Contacts of the helix formed by residues 131 - 143 (chain e) in PDB entry 5GJQ
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 GLY 131 (chain e).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1e THR 3.2 6.7 + - - -
2e THR* 3.2 24.7 - - - +
129e GLY 3.1 1.0 - - - -
130e SER* 1.3 76.0 + - - +
132e SER* 1.3 65.5 + - - +
133e VAL 3.2 2.7 - - - -
134e TYR* 2.9 28.3 + - - +
135e ALA 3.3 7.8 + - - -
163e ALA* 3.9 4.5 - - - +
167e ASP* 3.6 7.6 - - - -
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Residues in contact with SER 132 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26d VAL* 5.6 1.6 - - - +
2e THR* 4.3 1.8 - - - +
127e SER* 3.2 44.9 + - - -
128e VAL 4.5 0.9 - - - -
129e GLY* 2.6 28.6 + - - +
130e SER 3.5 0.2 - - - -
131e GLY* 1.3 78.1 - - - +
133e VAL* 1.3 69.5 + - - +
135e ALA 3.2 0.7 + - - -
136e TYR* 2.9 33.2 + - - -
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Residues in contact with VAL 133 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24d ASN* 5.7 2.5 - - - +
25d ILE* 3.9 21.1 - - + -
26d VAL* 3.6 26.2 - - + -
130e SER 4.6 6.9 + - - +
131e GLY 4.6 0.2 - - - +
132e SER* 1.3 82.8 + - - +
134e TYR* 1.3 83.3 + - + +
136e TYR* 3.6 6.2 + - - -
137e GLY 3.6 4.2 + - - -
137r PHE* 3.2 36.2 - - + +
138r LEU* 3.2 27.7 - - + +
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Residues in contact with TYR 134 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130e SER 4.2 6.1 - - - -
131e GLY* 2.9 19.6 + - - +
133e VAL* 1.3 84.5 - - + +
135e ALA* 1.3 65.1 + - - +
137e GLY 3.3 6.4 + - - -
138e VAL* 3.4 7.3 - - - +
163e ALA* 3.7 19.7 - - - +
166e ARG* 3.4 34.3 - - + -
167e ASP* 3.9 24.0 - - + -
32q ALA* 5.4 2.8 - - + +
33q GLN* 2.1 50.1 + - - +
137r PHE* 3.5 30.5 - + - -
140r LEU* 4.8 4.3 - - + -
141r SER* 2.9 34.6 + - - -
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Residues in contact with ALA 135 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2e THR* 4.2 10.5 - - + -
4e LEU* 4.2 18.8 - - + -
127e SER* 3.5 22.9 - - - +
131e GLY 3.3 6.5 + - - +
132e SER 3.2 2.3 + - - +
134e TYR* 1.3 76.5 - - - +
136e TYR* 1.3 65.0 + - - +
138e VAL* 3.4 3.8 + - - +
139e MET* 3.0 28.9 + - + +
159e ALA* 3.9 21.1 - - - +
163e ALA* 4.3 0.6 - - - +
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Residues in contact with TYR 136 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26d VAL* 3.4 36.3 - - + -
27d GLN 5.1 0.2 - - - -
28d MET* 2.4 40.1 - - + +
125e THR* 4.3 11.6 + - - -
126e PHE* 3.7 3.6 - - - -
127e SER* 3.2 26.1 + - - -
132e SER* 2.9 26.6 + - - +
133e VAL* 3.8 6.5 - - - +
134e TYR 3.2 0.2 - - - -
135e ALA* 1.3 76.8 - - - +
137e GLY* 1.3 63.6 + - - +
139e MET* 3.9 24.5 - - + -
140e ASP* 2.9 48.6 + - - +
138r LEU* 4.1 9.4 - - + -
166r GLU* 3.6 2.7 - - - +
170r ARG* 4.1 17.3 - - + -
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Residues in contact with GLY 137 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133e VAL 3.6 3.2 + - - -
