Contacts of the helix formed by residues 172 - 186 (chain M) in PDB entry 3EXG
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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138M VAL* 3.0 29.4 + - + +
139M GLY* 4.4 6.3 - - - -
169M ALA 3.1 17.7 + - - +
170M ALA 3.5 1.0 - - - -
171M ASN* 1.3 78.6 - - - +
173M GLY* 1.3 68.5 + - - +
174M GLN* 3.0 14.8 + - + +
175M ILE* 3.0 25.7 + - + +
176M PHE* 3.8 5.2 - - - -
60N MET* 4.9 0.5 - - - +
177O GLU* 3.6 3.2 + - - +
57P ILE* 2.8 29.4 + - - +
58P SER* 3.9 4.8 - - - +
59P GLU* 3.0 25.1 + - - -
88P GLN* 3.0 27.8 + - - +
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Residues in contact with GLY 173 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172M GLN* 1.3 70.0 + - - +
174M GLN* 1.4 52.2 + - - +
176M PHE* 2.8 35.9 + - - +
177M GLU 3.5 2.9 + - - -
173O GLY* 3.5 27.2 - - - -
174O GLN 4.5 0.2 - - - -
177O GLU* 2.7 35.2 + - - +
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Residues in contact with GLN 174 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139M GLY* 3.4 17.0 - - - +
140M ALA* 3.2 21.9 - - - +
143M PRO* 3.2 19.7 - - + +
172M GLN* 3.3 13.2 + - + +
173M GLY* 1.4 71.1 - - - +
175M ILE* 1.3 69.0 + - - +
177M GLU* 3.1 16.3 + - - +
178M ALA* 3.0 21.1 + - - +
60N MET* 3.5 33.5 - - + +
61N GLY* 4.9 0.6 - - - +
91N ASP* 4.8 1.0 + - - -
92N GLN* 2.9 28.2 + - - -
88P GLN* 3.3 24.4 + - - -
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Residues in contact with ILE 175 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139M GLY* 4.8 4.9 - - - -
142M VAL* 3.5 31.4 - - + -
165M TYR* 3.9 30.7 - - + -
169M ALA* 3.1 30.7 - - + +
170M ALA* 4.0 6.7 - - - +
172M GLN* 3.0 15.8 + - + +
174M GLN* 1.3 78.3 - - - +
176M PHE* 1.3 64.5 + - + +
178M ALA* 2.8 20.3 + - - +
179M TYR* 3.0 48.0 + - + +
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Residues in contact with PHE 176 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170M ALA 3.8 17.0 - - - -
171M ASN* 4.4 6.3 - - - -
172M GLN 3.8 15.5 - - - -
173M GLY 2.8 14.1 + - - +
175M ILE* 1.3 75.4 - - + +
177M GLU* 1.3 59.5 + - - +
179M TYR* 3.7 24.5 - + - +
180M ASN* 3.2 21.8 + - - +
216M ARG* 3.5 55.6 - - + -
219M PHE* 5.7 0.2 - - - -
171O ASN* 5.3 0.7 - - - +
173O GLY* 5.2 0.2 - - - -
176O PHE* 3.6 64.8 - + + -
177O GLU 5.6 0.2 - - - -
216O ARG* 5.5 0.7 + - - -
218O ASP* 6.1 0.2 - - - -
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Residues in contact with GLU 177 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173M GLY 3.5 1.3 + - - +
174M GLN* 3.1 13.7 + - - +
176M PHE* 1.3 74.9 - - - +
178M ALA* 1.3 65.9 + - - +
180M ASN* 4.1 4.3 - - - +
181M MET* 3.2 31.2 + - - +
58N SER* 3.5 28.6 - - - +
59N GLU 4.6 0.2 + - - -
60N MET* 3.8 6.8 + - - +
61N GLY* 2.7 38.8 + - - -
171O ASN 3.0 21.1 - - - +
172O GLN* 3.5 9.5 + - - -
173O GLY* 2.5 34.5 + - - +
174O GLN 4.6 0.3 + - - -
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Residues in contact with ALA 178 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142M VAL* 3.6 26.0 - - + -
143M PRO* 4.1 19.1 - - + -
146M ALA* 4.2 8.1 - - + +
174M GLN 3.0 9.5 + - - +
175M ILE 2.8 12.6 + - - +
177M GLU* 1.3 76.4 - - - +
179M TYR* 1.3 57.7 + - - +
181M MET* 4.3 2.3 - - - +
182M ALA* 2.8 33.1 + - - +
191M PHE* 3.6 10.0 - - + -
61N GLY* 5.2 0.8 - - - -
65N ILE* 5.3 3.6 - - - -
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Residues in contact with TYR 179 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165M TYR* 2.6 32.2 + - - -
170M ALA* 5.4 2.4 + - - +
