Contacts of the helix formed by residues 167 - 184 (chain X) in PDB entry 2W6C
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 ASN 167 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154X GLY 4.0 4.4 + - - -
155X PHE* 4.1 14.3 + - - +
166X GLY* 1.3 70.3 - - - +
168X VAL* 1.3 55.6 + - - +
169X GLY 3.2 2.7 - - - -
170X LEU* 2.6 40.6 + - + +
171X LEU* 2.9 14.0 + - + +
294X PRO* 3.2 12.8 - - - +
295X VAL* 2.9 50.1 + - - +
297X ASP* 3.1 26.5 + - - +
300X PHE* 3.7 18.3 - - + +
301X PHE* 4.3 1.4 - - - -
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Residues in contact with VAL 168 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45X PHE* 3.5 22.7 - - - +
46X ARG 3.6 7.9 - - - +
47X ARG* 3.9 20.6 - - + +
149X ARG* 3.5 30.5 - - - +
153X PHE 3.8 10.5 - - - +
154X GLY 3.4 11.9 + - - +
156X LEU 5.9 0.4 - - - +
165X PRO* 3.9 12.6 - - + -
166X GLY* 3.1 16.1 - - - +
167X ASN* 1.3 78.8 - - - +
169X GLY* 1.3 53.6 + - - +
171X LEU* 2.9 12.1 + - + +
172X ASP* 2.6 39.8 + - - +
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Residues in contact with GLY 169 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148X TYR* 3.6 4.4 - - - +
149X ARG 3.7 17.3 - - - -
154X GLY* 2.9 11.8 + - - -
155X PHE* 3.7 18.8 - - - -
168X VAL* 1.3 77.8 - - - +
170X LEU* 1.3 60.9 + - - +
172X ASP* 3.1 21.3 + - - +
173X GLN* 3.2 17.0 + - - +
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Residues in contact with LEU 170 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120X PHE* 4.9 2.2 - - + -
155X PHE* 3.8 11.0 - - + -
167X ASN* 2.6 28.2 + - - +
169X GLY* 1.3 70.7 - - - -
171X LEU* 1.3 54.2 + - - +
173X GLN* 3.1 26.4 + - - +
174X ARG* 3.1 22.9 + - - +
205X SER* 4.1 16.6 - - - +
208X MET* 4.1 15.0 - - + -
209X HIS* 3.6 11.3 - - - +
294X PRO* 3.7 30.5 - - + -
300X PHE* 3.6 39.5 - - + -
301X PHE* 4.0 9.6 - - + -
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Residues in contact with LEU 171 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47X ARG* 3.8 41.1 - - + +
48X PRO* 3.6 18.0 - - + +
166X GLY 5.0 2.7 - - - +
167X ASN* 2.9 14.4 + - + +
168X VAL* 2.9 18.4 + - + +
170X LEU* 1.3 73.3 - - - +
172X ASP* 1.3 64.2 + - - +
174X ARG* 3.4 37.6 - - - +
175X MET* 3.1 22.2 + - - +
300X PHE* 3.8 18.6 - - + -
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Residues in contact with ASP 172 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35X PHE* 3.5 14.6 - - + -
48X PRO* 3.4 14.3 - - - +
95X LEU* 3.6 16.0 - - + +
147X SER 4.2 2.2 - - - +
148X TYR* 3.7 15.3 - - + -
149X ARG* 2.8 67.0 + - - +
168X VAL 2.6 17.3 + - - +
169X GLY* 3.1 8.4 + - - +
171X LEU* 1.3 72.8 - - - +
173X GLN* 1.3 64.5 + - - +
175X MET* 3.1 9.9 + - - -
176X ALA* 3.1 10.7 + - - +
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Residues in contact with GLN 173 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115X ILE* 3.6 11.4 - - + +
120X PHE* 5.1 0.6 - - - -
146X LEU* 3.9 20.8 - - + +
148X TYR* 3.3 51.1 - - + -
155X PHE* 5.5 0.2 - - - -
169X GLY 3.2 10.4 + - - +
170X LEU* 3.1 15.8 + - - +
172X ASP* 1.3 79.7 - - - +
174X ARG* 1.3 64.3 + - - +
176X ALA* 3.2 4.4 + - - +
177X LEU* 3.0 25.9 + - + +
205X SER* 3.1 33.8 + - - -
209X HIS* 2.9 25.0 + - + +
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Residues in contact with ARG 174 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170X LEU 3.1 14.8 + - - +
171X LEU* 3.4 26.6 - - - +
172X ASP 3.1 0.4 - - - -
173X GLN* 1.3 78.4 - - - +
175X MET* 1.3 57.0 + - - +
177X LEU* 3.0 12.4 + - - +
178X GLN* 2.8 26.0 + - + +
209X HIS* 4.2 6.7 - - + -
212X SER* 2.9 27.7 + - - -
214X GLY* 3.1 32.0 + - - +
215X SER* 2.9 23.2 + - - +
218X LEU* 3.5 20.0 - - + +
300X PHE* 3.6 16.6 - - - +
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Residues in contact with MET 175 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35X PHE* 2.6 33.2 - - + +
36X ALA* 3.2 25.4 - - + -
48X PRO* 4.4 13.7 - - + +
49X GLU 3.2 14.8 - - - +
50X PRO* 3.5 26.2 - - + -
171X LEU 3.1 12.9 + - - +
172X ASP* 3.1 8.0 + - - +
174X ARG* 1.3 74.6 - - - +
176X ALA* 1.3 67.3 + - - +
