Contacts of the helix formed by residues 148 - 167 (chain s) 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 s).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8s PHE* 4.3 1.1 - - - -
10s HIS* 5.4 4.0 - - - -
146s ASP 4.9 3.4 - - - +
147s LEU* 1.3 75.6 - - - +
149s VAL* 1.3 54.5 + - - +
150s GLU* 3.4 3.9 - - + +
151s GLN* 2.6 43.7 + - + +
152s ALA* 2.7 33.4 + - - +
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Residues in contact with VAL 149 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8s PHE* 4.2 8.1 - - + -
10s HIS* 3.5 39.6 - - + -
147s LEU 4.2 0.2 + - - -
148s GLU* 1.3 74.9 - - - +
150s GLU* 1.3 59.6 + - + +
152s ALA* 3.2 0.9 + - - +
153s TYR* 2.9 66.7 + - + +
178s HIS* 4.0 13.5 - - + -
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Residues in contact with GLU 150 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148s GLU* 3.4 4.0 - - + +
149s VAL* 1.3 80.8 - - - +
151s GLN* 1.3 58.1 + - + +
153s TYR* 3.4 11.1 + - + +
154s ASP* 3.0 39.4 + - - +
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Residues in contact with GLN 151 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146s ASP 4.5 0.9 - - - +
147s LEU* 3.5 25.0 - - + +
148s GLU* 2.6 62.2 + - + +
150s GLU* 1.3 75.2 - - - +
152s ALA* 1.3 64.3 + - - +
154s ASP* 3.3 8.8 + - - +
155s LEU* 3.0 23.6 + - - +
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Residues in contact with ALA 152 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6s PHE* 3.6 18.8 - - + -
8s PHE* 3.5 37.7 - - + -
13s ILE* 4.0 12.8 - - + -
147s LEU* 4.5 5.6 - - + +
148s GLU 2.7 10.6 + - - +
149s VAL 3.4 7.6 - - - +
151s GLN* 1.3 71.3 - - - +
153s TYR* 1.3 67.0 + - - +
155s LEU* 3.1 5.4 + - - +
156s ALA* 3.0 21.5 + - - +
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Residues in contact with TYR 153 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13s ILE* 3.6 22.4 - - + -
149s VAL* 2.9 37.7 + - + +
150s GLU* 3.7 10.1 - - + +
152s ALA* 1.3 73.3 - - - +
154s ASP* 1.3 64.6 + - - +
156s ALA* 5.0 0.2 - - - -
157s ARG* 3.0 40.4 + - - +
176s LEU* 3.6 23.1 - - + +
178s HIS* 2.6 34.9 + + - -
180s ARG* 5.2 0.7 + - - -
185s ILE* 4.8 2.6 - - - +
187s VAL* 3.3 42.7 - - + +
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Residues in contact with ASP 154 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150s GLU* 3.0 27.2 + - - +
151s GLN* 3.7 6.9 - - - +
152s ALA 3.2 0.2 - - - -
153s TYR* 1.3 77.2 - - - +
155s LEU* 1.3 57.5 + - - +
157s ARG* 3.4 20.0 + - - +
158s ARG* 3.0 32.1 + - - +
198s LYS* 5.4 6.1 + - - -
199s TYR* 4.2 6.1 + - + +
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Residues in contact with LEU 155 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6s PHE* 4.3 15.7 - - + -
138s VAL* 3.8 32.5 - - + +
139s MET* 4.1 10.5 - - + +
142s GLY* 3.5 37.2 - - - +
143s TYR* 3.6 8.1 - - + +
147s LEU* 3.7 18.2 - - + -
151s GLN 3.0 13.2 + - - +
152s ALA 3.1 8.3 + - - +
154s ASP* 1.3 77.4 - - - +
156s ALA* 1.3 59.5 + - - +
158s ARG* 3.8 3.5 - - + +
159s ALA* 2.9 29.3 + - - +
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Residues in contact with ALA 156 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4s LEU* 4.1 3.4 - - + -
6s PHE* 3.8 12.1 - - + -
13s ILE* 3.5 32.1 - - + -
15s ALA* 4.1 9.4 - - + -
152s ALA 3.0 8.5 + - - +
153s TYR 4.0 1.3 - - - +
155s LEU* 1.3 81.6 - - - +
157s ARG* 1.3 57.6 + - - +
159s ALA* 3.2 6.2 + - - +
160s ILE* 2.9 36.2 + - - +
176s LEU* 3.9 11.4 - - + -
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Residues in contact with ARG 157 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153s TYR* 3.0 33.6 + - - +
154s ASP* 3.4 26.2 + - - +
156s ALA* 1.3 76.0 - - - +
158s ARG* 1.3 59.0 + - - +
160s ILE* 3.5 2.3 + - - +
161s TYR* 3.0 27.0 + - - +
174s VAL* 4.1 18.3 - - + +
176s LEU* 3.7 18.0 - - + +
187s VAL* 4.4 6.1 - - - +
188s SER* 3.0 25.5 + - - -
190s ASP* 3.0 25.2 + - - +
195s LEU* 3.8 25.8 - - + -
198s LYS* 5.9 3.7 - - - +
199s TYR* 3.6 16.6 + - - +
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Residues in contact with ARG 158 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144d ASP 4.8 2.0 + - - -
145d ARG* 3.5 55.6 + - - +
138s VAL* 4.4 6.3 - - + -
154s ASP 3.0 20.2 + - - +
155s LEU* 3.8 4.7 - - + +
157s ARG* 1.3 75.3 - - - +
159s ALA* 1.3 65.9 + - - +
