Contacts of the helix formed by residues 172 - 185 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A GLU* 4.0 5.0 + - - +
57B ILE* 2.8 34.7 + - - +
58B SER* 4.0 4.8 - - - +
59B GLU* 3.9 4.2 + - - -
88B GLN* 3.3 26.4 + - - +
138C VAL* 3.4 26.4 + - + +
139C GLY* 3.8 5.6 - - - -
169C ALA 2.9 16.8 + - - +
170C ALA 3.5 0.6 - - - -
171C ASN* 1.3 78.4 - - - +
173C GLY* 1.3 67.2 + - - +
174C GLN* 2.9 32.3 + - + +
175C ILE* 2.9 30.8 + - + +
176C PHE* 3.7 5.8 - - - -
60D MET* 5.5 0.2 - - - +
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Residues in contact with GLY 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A GLY* 3.1 36.4 - - - -
177A GLU* 2.6 27.9 + - - -
171C ASN 3.3 2.2 + - - -
172C GLN* 1.3 69.1 - - - +
174C GLN* 1.3 52.8 + - - +
176C PHE* 2.7 33.3 + - - +
177C GLU 3.3 6.4 + - - -
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Residues in contact with GLN 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A GLY* 4.2 0.8 - - - -
177A GLU* 4.4 0.6 + - - -
88B GLN* 3.4 13.7 + - - -
138C VAL 3.6 0.2 + - - -
139C GLY 3.2 30.0 - - - +
140C ALA* 3.3 6.1 - - - +
143C PRO* 3.3 16.2 - - + +
172C GLN* 2.9 30.9 + - + +
173C GLY* 1.3 71.3 - - - +
175C ILE* 1.3 64.6 + - - +
177C GLU* 3.0 15.9 + - - +
178C ALA* 2.8 24.9 + - - +
60D MET* 3.7 32.0 - - + +
61D GLY 4.8 0.4 - - - +
92D GLN* 3.3 24.9 + - - -
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Residues in contact with ILE 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C GLY* 4.6 3.4 - - - +
142C VAL* 3.7 41.5 - - + -
165C TYR* 3.9 21.8 - - + -
169C ALA* 3.2 29.8 - - + +
170C ALA* 4.2 6.5 - - - +
172C GLN* 2.9 20.7 + - + +
174C GLN* 1.3 79.2 - - - +
176C PHE* 1.3 62.3 + - + +
178C ALA* 3.2 2.4 + - - +
179C TYR* 2.8 62.2 + - + +
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Residues in contact with PHE 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ASN 5.6 0.2 - - - -
176A PHE* 3.7 65.6 - + + -
216A ARG* 5.8 0.7 + - - -
218A ASP* 6.6 0.2 - - + -
170C ALA 3.8 17.3 - - - -
171C ASN* 4.5 6.5 - - - -
172C GLN 3.7 15.5 - - - -
173C GLY* 2.7 14.3 + - - +
175C ILE* 1.3 70.9 - - + +
177C GLU* 1.3 63.5 + - - +
179C TYR* 3.9 23.5 - + - +
180C ASN* 3.2 22.0 + - - +
216C ARG* 3.5 57.2 - - + -
219C PHE* 5.7 0.5 - - - -
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Residues in contact with GLU 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ASN* 3.4 11.0 - - - +
172A GLN* 3.6 8.0 + - - +
173A GLY* 2.7 40.4 + - - +
173C GLY 3.3 3.0 + - - +
174C GLN* 3.0 10.9 + - - +
176C PHE* 1.3 76.8 - - - +
178C ALA* 1.3 62.1 + - - +
180C ASN* 3.3 13.9 + - - +
181C MET* 3.3 22.3 + - - +
58D SER* 3.2 33.9 + - - +
59D GLU 4.5 0.5 + - - -
60D MET* 3.5 7.9 + - - +
61D GLY* 2.5 40.1 + - - -
88D GLN* 5.2 1.2 + - - -
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Residues in contact with ALA 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C VAL* 4.1 15.3 - - + +
143C PRO* 3.8 29.4 - - + -
146C ALA* 4.3 11.6 - - + +
174C GLN 2.8 15.0 + - - +
175C ILE 3.6 4.0 - - - +
177C GLU* 1.3 75.7 - - - +
179C TYR* 1.3 63.4 + - - +
181C MET* 4.6 6.9 - - - +
182C ALA* 3.0 26.4 + - - +
191C PHE* 3.8 5.0 - - + -
61D GLY* 5.2 0.6 - - - -
65D ILE* 5.4 0.7 - - + -
