Contacts of the helix formed by residues 752 - 756 (chain B) in PDB entry 3ZHT
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 752 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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857A HIS* 3.1 24.3 + - + -
859A ARG* 4.6 6.0 - - + +
750B GLY 4.1 0.8 + - - -
751B ASP* 1.3 74.5 + - - +
753B PRO* 1.4 69.4 - - - +
754B SER* 2.8 26.9 + - - -
755B MET* 3.2 33.8 + - + +
756B THR* 5.1 0.2 + - - -
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Residues in contact with PRO 753 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680B ILE* 5.8 0.4 - - + -
743B ARG* 3.5 24.7 - - - +
745B ARG* 4.3 0.4 - - - -
746B GLY* 3.7 16.8 - - - +
751B ASP* 3.4 21.3 - - - +
752B ASP* 1.4 84.9 - - - +
754B SER* 1.3 57.3 + - - +
755B MET 3.2 0.8 + - - -
756B THR* 3.6 7.4 + - - +
757B GLN* 3.0 29.8 + - - +
761B TYR* 3.5 38.6 - - + -
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Residues in contact with SER 754 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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857A HIS* 2.7 32.7 + - - +
916A VAL 5.7 0.2 - - - +
918A ARG* 3.9 25.6 + - - -
752B ASP* 2.8 13.8 + - - -
753B PRO* 1.3 77.2 - - - +
755B MET* 1.4 63.4 + - - +
756B THR 3.3 0.4 - - - -
757B GLN 4.0 2.2 - - - -
758B PRO* 3.3 33.9 - - - +
761B TYR* 4.4 11.0 - - - +
762B ASP* 5.3 0.4 - - - -
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Residues in contact with MET 755 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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857A HIS* 3.4 35.2 - - + +
859A ARG* 4.3 13.9 - - + +
860A VAL* 3.9 26.9 - - + +
905A ARG* 4.0 13.7 - - - +
909A THR* 3.4 33.9 - - + -
912A HIS* 4.0 5.4 - - + -
916A VAL* 3.5 27.9 + - - +
750B GLY 4.6 2.0 - - - +
752B ASP* 3.2 37.1 + - + +
754B SER* 1.4 79.1 + - - +
756B THR* 1.3 63.8 + - + +
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Residues in contact with THR 756 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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904A GLN* 6.4 0.9 - - + -
905A ARG* 3.7 39.9 - - + -
914A VAL 6.1 0.9 - - - +
916A VAL* 4.2 20.8 - - + +
947A ASN* 6.2 1.6 - - - +
683B THR* 3.6 37.4 - - - +
751B ASP* 4.9 1.2 + - - -
753B PRO* 3.7 9.5 + - - +
755B MET* 1.3 78.5 - - - +
757B GLN* 1.4 76.7 + - - +
758B PRO* 3.5 8.0 - - - +
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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