Contacts of the helix formed by residues 147 - 163 (chain x) 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 SER 147 (chain x).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144x GLU* 5.2 6.3 - - - +
145x MET* 4.6 7.4 - - - +
146x ALA* 1.3 76.3 - - - +
148x ALA* 1.3 57.1 + - - +
149x GLN 3.5 0.9 - - - -
150x TYR* 2.9 56.6 + - - -
151x ILE* 3.6 6.4 - - - +
181x ALA* 3.9 18.3 - - - +
182x PHE* 4.9 4.7 - - - -
209x VAL* 5.7 1.4 - - - +
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Residues in contact with ALA 148 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146x ALA 3.1 2.6 + - - +
147x SER* 1.3 77.9 - - - +
149x GLN* 1.3 66.7 + - - +
150x TYR 3.2 3.2 + - - -
151x ILE* 3.6 1.8 + - - +
152x THR* 2.9 27.5 + - - -
209x VAL* 4.1 26.1 - - + +
212x GLN* 3.8 29.2 - - - +
213x LYS* 4.2 14.1 - - + -
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Residues in contact with GLN 149 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135x TYR* 3.3 27.4 + - - +
136x ALA 4.3 4.3 - - - +
137x GLY* 3.2 19.3 + - - +
140x ARG* 2.9 53.7 + - - +
146x ALA 3.8 11.6 + - - +
147x SER 3.5 1.0 - - - -
148x ALA* 1.3 80.1 - - - +
150x TYR* 1.3 62.2 + - + +
152x THR* 3.7 1.6 - - - -
153x ALA* 3.3 18.0 + - - +
213x LYS* 4.1 16.5 + - - +
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Residues in contact with TYR 150 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138x ALA 4.0 8.1 - - - +
140x ARG 4.9 0.9 - - - +
141x ALA* 3.3 31.4 - - + -
142x SER 5.5 1.1 - - - -
144x GLU* 6.2 0.2 - - - -
146x ALA 5.9 0.4 - - - -
147x SER* 2.9 46.1 - - - -
149x GLN* 1.3 76.9 - - + +
151x ILE* 1.3 80.2 + - + +
152x THR 3.1 2.2 - - - -
153x ALA* 2.5 27.7 + - - +
154x ALA* 2.6 19.4 + - - +
177x PHE* 3.3 61.2 - + + -
180x MET* 3.6 20.4 - - + +
181x ALA* 3.4 20.1 + - + -
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Residues in contact with ILE 151 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147x SER 3.6 7.2 - - - +
148x ALA 3.6 3.6 + - - +
150x TYR* 1.3 92.9 - - + +
152x THR* 1.3 62.6 + - - +
153x ALA 3.2 0.7 + - - -
154x ALA* 4.1 6.0 - - + +
155x LEU* 3.2 30.7 + - + +
174x LEU* 4.1 26.0 - - + +
177x PHE* 4.5 3.1 - - + +
178x LEU* 4.4 10.3 - - + +
181x ALA* 3.4 29.6 - - + -
182x PHE* 3.5 23.6 - - + -
206x MET* 4.8 13.0 - - - -
209x VAL* 4.6 19.7 - - + -
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Residues in contact with THR 152 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132x LEU* 3.8 6.6 - - + +
135x TYR* 3.3 32.5 - - + -
148x ALA 2.9 18.1 + - - -
149x GLN 3.7 0.4 - - - -
151x ILE* 1.3 78.0 - - - +
153x ALA* 1.3 59.7 + - - +
155x LEU* 4.0 4.0 - - - +
156x ARG* 3.5 18.2 + - - +
209x VAL* 3.8 16.1 + - - +
210x LEU* 4.2 23.9 + - + -
213x LYS* 3.6 25.5 - - + +
214x LEU* 4.5 8.7 - - + -
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Residues in contact with ALA 153 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135x TYR* 4.6 0.2 - - - -
137x GLY 3.7 0.2 - - - +
138x ALA* 3.6 23.6 - - + -
149x GLN 3.3 12.1 + - - +
150x TYR 2.5 19.1 + - - +
152x THR* 1.3 69.6 - - - +
154x ALA* 1.3 52.5 + - - +
155x LEU 2.8 4.3 - - - -
156x ARG* 2.4 63.7 + - - +
157x ASP* 2.9 10.8 + - - +
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Residues in contact with ALA 154 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138x ALA* 4.9 1.1 - - - +
150x TYR 2.6 12.1 + - - +
151x ILE* 4.1 6.3 - - - +
153x ALA* 1.3 72.2 - - - +
155x LEU* 1.3 53.0 + - - +
157x ASP* 3.8 5.6 - - - +
158x LEU* 2.8 36.7 + - - +
173x ILE* 3.9 9.0 - - + +
174x LEU* 3.8 26.2 - - + +
177x PHE* 3.2 36.4 - - + -
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Residues in contact with LEU 155 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119x VAL* 4.7 10.3 - - + -
122x ILE* 5.3 8.5 - - + -
132x LEU* 4.4 12.6 - - + -
151x ILE* 3.2 23.0 + - + +
152x THR 4.0 5.2 - - - +
153x ALA 2.7 0.6 + - - -
