Contacts of the helix formed by residues 138 - 152 (chain R) 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 LEU 138 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134R LEU* 2.6 52.2 + - + +
135R GLY* 4.8 0.2 - - - -
137R ARG* 1.3 73.1 - - + +
139R ASP* 1.3 66.3 + - - +
140R ILE 3.1 0.9 - - - -
141R VAL* 2.7 27.7 + - - +
142R PHE* 2.9 21.0 + - + -
164R ALA* 5.4 3.8 - - + -
167R LEU* 3.2 35.9 - - + -
168R ILE* 5.3 4.0 - - + -
176R ARG* 4.8 5.2 - - - -
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Residues in contact with ASP 139 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334J ARG* 3.8 8.6 + - - -
135R GLY* 2.7 30.7 + - - +
138R LEU* 1.3 71.9 - - - +
140R ILE* 1.3 61.5 + - - +
142R PHE* 3.0 30.4 + - + +
143R TYR* 3.0 9.0 + - - +
176R ARG* 2.9 44.4 + - - +
179R ARG* 6.0 0.2 - - - -
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Residues in contact with ILE 140 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105R MET* 5.9 7.2 - - + -
124R PHE* 3.5 38.1 - - + +
127R THR* 4.3 11.2 - - - +
128R TYR* 6.4 0.9 - - + -
131R THR* 5.4 1.3 - - + -
135R GLY 3.5 1.4 + - - -
136R HIS* 2.6 27.8 + - + +
137R ARG 4.9 0.2 - - - -
139R ASP* 1.3 79.1 - - - +
141R VAL* 1.3 60.8 + - + +
143R TYR* 2.2 35.5 - - + -
144R LEU* 2.9 7.8 + - + +
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Residues in contact with VAL 141 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137R ARG 3.2 23.8 + - - +
138R LEU* 2.7 18.7 + - - +
140R ILE* 1.3 74.4 - - - +
142R PHE* 1.3 53.7 + - - +
144R LEU* 2.7 31.3 + - + +
145R LEU* 2.9 14.8 + - - +
160R ASN* 4.8 13.1 - - + +
163R LYS* 4.3 22.0 - - + -
164R ALA* 4.8 13.7 - - + +
167R LEU* 5.8 1.1 - - + -
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Residues in contact with PHE 142 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138R LEU* 2.9 25.8 + - + -
139R ASP* 3.0 29.4 + - + +
141R VAL* 1.3 76.6 - - - +
143R TYR* 1.3 55.4 + - - +
145R LEU* 3.5 6.6 + - + +
146R ARG* 2.9 25.8 + - - +
164R ALA* 4.0 18.4 - - + -
168R ILE* 5.3 4.5 - - + -
176R ARG* 4.0 20.9 - - + -
179R ARG* 4.5 6.3 - - + -
180R LEU* 2.9 52.7 - - + -
183R TYR* 3.6 40.2 - + + +
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Residues in contact with TYR 143 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R ASN 4.4 13.9 - - - +
15R PRO* 4.8 1.9 - - + +
124R PHE* 4.0 24.7 - + + -
139R ASP 3.0 6.7 + - - +
140R ILE* 2.2 46.9 - - + -
142R PHE* 1.3 73.2 - - - +
144R LEU* 1.3 68.6 + - - +
146R ARG* 2.7 28.0 + - - +
147R ILE* 3.0 11.7 + - - +
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Residues in contact with LEU 144 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121R LEU* 4.8 13.7 - - + +
124R PHE* 3.7 39.3 - - + -
140R ILE* 2.9 24.2 + - + +
141R VAL* 2.7 18.0 + - + +
143R TYR* 1.3 72.5 - - - +
145R LEU* 1.3 61.4 + - - +
147R ILE* 3.2 23.9 - - - +
148R GLY* 3.6 1.9 + - - -
156R LEU* 4.7 6.6 - - - +
160R ASN* 5.0 10.5 - - - -
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Residues in contact with LEU 145 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141R VAL 2.9 10.4 + - - +
142R PHE* 3.7 9.2 - - - +
144R LEU* 1.3 73.4 - - - +
146R ARG* 1.3 58.7 + - - +
148R GLY* 2.3 32.9 + - - +
149R LEU* 3.0 8.0 + - + +
156R LEU 4.7 6.1 - - - -
157R ILE* 3.8 25.3 - - + +
160R ASN* 4.2 18.2 - - + -
161R THR* 5.4 2.2 - - - +
