Contacts of the helix formed by residues 172 - 186 (chain G) in PDB entry 3EXF
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 GLN 172 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177E GLU* 3.8 9.6 + - - +
57F ILE* 2.9 25.7 + - - +
59F GLU* 3.7 8.5 + - - +
88F GLN* 2.8 34.3 + - - +
138G VAL* 3.5 31.2 + - + +
139G GLY* 4.4 2.0 - - - -
169G ALA 3.0 15.2 + - - +
171G ASN* 1.3 76.6 - - - +
173G GLY* 1.3 68.9 + - - +
174G GLN* 3.3 22.2 + - + +
175G ILE* 2.8 32.5 + - + +
176G PHE* 3.7 4.1 - - - -
1012G TPP 4.2 3.6 - - - +
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Residues in contact with GLY 173 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173E GLY* 3.3 38.6 - - - -
174E GLN 4.4 0.2 - - - -
177E GLU* 3.0 27.3 + - - +
172G GLN* 1.3 68.3 + - - +
174G GLN* 1.3 61.5 + - - +
175G ILE 3.0 1.2 + - - -
176G PHE* 3.1 17.9 + - - +
177G GLU* 3.3 7.8 + - - -
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Residues in contact with GLN 174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F GLN* 2.8 28.9 + - - -
138G VAL 3.8 0.2 + - - -
139G GLY 3.6 5.8 - - - +
140G ALA* 3.3 29.4 - - - +
143G PRO* 3.1 31.7 - - + +
172G GLN* 3.3 16.1 + - + +
173G GLY* 1.3 70.5 - - - +
175G ILE* 1.3 65.3 + - - +
177G GLU* 3.7 13.4 + - - +
178G ALA* 3.2 20.4 + - - +
60H MET* 3.5 34.7 - - + +
61H GLY 4.9 1.1 - - - +
91H ASP* 5.5 0.4 + - - -
92H GLN* 3.3 13.2 + - - -
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Residues in contact with ILE 175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139G GLY* 4.4 12.1 - - - +
142G VAL* 3.7 28.1 - - + +
165G TYR* 4.2 16.4 - - + -
169G ALA 2.8 35.2 - - - +
170G ALA* 4.0 6.5 - - - +
172G GLN* 2.8 23.1 + - + +
174G GLN* 1.3 75.3 - - - +
176G PHE* 1.3 66.6 + - + +
178G ALA* 3.1 7.6 + - - +
179G TYR* 2.8 60.8 + - + +
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Residues in contact with PHE 176 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176E PHE* 3.5 67.4 - + + -
180E ASN* 6.5 0.2 - - + -
216E ARG* 5.7 0.7 + - - -
219E PHE* 6.0 2.5 - + - -
170G ALA 3.4 20.4 - - - -
171G ASN* 4.3 7.0 - - - -
172G GLN 3.7 16.4 - - - -
173G GLY 3.1 4.9 + - - +
175G ILE* 1.3 75.0 - - + +
177G GLU* 1.3 64.5 + - - +
179G TYR* 2.8 38.0 + + - +
180G ASN* 3.2 6.8 + - - +
216G ARG* 3.3 57.9 - - + -
219G PHE* 5.3 0.5 - - - -
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Residues in contact with GLU 177 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E ASN 3.2 17.5 - - - +
172E GLN* 3.8 4.7 - - - +
173E GLY* 2.7 39.9 + - - +
174E GLN 4.4 1.4 + - - -
176E PHE* 5.3 0.6 - - - -
173G GLY 3.3 2.2 + - - +
174G GLN* 3.7 11.6 - - - +
175G ILE 3.2 1.0 - - - -
176G PHE* 1.3 76.8 - - - +
178G ALA* 1.3 56.0 + - - +
180G ASN* 3.0 22.6 + - - +
181G MET* 3.2 21.2 + - + +
58H SER* 3.2 26.3 + - - +
59H GLU 4.9 0.2 + - - -
60H MET* 3.7 13.1 + - - +
61H GLY* 2.5 37.0 + - - -
88H GLN* 5.1 2.6 + - - -
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Residues in contact with ALA 178 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142G VAL* 4.0 21.3 - - + -
143G PRO* 4.3 9.6 - - + -
146G ALA* 4.2 17.9 - - + +
174G GLN 3.2 9.3 + - - +
175G ILE 3.1 9.1 + - - +
177G GLU* 1.3 75.7 - - - +
179G TYR* 1.3 63.2 + - - +
181G MET* 4.1 11.1 - - + +
182G ALA* 2.7 31.7 + - - +
191G PHE* 4.2 2.9 - - + -
61H GLY* 5.2 1.1 - - - -
65H ILE* 5.0 2.9 - - + -
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Residues in contact with TYR 179 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165G TYR* 2.3 34.3 + + - -
170G ALA* 5.3 1.9 - - - +
175G ILE* 2.8 37.0 + - + +
