Contacts of the helix formed by residues 142 - 154 (chain q) 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 CYS 142 (chain q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10q ALA* 3.3 33.4 - - - -
141q THR* 1.3 79.2 - - - +
143q ALA* 1.3 63.6 + - - +
145q GLN* 3.2 24.6 + - + +
146q MET* 3.1 32.4 + - - +
174q ALA 4.3 1.1 - - - +
175q VAL* 4.3 12.6 - - - -
178q ASP* 3.5 30.3 - - + +
181q SER* 4.0 2.5 - - - -
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Residues in contact with ALA 143 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22p GLU* 3.5 26.0 - - - +
25p VAL* 6.0 0.4 - - + -
138q VAL* 4.2 5.6 - - + +
139q SER* 5.3 1.1 - - - -
140q GLY 3.5 18.9 + - - +
141q THR 3.4 2.6 + - - +
142q CYS* 1.3 74.0 - - - +
144q GLU* 1.3 68.0 + - + +
146q MET* 3.3 14.1 + - - +
147q TYR* 2.9 33.3 + - + -
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Residues in contact with GLU 144 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140f SER 3.7 20.1 - - - +
141f ALA* 5.0 0.3 - - - -
143f ALA* 3.3 29.1 + - + +
144f MET* 3.4 31.3 - - + +
186f ASP* 5.2 2.4 - - - -
24p MET 4.2 5.2 - - - +
25p VAL* 3.4 34.4 - - + +
142q CYS 3.4 0.4 - - - -
143q ALA* 1.3 78.6 - - - +
145q GLN* 1.3 70.1 + - - +
147q TYR* 3.3 8.6 + - - +
148q GLY* 2.9 19.4 + - - -
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Residues in contact with GLN 145 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24e ALA* 6.0 0.4 - - - +
25e TYR* 3.3 33.0 - - + +
143f ALA* 3.7 22.8 - - - +
147f PRO* 4.1 11.0 - - + +
141q THR 4.5 2.6 + - - +
142q CYS* 3.2 33.3 - - + +
143q ALA 3.2 0.4 + - - -
144q GLU* 1.3 80.8 + - - +
146q MET* 1.3 63.4 + - - +
148q GLY* 3.0 3.8 + - - -
149q MET* 3.0 26.0 + - - +
174q ALA* 3.5 31.6 - - + +
177q ARG* 3.4 16.1 + - + -
178q ASP* 4.2 4.9 + - - +
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Residues in contact with MET 146 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10q ALA* 4.1 15.3 - - + -
11q VAL 4.0 2.5 - - - +
12q MET* 3.4 40.4 - - + -
138q VAL* 3.5 25.1 - - + -
139q SER 3.4 33.2 - - - +
142q CYS* 3.1 32.1 + - - +
143q ALA* 3.7 2.7 - - - +
145q GLN* 1.3 76.3 - - - +
147q TYR* 1.3 55.8 + - - +
149q MET* 3.4 1.8 + - - +
150q CYS* 2.9 37.7 + - - -
171q MET* 4.1 4.3 - - - +
174q ALA* 3.7 15.9 - - + -
175q VAL* 6.0 0.2 - - + -
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Residues in contact with TYR 147 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144f MET* 4.9 2.0 - - + -
185f ARG* 3.6 49.6 - - + -
22p GLU* 3.4 20.4 + - - -
25p VAL* 3.1 31.4 - - + -
26p VAL 3.6 6.5 - - - -
27p ALA* 2.9 31.7 + - - +
131q MET* 5.3 2.1 - - - +
136q PHE* 4.2 12.8 - + - -
137q VAL* 6.1 0.7 - - - -
138q VAL* 3.5 26.5 + - + +
143q ALA 2.9 24.8 + - - -
144q GLU* 3.4 7.6 - - - +
146q MET* 1.3 76.4 - - - +
148q GLY* 1.3 58.0 + - - +
150q CYS 3.8 0.2 - - - -
151q GLU* 2.9 36.6 + - - +
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Residues in contact with GLY 148 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144f MET* 3.6 34.6 - - - +
148f LEU* 5.2 1.9 - - - +
181f SER* 5.1 2.6 - - - -
185f ARG* 5.9 0.4 - - - -
144q GLU 2.9 14.5 + - - -
145q GLN 3.5 3.4 - - - -
147q TYR* 1.3 77.7 - - - +
