Contacts of the helix formed by residues 752 - 758 (chain B) in PDB entry 1GH6
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 ILE 752 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A MET* 4.0 9.9 - - + -
702B GLN* 4.4 14.8 - - + +
705B MET* 4.0 33.0 - - + -
706B CYS* 4.2 7.9 - - - -
721B PHE* 3.4 40.8 - - + -
725B VAL* 4.4 4.3 - - + -
739B PHE* 3.2 31.4 + - + +
742B VAL* 3.6 19.5 - - + +
751B SER* 1.3 71.3 + - - +
753B ILE* 1.3 71.3 + - + +
755B PHE* 3.0 10.6 + - + +
756B TYR* 2.8 32.6 + - - +
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Residues in contact with ILE 753 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A CYS* 3.8 23.6 - - + +
107A GLU* 4.5 15.0 - - + +
108A GLU* 5.1 1.6 - - - -
109A MET* 3.1 40.4 - - + +
721B PHE* 3.5 37.9 - - + -
751B SER* 2.6 11.4 + - - +
752B ILE* 1.3 77.4 - - - +
754B VAL* 1.3 66.3 + - + +
756B TYR* 2.9 17.6 + - - +
757B ASN* 2.9 35.1 + - - +
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Residues in contact with VAL 754 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744B ILE* 3.9 17.7 - - + -
750B ASP* 3.5 38.4 - - + +
751B SER* 2.4 27.9 + - - +
753B ILE* 1.3 71.8 - - + +
755B PHE* 1.3 62.3 + - - +
757B ASN* 4.6 5.4 - - - +
758B SER* 2.8 39.5 + - - +
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Residues in contact with PHE 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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694B LEU* 4.3 10.5 - - + -
698B ARG* 3.2 41.3 - - - -
702B GLN* 4.8 4.9 - - + -
703B ILE* 4.0 22.7 - - + -
706B CYS* 3.8 28.5 - - - -
742B VAL* 3.7 26.0 - - + -
743B LEU 3.7 14.1 - - - -
744B ILE* 3.5 13.3 - - + +
751B SER 3.1 4.0 + - - -
752B ILE* 3.0 12.9 + - + +
754B VAL* 1.3 76.3 - - - +
756B TYR* 1.3 57.9 + - - +
759B VAL* 2.9 33.8 + - + +
760B PHE* 2.9 31.3 + + + -
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Residues in contact with TYR 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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103A LEU* 2.8 33.5 + - - +
105A CYS* 4.4 1.3 - - + -
706B CYS* 3.9 23.3 - - + -
709B TYR* 3.2 32.2 - + - -
710B GLY* 3.4 29.1 - - - -
713B LYS* 4.7 0.5 - - - +
721B PHE* 3.9 16.2 - + + -
752B ILE 2.8 11.2 + - - +
753B ILE* 2.9 13.6 + - + +
755B PHE* 1.3 82.4 - - - +
757B ASN* 1.3 79.3 + - - +
760B PHE* 3.2 19.7 + + - -
761B MET* 2.7 47.2 + - + +
768B ILE* 5.3 1.1 - - + +
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Residues in contact with ASN 757 (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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104A PHE* 3.4 31.6 - - + -
105A CYS* 3.0 41.5 + - - +
753B ILE* 2.9 29.9 + - - +
754B VAL* 4.3 3.9 - - - +
756B TYR* 1.3 86.9 - - - +
758B SER* 1.3 60.6 + - - +
761B MET* 3.7 13.2 - - - +
762B GLN* 3.5 20.7 + - - +
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Residues in contact with SER 758 (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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744B ILE* 4.9 7.2 - - - -
754B VAL* 2.8 34.8 + - - +
757B ASN* 1.3 76.4 - - - +
759B VAL* 1.3 69.7 + - - +
762B GLN* 3.9 13.4 - - - +
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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