161s TYR* 3.2 5.0 + - - +
162s GLN* 2.9 53.5 + - + +
199s TYR* 3.4 64.7 + - + +
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Residues in contact with ALA 159 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4s LEU* 3.4 24.2 - - + -
135s ALA* 4.0 18.4 - - - +
138s VAL* 3.8 23.7 - - + +
139s MET* 4.4 6.5 - - + +
155s LEU 2.9 18.4 + - - +
156s ALA* 3.6 1.3 - - - +
158s ARG* 1.3 76.3 - - - +
160s ILE* 1.3 65.6 + - - +
162s GLN* 3.4 2.4 + - - +
163s ALA* 3.0 23.2 + - - +
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Residues in contact with ILE 160 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2s THR* 3.6 28.5 - - + +
4s LEU* 3.5 20.0 - - + +
15s ALA* 3.6 36.3 - - + +
16s ALA 3.9 2.5 - - - +
17s ASP* 3.8 23.1 - - + +
156s ALA 2.9 20.4 + - - +
159s ALA* 1.3 76.5 - - - +
161s TYR* 1.3 58.5 + - - +
163s ALA* 3.3 5.1 + - - +
164s THR* 2.9 30.8 + - + +
174s VAL* 3.7 28.9 - - + -
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Residues in contact with TYR 161 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204c MET* 4.9 8.9 + - - +
157s ARG 3.0 19.5 + - - +
158s ARG* 3.5 8.1 - - - +
159s ALA 3.2 0.2 - - - -
160s ILE* 1.3 74.1 - - - +
162s GLN* 1.3 84.1 + - - +
164s THR* 2.4 30.0 + - - -
165s TYR* 3.0 17.6 + + + +
174s VAL* 4.4 4.2 - - - +
192s VAL* 3.8 37.0 - - + -
195s LEU* 3.9 20.0 - - + -
196s HIS* 3.2 39.5 + - + +
199s TYR* 3.7 29.6 - + + +
200s SER* 5.4 1.4 + - - -
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Residues in contact with GLN 162 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141d SER* 4.6 13.9 - - - +
144d ASP* 3.1 41.3 + - - +
145d ARG* 4.5 6.5 - - + -
134s TYR* 4.9 2.7 - - - +
138s VAL* 4.1 21.3 - - + -
158s ARG* 2.9 61.1 + - + +
159s ALA 4.0 3.1 - - - +
161s TYR* 1.3 82.2 - - - +
163s ALA* 1.3 63.0 + - - +
165s TYR* 3.0 21.3 + - - +
166s ARG* 3.0 17.2 + - - +
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Residues in contact with ALA 163 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2s THR* 3.7 34.1 - - + +
131s GLY 4.0 10.5 - - - +
134s TYR* 3.8 15.2 - - + +
135s ALA 4.2 3.3 - - - +
159s ALA 3.0 14.5 + - - +
160s ILE 3.4 9.6 - - - +
162s GLN* 1.3 77.3 - - - +
164s THR* 1.3 57.0 + - - +
167s ASP* 2.9 34.5 + - - +
170s SER* 4.7 1.3 - - - -
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Residues in contact with THR 164 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204c MET 4.8 0.2 + - - -
205c ASP* 2.5 34.7 - - - +
2s THR* 6.0 0.2 - - - -
17s ASP* 4.2 15.3 - - + -
160s ILE* 2.9 19.3 + - + +
161s TYR* 2.4 27.4 + - - -
163s ALA* 1.3 75.3 - - + +
165s TYR* 1.3 59.7 + - - +
167s ASP 3.4 5.2 - - - +
170s SER* 3.6 15.9 - - - -
171s GLY* 3.7 25.8 - - - +
174s VAL* 5.0 0.2 - - + -
192s VAL* 4.0 24.8 - - + +
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Residues in contact with TYR 165 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34c MET* 4.0 29.9 - - + +
37c THR* 3.7 19.6 + - + +
183c MET* 3.5 28.8 - - + +
204c MET* 3.4 36.2 - - + +
205c ASP 4.7 2.1 - - - +
144d ASP* 3.6 33.7 - - - -
161s TYR* 3.0 23.3 + + + +
162s GLN* 3.1 17.7 - - - +
164s THR* 1.3 80.4 + - - +
166s ARG* 1.3 66.3 + - - +
167s ASP 5.0 0.3 - - - +
196s HIS* 6.0 2.2 - + - -
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Residues in contact with ARG 166 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27c ARG* 5.2 0.2 + - - -
32c ALA 3.4 13.7 - - - +
33c GLN* 4.1 3.2 - - - -
34c MET* 2.5 77.1 + - - +
35c VAL* 3.9 8.7 + - - +
129d PHE* 3.4 25.9 + - - -
140d LEU* 3.1 49.6 - - + +
141d SER* 5.0 2.9 - - - +
144d ASP* 3.1 25.1 + - - +
134s TYR* 3.5 38.6 - - + -
162s GLN 3.0 9.4 + - - +
165s TYR* 1.3 85.2 - - + +
167s ASP* 1.3 61.9 + - - +
168s ALA* 5.2 0.2 - - - +
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Residues in contact with ASP 167 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32c ALA* 4.1 10.2 - - - +
205c ASP 3.6 0.3 - - - +
130s SER* 2.5 39.7 + - - +
131s GLY* 3.3 17.1 + - - -
134s TYR* 4.0 10.2 - - + -
163s ALA 2.9 16.7 + - - +
164s THR 3.4 7.4 - - - +
165s TYR 5.1 0.2 - - - -
166s ARG* 1.3 76.8 - - - +
168s ALA* 1.3 71.0 + - - +
169s TYR* 3.1 16.7 + - - -
170s SER* 2.9 39.7 + - - +
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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