Contacts of the helix formed by residues 148 - 167 (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 GLU 148 (chain e).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8e PHE* 4.4 2.0 - - - -
10e HIS* 5.0 5.8 - - - +
146e ASP 5.1 2.5 - - - +
147e LEU* 1.3 76.6 - - - +
149e VAL* 1.3 56.5 + - - +
150e GLU* 3.4 6.8 + - - +
151e GLN* 2.7 42.6 + - + +
152e ALA* 2.7 34.5 + - - +
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Residues in contact with VAL 149 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8e PHE* 4.6 2.7 - - + -
10e HIS* 3.4 37.0 - - + -
148e GLU* 1.3 73.5 - - - +
150e GLU* 1.3 59.8 + - - +
152e ALA* 3.3 5.6 + - - +
153e TYR* 2.9 67.1 + - + +
178e HIS* 4.3 10.8 - - + -
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Residues in contact with GLU 150 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148e GLU* 3.4 6.5 - - - +
149e VAL* 1.3 79.6 - - - +
151e GLN* 1.3 58.3 + - + +
153e TYR* 3.4 10.7 + - + +
154e ASP* 3.0 39.9 + - - +
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Residues in contact with GLN 151 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146e ASP 4.5 1.6 - - - +
147e LEU* 3.6 23.7 - - + +
148e GLU* 2.7 58.9 + - + +
150e GLU* 1.3 76.4 - - + +
152e ALA* 1.3 60.4 + - - +
154e ASP* 3.3 9.1 + - - +
155e LEU* 2.9 28.5 + - - +
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Residues in contact with ALA 152 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6e PHE* 3.5 17.0 - - + -
8e PHE* 3.4 39.7 - - + -
13e ILE* 3.9 12.1 - - + -
147e LEU* 4.2 9.1 - - + +
148e GLU 2.7 12.4 + - - +
149e VAL 3.5 4.3 - - - +
151e GLN* 1.3 72.4 - - - +
153e TYR* 1.3 63.6 + - - +
155e LEU* 3.1 3.2 + - - +
156e ALA* 3.0 21.8 + - - +
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Residues in contact with TYR 153 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13e ILE* 3.4 30.5 - - + -
149e VAL* 2.9 38.1 + - + +
150e GLU* 3.7 12.1 - - + +
151e GLN 3.3 0.2 - - - -
152e ALA* 1.3 74.8 - - - +
154e ASP* 1.3 64.6 + - - +
156e ALA* 3.4 0.8 + - - -
157e ARG* 3.0 39.1 + - - +
176e LEU* 3.6 24.9 - - + +
177e TYR 5.3 0.4 - - - -
178e HIS* 2.5 27.2 + - - +
180e ARG* 5.2 1.0 + - - -
187e VAL* 3.3 41.4 - - + +
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Residues in contact with ASP 154 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150e GLU* 3.0 27.7 + - - +
151e GLN* 3.6 8.3 - - - +
153e TYR* 1.3 77.3 - - - +
155e LEU* 1.3 57.9 + - - +
157e ARG* 3.5 20.0 + - - +
158e ARG* 3.0 32.4 + - - +
198e LYS* 4.5 9.2 + - - -
199e TYR* 4.2 6.1 + - + +
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Residues in contact with LEU 155 (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* 4.4 14.6 - - + -
138e VAL* 3.9 20.2 - - + +
139e MET* 4.0 13.7 - - + +
142e GLY* 3.5 44.6 - - - +
143e TYR* 3.6 15.3 - - + +
147e LEU* 3.7 12.8 - - + -
151e GLN 2.9 14.0 + - - +
152e ALA* 3.1 10.3 + - - +
154e ASP* 1.3 73.2 - - - +
156e ALA* 1.3 67.7 + - - +
158e ARG* 3.3 4.1 + - + +
159e ALA* 2.9 22.9 + - - +
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Residues in contact with ALA 156 (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* 4.0 13.9 - - + -
6e PHE* 3.8 13.4 - - + -
13e ILE* 3.6 31.2 - - + -
15e ALA* 4.1 2.5 - - + -
152e ALA 3.0 9.7 + - - +
153e TYR 4.0 2.7 - - - +
155e LEU* 1.3 76.6 - - - +
157e ARG* 1.3 65.0 + - - +
159e ALA* 3.2 4.7 + - - +
160e ILE* 3.0 29.2 + - - +
176e LEU* 4.0 9.4 - - + -
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Residues in contact with ARG 157 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153e TYR* 3.0 31.5 + - - +
154e ASP* 3.5 25.7 + - - +
156e ALA* 1.3 77.6 - - - +
158e ARG* 1.3 62.6 + - - +
160e ILE* 3.5 2.4 + - - +
161e TYR* 3.0 23.0 + - - +
174e VAL* 4.1 19.1 + - + +
176e LEU* 3.6 19.5 - - + +
187e VAL* 4.5 4.4 - - - +
188e SER* 3.0 27.9 + - - -
190e ASP* 3.1 23.1 + - - -
195e LEU* 3.6 32.3 - - + -
198e LYS* 4.1 13.7 - - - +
199e TYR* 3.7 10.3 + - - +
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Residues in contact with ARG 158 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138e VAL* 4.3 10.1 - - + -
154e ASP 3.0 19.4 + - - +
155e LEU* 3.8 4.9 - - + +
157e ARG* 1.3 77.1 - - - +
159e ALA* 1.3 64.0 + - - +
161e TYR* 3.2 2.9 + - - +
162e GLN* 2.9 57.8 + - + +
199e TYR* 3.3 63.9 + - + +
144r ASP 5.0 1.0 + - - -
145r ARG* 3.1 58.4 + - - +