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Residues in contact with TYR 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C TYR* 2.8 25.0 + - - -
170C ALA* 5.4 2.9 + - - +
175C ILE* 2.8 46.7 + - + +
176C PHE* 3.9 32.5 - + - +
177C GLU 3.4 0.4 - - - -
178C ALA* 1.3 73.6 - - - +
180C ASN* 1.3 62.8 + - - +
182C ALA* 3.5 2.2 - - - +
183C ALA* 3.0 21.1 + - - +
191C PHE* 3.8 36.1 - + - -
213C TYR 5.1 0.2 + - - -
216C ARG* 4.0 11.5 - - + +
217C GLY* 3.8 20.9 - - - +
219C PHE* 3.7 7.8 - - + -
220C ILE* 3.3 27.2 - - + +
252C LEU* 3.9 19.8 - - + +
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Residues in contact with ASN 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ASN* 3.5 28.4 - - + +
207A ALA 3.1 21.4 + - - -
208A ALA* 3.8 2.1 - - - -
209A ALA* 3.0 30.1 + - - +
216A ARG* 4.3 4.3 + - - +
176C PHE 3.2 11.3 + - - +
177C GLU* 3.5 10.7 + - - +
178C ALA 3.1 0.6 - - - -
179C TYR* 1.3 80.7 - - - +
181C MET* 1.3 58.9 + - - +
183C ALA* 3.3 3.6 + - - +
184C LEU* 2.9 29.5 + - - +
219C PHE* 4.0 14.0 - - + -
56D PRO* 3.7 17.2 - - - +
58D SER* 4.9 0.8 + - - -
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Residues in contact with MET 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C GLU 3.3 21.4 + - - +
178C ALA* 4.6 1.1 - - - +
180C ASN* 1.3 73.9 - - - +
182C ALA* 1.3 66.0 + - - +
184C LEU* 3.8 6.5 - - - -
185C TRP* 3.0 63.7 + - + +
187C LEU* 4.3 0.7 - - - -
55D THR* 4.5 0.2 - - - -
56D PRO* 3.3 36.1 - - + -
58D SER* 4.3 8.3 - - - +
61D GLY* 3.6 8.3 - - - -
62D PHE* 3.5 41.1 - - + +
65D ILE* 3.6 20.2 - - + -
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Residues in contact with ALA 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C ALA* 5.1 0.9 - - + -
178C ALA 3.0 22.3 + - - +
179C TYR 3.5 4.9 - - - +
181C MET* 1.3 76.5 - - - +
183C ALA* 1.3 62.9 + - - +
186C LYS* 3.1 4.2 + - - -
187C LEU* 2.9 49.0 + - + +
189C CYS* 5.2 1.1 - - + -
191C PHE* 3.6 25.8 - - + -
250C PRO* 3.4 12.5 - - + +
65D ILE* 5.5 0.2 - - - +
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Residues in contact with ALA 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ALA* 3.7 6.7 - - + -
179C TYR 3.0 5.9 + - - +
180C ASN 3.7 1.3 - - - +
182C ALA* 1.3 80.3 - - - +
184C LEU* 1.3 61.7 - - - +
186C LYS* 3.2 19.2 + - - +
219C PHE* 3.5 38.8 - - + -
220C ILE* 4.2 3.6 - - + -
250C PRO* 3.5 18.7 - - + +
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Residues in contact with LEU 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ARG* 3.8 26.0 - - - +
207A ALA* 3.1 23.8 - - - +
208A ALA 3.8 24.0 - - - +
209A ALA* 4.0 6.7 - - + +
180C ASN* 2.9 18.4 + - - +
181C MET* 3.6 6.5 - - - +
183C ALA* 1.3 77.6 - - - +
185C TRP* 1.3 80.7 + - + +
186C LYS* 5.0 3.2 - - - +
54D ASP 6.0 0.2 - - - +
56D PRO* 4.2 16.6 - - + -
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Residues in contact with TRP 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C LEU* 4.9 11.2 - - + -
153C LYS* 2.8 26.0 + - - +
181C MET* 3.0 40.8 + - + +
184C LEU* 1.3 101.2 - - + +
186C LYS* 1.3 71.3 + - - +
187C LEU* 3.4 24.4 - - + +
26D LEU* 5.0 5.2 - - + -
53D ILE* 3.5 29.6 - - + +
54D ASP 3.7 14.8 + - - -
55D THR* 3.6 22.7 - - + -
56D PRO* 4.2 9.4 - - + -
65D ILE* 4.0 22.0 - - + -
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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