.0 9.8 - - - +
872D TRP* 1.3 79.3 - - - +
874D ASP* 1.3 75.5 + - - +
875D ALA 3.2 1.8 + - - -
876D LYS* 3.6 10.7 + - - -
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Residues in contact with ASP 874 (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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867D HIS* 4.8 1.0 - - - +
868D TYR 3.5 13.2 + - - +
869D GLY* 3.8 15.7 - - - -
870D SER* 3.7 8.8 + - - -
871D THR* 2.8 40.0 + - - +
873D TYR* 1.3 87.7 - - - +
875D ALA* 1.3 55.9 + - - +
876D LYS* 2.9 14.0 + - - +
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Residues in contact with ALA 875 (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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649D ILE* 4.4 12.3 - - + +
651D ALA* 3.9 30.7 - - + +
867D HIS* 3.5 25.3 - - - +
868D TYR* 4.1 8.7 - - - +
871D THR 3.4 5.4 + - - +
872D TRP* 3.0 22.5 + - + +
874D ASP* 1.3 75.1 - - - +
876D LYS* 1.3 70.5 - - - +
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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