176G PHE* 2.8 37.9 + + - +
178G ALA* 1.3 71.8 - - - +
180G ASN* 1.3 57.2 + - - +
182G ALA* 4.3 0.7 - - - -
183G ALA* 3.0 24.1 + - - +
191G PHE* 3.8 38.1 - + - -
213G TYR 5.1 0.2 + - - -
216G ARG* 4.0 12.8 - - + +
217G GLY* 3.7 26.7 - - - +
219G PHE* 4.0 11.0 - - + -
220G ILE* 3.2 25.5 - - + +
252G LEU* 3.8 15.1 - - + +
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Residues in contact with ASN 180 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E ASN* 3.6 27.4 - - + +
207E ALA 3.0 23.8 + - - -
208E ALA* 3.6 5.1 - - - +
209E ALA* 3.3 26.2 + - - +
210E SER 4.9 0.2 + - - -
216E ARG* 4.0 10.7 + - - +
176G PHE 3.2 5.3 + - - +
177G GLU* 3.0 12.6 + - - +
179G TYR* 1.3 75.8 - - - +
181G MET* 1.3 54.6 + - - +
183G ALA* 3.1 2.4 + - - +
184G LEU* 2.7 37.1 + - - +
219G PHE* 3.6 13.8 - - + -
56H PRO* 3.7 14.6 - - - +
58H SER* 5.1 0.2 + - - -
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Residues in contact with MET 181 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177G GLU 3.2 31.4 + - - +
178G ALA* 4.1 3.8 - - - +
180G ASN* 1.3 79.0 - - - +
182G ALA* 1.3 54.3 + - - +
184G LEU* 3.9 6.5 - - - -
185G TRP* 2.6 65.1 + - + +
55H THR* 5.0 0.2 - - - -
56H PRO* 3.5 28.9 - - + -
58H SER* 3.5 29.2 - - - +
61H GLY* 3.9 6.5 - - - -
62H PHE* 3.8 31.9 - - - +
65H ILE* 3.6 21.5 - - + -
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Residues in contact with ALA 182 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146G ALA* 5.2 2.5 - - + -
178G ALA* 2.7 23.1 + - - +
179G TYR 3.6 3.8 - - - +
181G MET* 1.3 77.0 - - - +
183G ALA* 1.3 60.7 + - - +
186G LYS 3.1 2.3 + - - -
187G LEU* 3.0 46.6 + - + +
189G CYS* 5.1 1.6 - - + -
191G PHE* 3.6 26.7 - - + -
250G PRO* 3.4 11.4 - - + +
65H ILE* 5.2 1.0 - - - +
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Residues in contact with ALA 183 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209E ALA* 3.8 5.8 - - + -
179G TYR 3.0 9.7 + - - +
180G ASN 3.7 0.7 - - - +
182G ALA* 1.3 71.2 - - - +
184G LEU* 1.3 67.8 + - - +
186G LYS* 2.9 20.4 + - - +
219G PHE* 3.4 39.3 - - + +
220G ILE* 4.1 9.0 - - + -
250G PRO* 3.6 12.8 - - + +
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Residues in contact with LEU 184 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205E GLU 4.4 3.6 - - - +
206E ARG 3.4 28.0 - - - +
207E ALA 3.8 12.8 - - - +
208E ALA 3.6 31.6 - - - +
209E ALA* 3.9 7.0 - - + +
180G ASN 2.7 22.3 + - - +
181G MET* 3.4 4.9 - - - +
183G ALA* 1.3 72.8 - - - +
185G TRP* 1.3 82.0 + - + +
186G LYS* 4.7 3.3 - - - +
54H ASP 5.5 1.6 - - - +
56H PRO* 4.1 18.4 - - + -
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Residues in contact with TRP 185 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150G LEU* 4.9 14.1 - - + -
153G LYS* 3.1 26.4 + - - +
181G MET* 2.6 52.6 + - + +
184G LEU* 1.3 97.9 - - + +
186G LYS* 1.3 71.5 + - - +
187G LEU* 3.8 26.9 - - + +
26H LEU* 4.8 5.6 - - + -
53H ILE* 3.4 31.9 - - + +
54H ASP 3.9 10.8 + - - -
55H THR* 3.8 23.1 - - + -
56H PRO* 4.4 2.2 - - + -
65H ILE* 4.2 21.3 - - + -
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Residues in contact with LYS 186 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLU* 5.3 8.0 + - - +
153G LYS* 3.8 12.1 - - - +
182G ALA 3.1 3.3 + - - -
183G ALA 2.9 15.1 + - - +
184G LEU 4.7 3.1 - - - +
185G TRP* 1.3 82.4 - - - +
187G LEU* 1.3 63.9 + - - +
188G PRO* 3.7 6.1 - - - +
247G GLY* 3.8 25.0 + - - +
248G LYS* 4.3 13.6 - - - +
249G GLY* 3.7 17.8 + - - +
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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