175M ILE* 3.0 31.3 + - + +
176M PHE* 3.7 34.7 - + - +
177M GLU 3.3 0.2 - - - -
178M ALA* 1.3 75.9 - - - +
180M ASN* 1.3 64.8 + - - +
183M ALA* 3.0 20.4 + - - +
191M PHE* 3.8 30.1 - + - -
216M ARG* 3.5 32.2 - - + +
217M GLY* 3.9 4.7 - - - +
219M PHE* 4.1 7.6 - - + -
220M ILE* 3.3 28.4 - - + +
252M LEU* 3.6 24.3 - - + +
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Residues in contact with ASN 180 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176M PHE 3.2 15.1 + - - +
177M GLU* 4.1 5.4 - - - +
178M ALA 3.2 0.2 - - - -
179M TYR* 1.3 80.3 - - - +
181M MET* 1.3 59.9 + - + +
183M ALA* 3.2 3.5 + - - +
184M LEU* 2.9 30.2 + - - +
219M PHE* 3.8 15.4 - - + -
56N PRO* 3.9 11.3 - - - +
58N SER* 5.4 0.2 + - - -
171O ASN* 3.5 22.7 - - + +
207O ALA 2.9 26.8 + - - -
208O ALA* 3.7 2.8 - - - +
209O ALA* 3.1 23.7 + - - +
216O ARG* 3.8 14.9 + - - +
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Residues in contact with MET 181 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177M GLU 3.2 28.5 + - - +
178M ALA 4.3 0.2 - - - +
180M ASN* 1.3 76.0 - - - +
182M ALA* 1.3 66.9 + - - +
184M LEU* 3.9 5.4 - - + -
185M TRP* 3.0 58.7 + - + +
187M LEU* 4.5 1.3 - - - -
56N PRO* 3.8 23.3 - - + -
58N SER* 3.4 33.2 - - - +
61N GLY 4.0 4.5 - - - -
62N PHE* 3.6 37.0 - - + +
65N ILE* 3.7 19.1 - - + -
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Residues in contact with ALA 182 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146M ALA* 5.0 1.8 - - + +
178M ALA 2.8 23.9 + - - +
179M TYR 3.9 0.7 - - - +
181M MET* 1.3 72.3 - - - +
183M ALA* 1.3 58.8 + - - +
186M LYS* 2.8 24.9 + - - -
187M LEU* 3.0 34.0 + - + +
189M CYS* 4.8 2.5 - - + -
191M PHE* 3.5 28.5 - - + -
250M PRO* 3.7 14.6 - - + +
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Residues in contact with ALA 183 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179M TYR 3.0 17.4 + - - +
180M ASN 3.7 0.2 - - - +
182M ALA* 1.3 75.2 - - - +
184M LEU* 1.3 67.4 + - - +
186M LYS* 3.1 20.6 + - - +
219M PHE* 3.5 27.1 - - + -
220M ILE* 4.1 7.4 - - + -
250M PRO* 3.9 12.0 - - + +
209O ALA* 3.6 12.1 - - + -
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Residues in contact with LEU 184 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180M ASN* 2.9 17.2 + - - +
181M MET* 3.6 6.5 - - - +
183M ALA* 1.3 78.2 - - - +
185M TRP* 1.3 80.0 + - + +
186M LYS* 3.5 12.8 + - - +
54N ASP 5.9 0.2 - - - +
56N PRO* 4.1 15.9 - - + -
207O ALA* 3.3 35.9 - - - +
208O ALA 4.1 8.7 - - - +
209O ALA* 4.0 25.8 - - - +
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Residues in contact with TRP 185 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150M LEU* 4.1 23.3 - - + -
153M LYS* 2.8 34.4 + - - +
181M MET* 3.0 58.4 + - + +
184M LEU* 1.3 93.3 - - + +
186M LYS* 1.3 68.9 + - - +
187M LEU* 3.4 18.4 - - + -
26N LEU* 4.8 7.2 - - + -
53N ILE* 3.7 31.0 - - + +
54N ASP 3.8 16.0 + - - -
55N THR* 4.3 15.0 - - + -
56N PRO* 4.5 1.3 - - + -
65N ILE* 4.2 20.9 - - + -
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Residues in contact with LYS 186 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153M LYS* 3.8 16.4 - - - +
182M ALA 2.8 10.8 + - - -
183M ALA 3.1 14.5 + - - +
184M LEU 4.0 12.6 - - - +
185M TRP* 1.3 82.6 - - - +
187M LEU* 1.3 62.2 + - - +
188M PRO* 3.9 2.3 - - - +
247M GLY* 4.5 12.8 - - - +
248M LYS 4.6 12.8 + - - +
249M GLY* 4.0 14.8 + - - -
250M PRO* 5.8 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
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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