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Residues in contact with ARG 146 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R ASN* 3.8 23.4 - - - +
15R PRO* 3.4 29.3 + - + +
16R ASP* 4.2 1.0 - - - +
17R LEU* 3.6 35.0 - - + +
142R PHE 2.9 15.2 + - - +
143R TYR* 2.7 20.4 + - - +
145R LEU* 1.3 74.8 - - - +
147R ILE* 1.3 60.5 + - - +
149R LEU* 2.9 15.2 + - - +
150R PHE* 2.9 20.0 + - - +
183R TYR* 3.5 18.3 + - - -
212R GLU* 2.8 30.5 + - - +
213R LEU* 2.6 48.1 - - - +
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Residues in contact with ILE 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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15R PRO* 4.8 15.3 - - + -
112R CYS* 5.8 4.7 - - + -
117R LYS* 4.8 22.9 - - + -
120R ALA* 5.4 12.6 - - + -
121R LEU* 5.1 9.2 - - + -
124R PHE* 5.7 4.9 - - + -
143R TYR 3.0 14.4 + - - +
144R LEU* 3.2 17.9 - - - +
146R ARG* 1.3 74.4 - - - +
148R GLY* 1.3 63.3 + - - +
150R PHE* 2.8 20.2 + - - +
151R TYR* 2.9 22.7 + - + -
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Residues in contact with GLY 148 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117R LYS* 5.2 1.1 - - - -
144R LEU 3.6 1.8 + - - -
145R LEU 2.3 22.5 + - - -
147R ILE* 1.3 73.2 - - - +
149R LEU* 1.3 62.4 + - - -
150R PHE 3.0 0.5 + - - -
151R TYR* 3.1 2.0 + - - -
152R MET 3.1 18.5 + - - -
153R ASP* 3.3 14.6 + - - +
156R LEU* 4.2 14.8 - - - +
157R ILE* 3.5 20.1 - - - +
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Residues in contact with LEU 149 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17R LEU* 4.2 17.1 - - + +
20R ALA* 5.4 1.0 - - - +
145R LEU* 3.0 8.7 + - + +
146R ARG* 2.9 16.2 + - - +
148R GLY* 1.3 75.8 - - - +
150R PHE* 1.3 64.0 + - - +
151R TYR 3.5 0.2 + - - -
152R MET* 3.5 11.2 + - - +
157R ILE* 3.4 17.1 - - + +
183R TYR* 5.1 18.4 - - + +
186R LEU* 5.5 11.7 - - + -
187R TYR* 6.3 3.1 - - + -
213R LEU* 5.7 1.3 - - + -
286R TRP* 5.4 10.5 + - + +
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Residues in contact with PHE 150 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15R PRO* 4.7 20.2 - - + -
16R ASP 4.1 17.7 - - - -
17R LEU* 4.3 11.4 - - + -
19R ILE* 4.1 2.7 - - + -
20R ALA* 3.5 49.5 - - + +
23R ARG* 5.7 3.8 + - - -
53R TYR* 2.6 45.5 - + - -
115R GLY* 5.3 9.0 - - - -
146R ARG 2.9 10.5 + - - +
147R ILE* 2.8 15.6 + - - +
149R LEU* 1.3 81.7 - - - +
151R TYR* 1.3 90.4 + + - +
152R MET* 3.6 5.0 + - - +
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Residues in contact with TYR 151 (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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23R ARG* 4.9 14.0 + - - +
52R PRO* 5.2 3.5 - - - +
53R TYR* 6.4 0.7 - + - -
115R GLY 2.8 27.4 + - - -
116R ASP* 4.2 1.7 + - - -
117R LYS* 3.2 63.1 + - + +
147R ILE* 2.9 23.6 + - + +
148R GLY 4.1 2.0 - - - +
150R PHE* 1.3 98.3 - + - +
152R MET* 1.3 72.3 + - - +
153R ASP* 4.5 4.5 - - + +
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Residues in contact with MET 152 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23R ARG* 4.6 16.4 - - - +
24R PHE* 6.2 4.5 - - + -
148R GLY 3.1 5.5 + - - -
149R LEU* 3.5 7.4 + - - +
150R PHE 3.4 8.3 - - - +
151R TYR* 1.3 84.5 - - - +
153R ASP* 1.3 67.4 + - - +
286R TRP* 6.3 4.7 - - + -
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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
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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