149q MET* 1.3 61.2 + - - +
151q GLU* 3.7 3.9 + - - +
152q SER* 3.4 22.3 + - - -
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Residues in contact with MET 149 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147f PRO* 3.5 21.8 - - + +
148f LEU* 3.5 38.1 - - + -
151f ASN* 4.1 11.0 - - + +
145q GLN 3.0 14.4 + - - +
146q MET 4.0 2.9 - - - +
148q GLY* 1.3 74.3 - - - +
150q CYS* 1.3 61.8 + - - +
152q SER* 3.1 4.0 + - - -
153q LEU* 2.9 59.2 + - + +
169q GLN 3.8 17.3 - - - +
170q ALA* 3.7 28.5 - - + +
173q ASN* 3.8 13.2 - - + +
174q ALA 4.2 3.6 - - - +
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Residues in contact with CYS 150 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12q MET* 3.7 23.3 - - - -
14q MET* 3.2 32.5 - - + -
136q PHE* 3.4 35.1 - - + -
138q VAL* 4.9 0.4 - - - -
146q MET 2.9 25.9 + - - +
149q MET* 1.3 78.1 - - - +
151q GLU* 1.3 62.2 + - - +
153q LEU* 4.0 2.5 - - - +
154q TRP* 3.1 28.8 + - - +
170q ALA* 4.1 4.9 - - - -
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Residues in contact with GLU 151 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181f SER* 3.5 24.6 + - - +
184f GLU* 3.9 10.5 - - - +
185f ARG* 2.4 55.8 + - + +
29p LYS* 2.7 17.8 + - - -
195p LYS* 3.5 31.4 + - - -
198p ARG* 4.0 13.5 + - - -
136q PHE* 3.6 9.6 - - + -
147q TYR 2.9 19.7 + - - +
148q GLY* 4.2 2.9 - - - +
149q MET 3.2 0.2 - - - -
150q CYS* 1.3 76.7 - - - +
152q SER* 1.3 59.8 + - - +
154q TRP 4.6 1.0 - - - +
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Residues in contact with SER 152 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148f LEU* 3.4 37.4 - - - +
177f ASP* 5.0 1.6 + - - -
178f VAL* 5.0 2.6 - - - -
181f SER* 3.2 20.7 + - - -
198p ARG* 3.6 16.9 + - - +
202p TYR* 3.9 17.9 - - - -
148q GLY 3.4 12.6 + - - -
149q MET 3.1 7.2 + - - -
151q GLU* 1.3 80.4 - - - +
153q LEU* 1.3 65.5 + - - +
154q TRP 3.7 0.2 - - - -
155q GLU* 5.5 1.0 - - - +
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Residues in contact with LEU 153 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148f LEU* 4.7 9.9 - - + -
151f ASN* 4.4 4.0 - - - +
152f GLN* 4.8 4.0 - - - +
198p ARG* 3.9 1.6 - - - -
202p TYR* 4.3 23.8 - - + +
204p CYS* 5.0 13.0 - - - -
149q MET* 2.9 42.7 + - + +
150q CYS* 4.9 1.6 - - - -
152q SER* 1.3 87.1 - - - +
154q TRP* 1.3 63.1 + - - +
155q GLU* 3.3 16.2 + - - +
158q MET* 4.8 0.3 - - - +
166q THR* 3.7 35.1 + - + +
169q GLN* 3.9 22.9 - - + -
170q ALA* 4.2 2.5 - - + +
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Residues in contact with TRP 154 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198p ARG* 2.6 24.7 + - - +
14q MET* 3.7 26.9 - - + -
15q LYS* 3.3 22.7 + - + -
134q ASP* 3.5 21.8 - - + -
135q ASP* 3.6 34.3 + - + -
136q PHE* 4.1 11.7 - + + -
150q CYS* 3.1 22.9 + - + +
151q GLU 5.1 0.3 - - - +
152q SER 3.7 0.6 - - - -
153q LEU* 1.3 76.5 - - - +
155q GLU* 1.3 73.3 + - - +
156q PRO* 3.6 35.7 - - + +
158q MET* 4.0 8.9 - - - -
166q THR* 4.3 6.0 - - + +
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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
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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