134e TYR 3.3 8.0 + - - -
135e ALA 3.2 1.0 - - - -
136e TYR* 1.3 81.9 - - - +
138e VAL* 1.3 60.1 + - - +
141e ARG* 3.4 26.3 + - - +
138r LEU 3.7 15.9 - - - -
141r SER* 4.3 0.9 - - - -
142r ILE* 3.6 12.3 - - - +
166r GLU* 3.4 20.8 - - - +
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Residues in contact with VAL 138 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134e TYR 3.4 18.4 - - - +
135e ALA* 3.6 8.7 - - - +
137e GLY* 1.3 74.3 - - - +
139e MET* 1.3 65.2 + - - +
141e ARG* 3.2 6.4 + - - +
142e GLY* 2.9 21.5 + - - -
155e LEU* 3.9 9.5 - - + +
158e ARG* 4.3 14.4 - - + -
159e ALA* 3.7 34.1 - - + +
162e GLN* 4.3 12.3 - - + -
141r SER* 4.0 16.1 + - - +
142r ILE* 5.0 2.5 - - - +
145r ARG* 5.5 13.0 - - + -
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Residues in contact with MET 139 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4e LEU* 3.8 32.5 - - + -
6e PHE* 3.9 19.5 - - + -
125e THR* 3.9 28.0 - - + +
126e PHE 3.9 16.4 - - - +
127e SER* 4.3 6.3 - - - -
135e ALA 3.0 19.9 + - - +
136e TYR* 3.9 26.7 - - + +
138e VAL* 1.3 80.3 - - - +
140e ASP* 1.3 57.7 + - - +
143e TYR* 2.8 40.8 + - + +
155e LEU* 4.0 17.2 - - + +
159e ALA* 4.2 7.2 - - + -
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Residues in contact with ASP 140 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125e THR* 4.1 17.5 + - - +
136e TYR* 2.9 30.1 + - - +
139e MET* 1.3 77.5 - - - +
141e ARG* 1.3 68.5 + - - +
142e GLY 3.5 0.5 + - - -
143e TYR* 3.8 13.9 + - - +
166r GLU* 3.3 14.9 - - - +
169r LYS* 3.5 32.7 - - + +
170r ARG* 3.0 38.4 + - - +
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Residues in contact with ARG 141 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137e GLY 3.4 17.3 + - - +
138e VAL* 3.2 7.2 + - - +
140e ASP* 1.3 82.5 + - - +
142e GLY* 1.3 58.1 + - - +
143e TYR 3.6 0.2 - - - -
142r ILE* 4.5 19.5 - - + -
146r TYR* 4.4 22.5 + - + +
162r LYS* 4.5 31.6 + - - +
165r GLU* 2.1 44.5 + - - +
166r GLU* 4.4 10.5 + - - +
169r LYS* 4.2 21.4 - - - +
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Residues in contact with GLY 142 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138e VAL 2.9 10.4 + - - -
141e ARG* 1.3 79.6 - - - +
143e TYR* 1.3 64.0 + - - +
144e SER* 3.5 2.6 + - - -
147e LEU* 3.9 13.5 - - - +
155e LEU* 3.5 26.7 - - - +
146r TYR* 5.6 1.6 - - - -
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Residues in contact with TYR 143 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6e PHE* 3.6 30.1 - + - -
7e LYS 2.4 33.6 + - - -
8e PHE* 4.4 1.6 - - + -
124e ALA* 4.0 14.1 - - + +
125e THR* 3.8 27.6 - - + -
139e MET* 2.8 21.4 + - + +
140e ASP* 3.8 11.3 + - - +
141e ARG 3.6 1.6 - - - -
142e GLY* 1.3 79.2 - - - +
144e SER* 1.3 79.3 + - - +
145e TYR* 3.7 24.4 - - + -
147e LEU* 4.8 0.2 - - + -
155e LEU* 3.6 9.6 - - + -
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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