154x ALA* 1.3 79.0 - - - +
156x ARG* 1.3 63.6 + - - +
157x ASP 3.2 0.4 - - - -
158x LEU* 4.5 3.8 - - + +
159x PHE* 3.1 71.1 + - + +
174x LEU* 5.5 8.5 - - + -
206x MET* 3.8 32.5 - - + -
209x VAL* 6.2 0.7 - - + -
210x LEU* 4.2 21.8 - - + -
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Residues in contact with ARG 156 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132x LEU* 3.6 42.9 - - + +
133x LYS* 5.5 2.4 - - - -
135x TYR* 3.5 25.7 + - + +
136x ALA* 3.1 11.7 + - - +
137x GLY 2.9 41.7 + - - +
138x ALA* 4.4 2.5 - - - -
152x THR 3.5 10.6 + - - +
153x ALA* 2.4 46.3 + - - +
155x LEU* 1.3 75.7 - - - +
157x ASP* 1.3 83.2 + - - +
159x PHE* 3.9 1.6 - - - +
160x ASP* 3.2 28.9 + - - +
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Residues in contact with ASP 157 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138x ALA* 4.0 17.2 - - - +
153x ALA 2.9 6.3 + - - +
154x ALA* 4.0 7.9 - - - +
156x ARG* 1.3 98.4 + - - +
158x LEU* 1.3 60.8 + - - +
159x PHE 3.0 4.7 - - - -
160x ASP* 3.3 7.1 + - - +
161x SER* 3.0 25.1 + - - -
173x ILE* 5.4 4.5 - - + -
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Residues in contact with LEU 158 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106x LEU* 4.0 12.1 - - + -
119x VAL* 4.8 13.7 - - + -
154x ALA 2.8 22.1 + - - +
155x LEU* 4.4 4.3 - - + +
157x ASP* 1.3 74.2 - - - +
159x PHE* 1.3 60.6 + - + +
161x SER* 3.6 6.2 - - - -
162x MET* 3.1 59.4 + - + +
169x ILE* 4.5 12.6 - - + +
170x PRO 4.8 1.3 - - - +
171x PRO* 3.6 35.0 - - + -
173x ILE* 3.4 27.9 - - + +
174x LEU* 4.4 8.7 - - + -
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Residues in contact with PHE 159 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119x VAL* 4.0 19.7 - - + -
122x ILE* 4.5 6.7 - - + -
123x ARG* 3.5 49.6 - - + +
128x LEU* 6.0 1.1 - - + -
129x LYS* 4.1 24.5 - - + -
132x LEU* 3.6 23.1 - - + -
155x LEU* 3.1 48.5 + - + +
156x ARG* 3.9 4.7 - - - +
157x ASP 3.0 0.2 - - - -
158x LEU* 1.3 82.9 - - + +
160x ASP* 1.3 54.7 + - - +
161x SER 2.7 14.3 + - - -
162x MET* 3.1 6.5 + - - -
163x ASP* 2.4 38.5 + - - +
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Residues in contact with ASP 160 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133x LYS* 3.9 37.3 + - - +
156x ARG* 3.2 18.8 + - - +
157x ASP* 3.3 8.7 + - - +
159x PHE* 1.3 79.2 - - - +
161x SER* 1.3 58.0 + - - +
163x ASP* 4.3 7.3 - - - +
164x LYS* 3.5 39.7 + - - +
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Residues in contact with SER 161 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157x ASP 3.0 15.1 + - - -
158x LEU* 3.6 9.0 - - - -
159x PHE 2.7 1.4 + - - -
160x ASP* 1.3 78.2 - - - +
162x MET* 1.3 64.8 + - - -
163x ASP 3.0 1.6 - - - -
164x LYS* 2.9 24.8 + - - +
165x THR* 3.8 3.3 + - - -
169x ILE* 3.0 26.4 - - - +
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Residues in contact with MET 162 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104x CYS* 3.4 34.9 - - - +
105x GLY 3.2 12.8 - - - +
106x LEU* 3.2 29.2 - - + -
119x VAL* 5.4 2.2 - - - -
120x GLN* 3.6 10.1 - - + +
123x ARG* 2.9 37.2 + - - +
158x LEU* 3.1 43.5 + - + +
159x PHE* 3.1 8.6 + - - +
161x SER* 1.3 78.6 - - - +
163x ASP* 1.3 51.8 + - - +
164x LYS 2.8 11.1 + - - -
165x THR 3.4 10.2 + - - +
169x ILE* 3.1 26.3 - - + +
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Residues in contact with ASP 163 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123x ARG* 3.4 21.8 + - - +
129x LYS* 4.2 18.6 + - - +
133x LYS* 4.7 17.3 + - - +
159x PHE* 2.4 38.0 + - - +
160x ASP* 4.4 8.7 - - - +
161x SER 2.9 0.8 + - - -
162x MET* 1.3 74.1 - - - +
164x LYS* 1.3 70.2 + - + +
165x THR 4.1 0.2 - - - -
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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
------------------------------------------------------------
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