Contacts of the helix formed by residues 81 - 91 (chain R) in PDB entry 1G4Y
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 SER 81 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491B HIS* 2.6 30.9 + - - -
493B HIS* 4.0 22.7 + - - +
80R ASP* 1.3 73.0 - - - +
82R GLU* 1.3 65.6 + - - +
83R GLU 3.4 2.0 - - - -
84R GLU* 3.2 20.4 + - - +
85R ILE* 3.0 38.8 + - - +
146R THR* 4.9 2.2 - - - +
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Residues in contact with GLU 82 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80R ASP* 3.0 21.1 + - - +
81R SER* 1.3 77.6 - - - +
83R GLU* 1.3 58.4 + - - +
85R ILE 3.2 0.3 + - - -
86R ARG* 2.9 41.4 + - - +
139R GLU 5.1 0.4 - - - +
142R VAL* 3.6 16.7 - - + +
143R GLN* 3.0 42.4 + - + +
146R THR* 3.7 33.2 + - - +
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Residues in contact with GLU 83 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80R ASP* 4.5 1.8 + - - -
81R SER 3.4 0.4 - - - -
82R GLU* 1.3 80.0 - - - +
84R GLU* 1.3 62.2 + - + +
86R ARG* 3.2 36.6 + - - +
87R GLU* 3.0 49.0 + - - +
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Residues in contact with GLU 84 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B HIS* 5.3 6.1 + - - +
80R ASP 5.6 0.2 - - - +
81R SER* 3.2 23.0 + - - +
83R GLU* 1.3 83.2 - - + +
85R ILE* 1.3 65.1 + - + +
87R GLU* 3.4 7.9 + - - +
88R ALA* 3.1 19.8 + - - +
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Residues in contact with ILE 85 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491B HIS* 4.3 22.9 - - + +
81R SER* 3.0 35.8 + - - +
82R GLU 3.7 3.6 - - - +
84R GLU* 1.3 76.0 - - + +
86R ARG* 1.3 65.4 + - - +
88R ALA* 3.0 18.1 + - + +
89R PHE* 3.1 23.8 + - + -
142R VAL* 3.7 24.0 - - + -
145R MET* 5.2 5.8 - - + -
146R THR* 4.1 21.3 - - + -
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Residues in contact with ARG 86 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82R GLU* 2.9 41.1 + - - +
83R GLU* 3.2 45.5 + - - +
85R ILE* 1.3 76.2 - - - +
87R GLU* 1.3 60.8 + - + +
89R PHE* 3.1 5.6 + - - +
90R ARG* 2.9 27.9 + - + +
138R TYR* 3.8 20.3 - - + +
139R GLU* 3.7 45.2 + - - +
142R VAL* 4.1 13.9 - - + +
143R GLN* 4.1 3.0 - - - +
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Residues in contact with GLU 87 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83R GLU* 3.0 40.5 + - - +
84R GLU* 3.5 11.4 - - - +
85R ILE 3.2 0.4 - - - -
86R ARG* 1.3 80.8 + - - +
88R ALA* 1.3 61.0 + - - +
90R ARG* 3.3 42.4 + - - +
91R VAL* 3.4 15.3 + - - +
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Residues in contact with ALA 88 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84R GLU 3.1 11.3 + - - +
85R ILE* 3.0 14.9 + - + +
87R GLU* 1.3 72.9 - - - +
89R PHE* 1.3 68.6 + - + +
91R VAL* 3.3 23.4 + - - +
92R PHE* 3.7 12.7 - - + -
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Residues in contact with PHE 89 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85R ILE* 3.1 36.1 + - + -
86R ARG 3.1 6.9 + - - +
88R ALA* 1.3 78.7 - - + +
90R ARG* 1.3 57.9 + - - +
91R VAL 3.0 0.2 - - - -
92R PHE* 2.9 24.7 + + - +
93R ASP 3.6 0.3 + - - -
100R ILE* 3.5 29.8 - - + +
105R LEU* 4.8 11.9 - - + -
124R MET* 4.2 20.2 - - + -
136R VAL* 5.3 2.7 - - + -
138R TYR* 3.5 31.6 - - + -
141R PHE* 3.8 32.1 - + - -
142R VAL* 3.5 25.6 - - + -
145R MET* 4.2 6.3 - - + -
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Residues in contact with ARG 90 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86R ARG* 2.9 14.0 + - + +
87R GLU* 3.6 36.7 + - - +
88R ALA 3.3 0.4 - - - -
89R PHE* 1.3 75.9 - - - +
91R VAL* 1.3 62.6 + - - +
92R PHE 3.1 0.2 - - - -
93R ASP* 3.1 20.0 + - + +
96R GLY* 6.1 2.2 - - - -
138R TYR* 3.6 27.8 - - + +
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Residues in contact with VAL 91 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87R GLU 3.4 15.1 + - - +
88R ALA* 3.4 15.7 - - - +
89R PHE 3.0 0.8 + - - -
90R ARG* 1.3 77.4 - - - +
92R PHE* 1.3 82.1 + - + +
93R ASP 3.8 1.6 + - - -
94R LYS* 5.8 0.5 - - - -
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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