Contacts of the helix formed by residues 138 - 147 (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 TYR 138 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86R ARG* 3.8 31.2 - - + -
89R PHE* 3.5 38.4 - + + -
90R ARG* 3.6 23.1 - - + +
93R ASP* 2.7 38.3 + - + +
98R GLY* 3.3 32.5 + - - -
99R TYR 3.9 0.2 - - - -
100R ILE* 3.9 19.5 - - + -
136R VAL* 3.1 18.1 + - + -
137R ASN* 1.3 68.2 - - - +
139R GLU* 1.3 71.8 + - + +
141R PHE* 3.8 2.2 - - - +
142R VAL* 2.9 27.9 + - - +
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Residues in contact with GLU 139 (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* 5.1 0.5 - - - +
86R ARG* 3.7 39.4 + - + +
98R GLY 4.9 0.8 + - - +
137R ASN* 3.4 7.8 + - - +
138R TYR* 1.3 84.0 - - + +
140R GLU* 1.3 64.9 + - + +
142R VAL* 4.0 1.5 - - - +
143R GLN* 3.1 47.7 + - - +
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Residues in contact with GLU 140 (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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130R ILE* 5.5 11.4 - - + +
131R ASP* 4.9 7.4 - - - +
137R ASN* 3.0 41.8 + - + +
139R GLU* 1.3 78.9 - - + +
141R PHE* 1.3 62.1 + - - +
143R GLN* 3.3 15.5 + - - +
144R MET* 3.1 22.6 + - - +
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Residues in contact with PHE 141 (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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89R PHE* 3.8 25.8 - + - -
105R LEU* 5.9 0.2 - - + -
124R MET* 4.2 27.6 - - + -
127R GLU* 4.3 6.7 - - + -
128R ALA* 3.6 45.8 - - + +
130R ILE* 5.2 6.0 - - + +
136R VAL* 4.2 11.4 - - + -
137R ASN 3.1 15.4 + - - +
138R TYR* 3.8 3.8 - - - +
140R GLU* 1.3 77.5 - - - +
142R VAL* 1.3 62.3 + - + +
144R MET* 3.3 22.9 + - + +
145R MET* 3.0 61.8 + - + +
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Residues in contact with VAL 142 (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* 3.6 34.3 - - + +
85R ILE* 3.7 18.8 - - + -
86R ARG* 4.1 10.3 - - + +
89R PHE* 3.5 39.7 - - + -
138R TYR 2.9 22.6 + - - +
139R GLU* 4.0 4.3 - - - +
141R PHE* 1.3 73.2 - - - +
143R GLN* 1.3 60.4 + - - +
145R MET* 3.2 8.6 + - + +
146R THR* 2.9 38.3 + - + +
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Residues in contact with GLN 143 (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* 3.0 29.8 + - - +
86R ARG* 4.1 2.0 - - - +
139R GLU* 3.1 48.5 + - - +
140R GLU* 3.5 16.9 - - - +
141R PHE 3.3 0.2 - - - -
142R VAL* 1.3 77.7 - - - +
144R MET* 1.3 55.7 + - - +
146R THR* 3.5 6.4 + - - -
147R ALA* 2.9 32.4 + - - +
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Residues in contact with MET 144 (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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127R GLU* 3.2 39.5 - - + +
130R ILE* 5.6 5.6 - - + -
140R GLU 3.1 13.2 + - - +
141R PHE* 3.6 31.0 - - + +
142R VAL 3.2 0.2 - - - -
143R GLN* 1.3 75.2 - - - +
145R MET* 1.3 72.4 + - + +
146R THR 3.4 0.2 + - - -
147R ALA* 3.6 17.1 + - - +
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Residues in contact with MET 145 (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* 4.0 30.2 + - + +
85R ILE* 5.2 5.2 - - + -
89R PHE* 4.2 16.6 - - + -
124R MET* 5.9 0.4 - - + -
141R PHE* 3.0 68.0 + - + +
142R VAL* 3.2 11.9 + - + +
144R MET* 1.3 85.2 - - + +
146R THR* 1.3 60.7 + - + +
147R ALA 3.5 2.5 + - - +
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Residues in contact with THR 146 (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 14.8 - - + +
492B HIS* 5.8 1.9 + - - -
80R ASP* 5.7 8.1 - - - +
81R SER 4.9 1.3 - - - +
82R GLU* 3.7 37.5 + - - +
85R ILE* 4.1 26.9 - - + -
142R VAL* 2.9 22.7 + - + +
143R GLN* 3.5 4.7 + - - -
145R MET* 1.3 78.3 - - + +
147R ALA* 1.3 69.0 + - - +
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Residues in contact with ALA 147 (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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143R GLN 2.9 19.0 + - - +
144R MET* 3.6 13.1 + - - +
145R MET 3.5 4.5 - - - +
146R THR* 1.3 83.2 - - - +
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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