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Residues in contact with ALA 159 (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* 3.6 22.0 - - + -
135e ALA* 3.9 20.7 - - - +
138e VAL* 3.7 23.3 - - + +
139e MET* 4.2 9.0 - - + -
155e LEU 2.9 17.5 + - - +
156e ALA* 3.7 0.9 - - - +
158e ARG* 1.3 75.8 - - - +
160e ILE* 1.3 67.0 + - - +
162e GLN* 3.4 1.6 + - - +
163e ALA* 3.0 23.8 + - - +
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Residues in contact with ILE 160 (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* 3.6 30.1 - - + +
4e LEU* 3.6 20.6 - - + +
15e ALA* 3.6 33.4 - - + +
16e ALA 4.0 0.2 - - - -
17e ASP* 3.9 25.1 - - + +
156e ALA 3.0 16.9 + - - +
157e ARG 3.9 0.2 - - - +
159e ALA* 1.3 75.7 - - - +
161e TYR* 1.3 62.9 + - - +
163e ALA* 3.3 6.9 + - - +
164e THR* 3.0 27.4 + - + +
174e VAL* 3.6 32.3 - - + -
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Residues in contact with TYR 161 (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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157e ARG 3.0 19.1 + - - +
158e ARG* 3.4 7.2 - - - +
159e ALA 3.1 0.2 - - - -
160e ILE* 1.3 73.6 - - - +
162e GLN* 1.3 92.8 + - + +
164e THR* 2.3 29.5 + - - -
165e TYR* 3.0 22.3 + + + +
174e VAL* 4.8 3.6 - - - -
192e VAL* 3.7 37.9 - - + -
195e LEU* 3.8 20.6 - - + -
196e HIS* 3.4 38.7 + - + +
199e TYR* 3.7 28.8 - + + +
200e SER 5.6 0.3 + - - -
204q MET* 5.0 4.4 + - - +
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Residues in contact with GLN 162 (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* 4.8 2.2 - - - -
138e VAL* 4.3 11.0 - - + -
158e ARG* 2.9 53.4 + - + +
159e ALA 4.1 2.2 - - - +
161e TYR* 1.3 93.2 - - - +
163e ALA* 1.3 63.4 + - - +
165e TYR* 2.9 21.6 + - - +
166e ARG* 3.1 17.3 + - - +
141r SER* 4.0 23.6 - - - +
144r ASP* 3.6 32.7 + - - +
145r ARG* 4.3 6.3 - - + -
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Residues in contact with ALA 163 (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* 3.5 32.3 - - + +
131e GLY 3.9 10.8 - - - +
134e TYR* 3.7 15.0 - - + +
135e ALA 4.3 2.9 - - - +
159e ALA 3.0 14.5 + - - +
160e ILE 3.3 10.8 - - - +
162e GLN* 1.3 78.2 - - - +
164e THR* 1.3 57.0 + - - +
166e ARG* 3.3 1.2 + - - +
167e ASP* 2.9 35.2 + - - +
170e SER* 4.7 0.9 - - - -
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Residues in contact with THR 164 (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* 5.7 0.2 - - - -
17e ASP* 4.4 13.5 - - + -
160e ILE* 3.0 17.7 + - + +
161e TYR* 2.3 29.1 + - - -
163e ALA* 1.3 76.1 - - + +
165e TYR* 1.3 61.6 + - - +
167e ASP 3.3 5.4 - - - +
170e SER* 3.6 15.0 - - - -
171e GLY* 3.7 22.0 - - - +
192e VAL* 4.0 20.2 - - + +
205q ASP* 2.5 44.3 - - - +
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Residues in contact with TYR 165 (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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161e TYR* 3.9 20.6 - + + +
162e GLN* 2.9 22.5 + - - +
164e THR* 1.3 84.9 + - - +
166e ARG* 1.3 64.8 + - - +
167e ASP 5.1 0.3 - - - -
196e HIS* 6.0 2.7 - + - -
34q MET* 3.8 27.0 - - + +
37q THR* 3.6 18.7 + - - +
183q MET* 3.5 33.1 - - + +
204q MET* 3.2 39.3 - - + +
205q ASP 4.8 0.5 - - - +
144r ASP* 3.6 30.1 - - - -
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Residues in contact with ARG 166 (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 41.3 + - + +
162e GLN 3.1 9.9 + - - +
165e TYR* 1.3 84.3 - - + +
167e ASP* 1.3 57.8 + - - +
168e ALA 3.7 0.2 + - - -
27q ARG* 5.0 0.3 + - - -
32q ALA 3.4 5.5 - - - +
33q GLN* 3.6 4.0 - - - +
34q MET* 2.8 84.4 + - - +
35q VAL* 3.8 7.7 + - - +
129r PHE* 3.2 34.6 + - - -
140r LEU* 3.4 35.9 - - + +
141r SER* 4.6 4.9 - - - +
144r ASP* 2.6 27.1 + - - +
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Residues in contact with ASP 167 (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* 2.5 39.3 + - - +
131e GLY* 3.3 7.4 + - - -
134e TYR* 3.9 18.1 - - + -
163e ALA 2.9 17.6 + - - +
164e THR 3.3 6.9 - - - +
165e TYR 5.1 0.7 - - - -
166e ARG* 1.3 75.7 - - - +
168e ALA* 1.3 71.9 + - - +
169e TYR* 3.2 17.1 + - - -
170e SER* 3.0 38.4 + - - +
32q ALA* 3.8 11.5 - - - +
205q ASP 3.5 1.0 - - - +
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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
------------------------------------------------------------
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