177X LEU 2.9 1.6 - - - -
178X GLN* 2.9 14.8 + - + +
179X TRP* 2.8 22.9 + - + +
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Residues in contact with ALA 176 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35X PHE* 3.6 36.6 - - + -
97X LEU* 4.2 6.8 - - + +
146X LEU* 3.5 33.2 - - + -
172X ASP 3.1 6.9 + - - +
173X GLN 3.6 7.9 - - - +
175X MET* 1.3 77.0 - - - +
177X LEU* 1.3 58.1 + - - +
179X TRP* 3.2 2.6 + - - +
180X VAL* 3.0 32.1 + - + +
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Residues in contact with LEU 177 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113X VAL* 3.8 26.7 - - + -
115X ILE* 5.3 2.0 - - + -
146X LEU* 4.2 6.7 - - + -
173X GLN 3.0 16.7 + - - +
174X ARG* 3.0 14.9 + - - +
175X MET 2.9 0.8 - - - -
176X ALA* 1.3 76.7 - - - +
178X GLN* 1.3 64.5 + - - +
180X VAL* 3.5 4.9 + - + +
181X HIS* 3.0 24.4 + - - +
194X VAL* 5.1 2.7 - - + -
196X ILE* 3.5 32.8 - - + -
209X HIS* 4.4 25.6 - - + +
215X SER* 5.4 1.8 - - - +
218X LEU* 4.4 25.9 - - + +
219X PHE* 4.6 13.7 - - + -
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Residues in contact with GLN 178 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174X ARG* 2.8 12.9 + - + +
175X MET* 3.2 19.5 - - + +
177X LEU* 1.3 75.1 - - - +
179X TRP* 1.3 64.2 + - + +
181X HIS* 3.2 13.4 + - - +
182X ASP* 2.9 62.8 + - - +
218X LEU* 3.5 27.3 - - + +
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Residues in contact with TRP 179 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X THR* 4.2 13.7 - - + -
12X SER* 3.3 25.8 + - - -
15X VAL* 5.8 1.1 - - + -
33X ILE* 4.0 26.9 - - + -
34X PRO 4.4 5.8 + - - -
35X PHE* 4.1 25.8 - - + +
51X LYS* 6.4 0.4 - - + -
54X TRP* 5.5 1.8 - + - -
97X LEU* 3.7 28.0 - - + -
99X ILE* 4.3 10.5 - - + -
175X MET* 2.8 14.5 + - + +
176X ALA 3.6 4.5 - - - +
177X LEU 3.1 0.2 - - - -
178X GLN* 1.3 79.9 - - + +
180X VAL* 1.3 64.9 + - + +
182X ASP* 3.1 2.8 + - - -
183X ASN* 2.8 68.0 + - + +
184X ILE* 5.3 1.8 - - + -
187X PHE* 4.0 21.8 - + - -
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Residues in contact with VAL 180 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97X LEU* 4.7 2.5 - - + -
111X VAL* 4.4 6.7 - - + -
113X VAL* 4.3 22.7 - - + -
144X VAL* 4.2 28.0 - - + -
176X ALA* 3.0 18.8 + - + +
177X LEU* 3.8 7.4 - - + +
179X TRP* 1.3 85.5 - - + +
181X HIS* 1.3 67.9 + - - +
184X ILE* 2.8 56.9 + - + +
194X VAL* 4.6 12.1 - - + -
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Residues in contact with HIS 181 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177X LEU 3.0 17.9 + - - +
178X GLN* 3.5 15.9 + - - +
180X VAL* 1.3 79.1 - - - +
182X ASP* 1.3 86.3 + - - +
185X GLN* 4.7 1.9 - - - +
191X PRO* 3.4 37.6 - - + +
194X VAL* 5.7 2.5 - - + -
217X ASP 4.7 14.5 + - - -
218X LEU* 4.7 20.6 - - + +
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Residues in contact with ASP 182 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11X LYS* 2.7 43.3 + - + +
178X GLN* 2.9 41.0 + - - +
179X TRP* 4.5 1.1 - - - -
180X VAL 3.0 0.2 - - - -
181X HIS* 1.3 110.2 + - - +
183X ASN* 1.3 72.0 + - - +
185X GLN* 3.7 8.5 - - - +
186X PHE* 4.0 1.0 - - - -
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Residues in contact with ASN 183 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10X THR* 3.4 4.6 - - - -
11X LYS* 2.7 44.3 + - - +
12X SER* 4.7 1.4 + - - -
179X TRP* 2.8 73.4 + - + +
182X ASP* 1.3 84.7 - - - +
184X ILE* 1.3 68.3 + - - +
185X GLN 3.0 4.9 + - - -
186X PHE* 3.1 22.3 + - + -
187X PHE* 3.4 10.9 - - - -
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Residues in contact with ILE 184 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99X ILE* 4.0 22.4 - - + -
111X VAL* 4.0 24.2 - - + -
142X VAL* 3.9 19.7 - - + -
144X VAL* 4.0 19.3 - - + -
179X TRP* 5.4 1.6 - - + -
180X VAL* 2.8 45.0 + - + +
182X ASP 3.7 0.4 - - - -
183X ASN* 1.3 79.7 - - - +
185X GLN* 1.3 65.2 + - - +
187X PHE* 3.0 18.3 + - + +
189X GLY* 3.1 20.9 + - - -
191X PRO* 3.9 28.7 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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