Contacts of the helix formed by residues 180 - 198 (chain B) in PDB entry 3G4C
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 180 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B PHE* 3.6 17.0 - - + -
72B VAL* 6.2 0.4 - - + -
75B GLN* 3.2 22.2 + - - +
105B ARG* 4.2 0.8 - - - +
179B ALA* 1.3 73.6 - - - +
181B TRP* 1.3 65.6 + - - +
182B GLU* 3.0 31.0 + - + +
183B ILE* 3.0 18.2 + - + +
184B GLN* 3.2 9.7 + - - +
90C ARG* 3.4 27.6 - - - +
144C GLU* 3.1 43.9 + - - +
145C VAL* 4.3 2.0 - - - +
147C ARG* 2.8 26.8 + - - -
313C UMP 4.4 1.8 + - - -
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Residues in contact with TRP 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 3.5 27.1 - - + -
99B TYR* 3.8 12.8 - + - -
102B SER* 5.8 3.8 - - - -
105B ARG* 3.6 47.5 - - + +
179B ALA 3.4 3.0 + - - -
180B GLN* 1.3 72.4 - - - +
182B GLU* 1.3 78.9 + - - +
184B GLN* 3.2 27.7 + - - +
185B GLN* 3.1 54.8 + - + +
144C GLU* 4.6 2.6 + - - +
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Residues in contact with GLU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 3.9 10.9 - - + +
71B PHE* 3.8 8.3 - - + -
72B VAL* 3.8 19.7 - - + -
99B TYR* 2.5 49.4 + - + +
105B ARG* 2.6 32.1 + - - +
180B GLN* 3.0 27.3 + - + +
181B TRP* 1.3 84.4 - - + +
183B ILE* 1.3 60.6 + - - +
185B GLN* 3.4 9.9 + - - +
186B TYR* 3.2 21.5 - - - -
145C VAL* 4.4 4.6 - - - +
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Residues in contact with ILE 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 3.8 38.3 - - + +
75B GLN* 3.6 24.2 - - + +
76B TRP* 4.0 30.5 - - + +
170B PHE* 4.6 2.2 - - + -
174B ARG* 4.0 33.4 - - + +
179B ALA* 3.8 19.5 - - + -
180B GLN* 3.0 14.3 + - - +
182B GLU* 1.3 73.3 - - - +
184B GLN* 1.3 70.6 + - - +
185B GLN 3.1 1.1 - - - -
186B TYR* 3.0 5.7 + - + +
187B ALA* 2.8 22.0 + - - +
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Residues in contact with GLN 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ARG 3.3 15.5 - - - +
176B ASP 3.6 19.8 + - - +
177B SER* 3.6 19.6 + - - +
179B ALA* 2.9 22.6 + - + +
180B GLN 3.2 9.8 + - - +
181B TRP* 3.2 32.8 - - + +
183B ILE* 1.3 78.2 - - - +
185B GLN* 1.3 61.2 + - - +
187B ALA* 3.1 3.5 + - - +
188B LEU* 2.9 34.4 + - + +
214B ILE* 3.9 23.6 - - + +
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Residues in contact with GLN 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 3.6 28.8 - - + +
6B LEU* 4.3 4.2 - - + +
181B TRP* 3.1 60.4 + - + +
182B GLU 3.4 9.4 - - - +
183B ILE 3.1 0.4 - - - -
184B GLN* 1.3 80.9 - - - +
186B TYR* 1.3 61.8 + - - +
188B LEU* 3.4 32.3 + - - +
189B ALA 3.5 8.1 + - - -
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Residues in contact with TYR 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ILE* 3.7 29.2 + - + +
6B LEU* 3.7 19.2 - - + +
9B GLY* 3.4 13.3 - - - -
10B PHE 3.8 6.7 - - - -
11B VAL* 3.6 18.9 - - + +
66B VAL* 3.8 10.8 - - + -
67B LYS 2.6 28.8 + - - -
68B ALA* 3.3 13.3 - - + -
69B PRO* 3.7 5.0 - - + +
72B VAL* 4.0 17.5 - - + -
76B TRP* 3.4 28.3 - + + -
155B TYR* 3.9 0.7 - - - -
182B GLU 3.2 19.3 - - - -
183B ILE* 3.0 8.4 + - + +
185B GLN* 1.3 74.1 - - - +
187B ALA* 1.3 65.2 + - - +
189B ALA* 3.1 6.1 + - - +
190B ILE* 3.0 26.0 + - - +
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Residues in contact with ALA 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B PHE* 4.0 17.7 - - + -
171B LEU* 3.2 12.7 - - + +
174B ARG* 3.7 13.7 - - + -
175B ALA* 3.6 33.8 - - + +
183B ILE 2.8 15.8 + - - +
184B GLN 3.5 8.1 - - - +
186B TYR* 1.3 74.2 - - - +
188B LEU* 1.3 56.9 + - - +
190B ILE* 3.4 0.6 + - - -
191B ALA* 2.9 24.1 + - - +
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Residues in contact with LEU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B ALA* 5.4 0.2 - - + -
184B GLN* 2.9 15.3 + - + +
185B GLN* 3.6 35.7 - - - +
186B TYR 3.2 0.2 - - - -
187B ALA* 1.3 73.8 - - - +
189B ALA* 1.3 61.2 + - - +
191B ALA* 3.4 6.0 + - - +
192B ARG* 3.0 26.0 + - - +
214B ILE* 4.1 19.1 - - + -
215B LEU* 3.7 21.7 - - + +
218B VAL* 3.4 40.8 - - + -
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Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B ILE* 3.6 33.2 - - + +
5B ILE* 3.4 32.5 - - + -
11B VAL* 4.1 9.2 - - + -
185B GLN 3.5 1.4 + - - -
186B TYR 3.1 7.0 + - - +
188B LEU* 1.3 77.3 - - - +
190B ILE* 1.3 64.7 + - - +
192B ARG* 3.1 5.9 + - - +
193B ILE* 3.0 21.8 + - - +
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Residues in contact with ILE 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL* 3.7 13.2 - - + -
64B PHE* 3.6 35.3 - - + -
76B TRP* 4.1 13.7 - - + -
160B TRP* 3.8 14.8 - - + -
167B LEU* 3.0 42.4 - - + -
170B PHE* 4.0 16.2 - - + -
171B LEU* 4.0 10.3 - - + -
186B TYR 3.0 18.8 + - - +
187B ALA 3.6 7.6 - - - +
189B ALA* 1.3 76.2 - - - +
191B ALA* 1.3 58.5 + - - +
193B ILE* 3.3 2.3 + - - +
194B PHE* 2.9 26.2 + - - +
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Residues in contact with ALA 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B LEU* 4.0 10.5 - - + +
187B ALA 2.9 17.4 + - - +
188B LEU 3.6 4.0 - - - +
189B ALA 3.2 0.2 - - - -
190B ILE* 1.3 76.6 - - - +
192B ARG* 1.3 56.2 + - - +
194B PHE* 3.6 2.3 - - - +
195B LYS* 2.9 31.5 + - - +
202B PHE* 3.6 21.2 - - + -
215B LEU* 3.5 34.5 - - + -
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Residues in contact with ARG 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 5.0 7.4 - - + -
3B ILE* 4.3 22.4 - - + -
188B LEU 3.0 15.1 + - - +
189B ALA* 3.1 11.9 + - - +
191B ALA* 1.3 73.3 - - - +
193B ILE* 1.3 62.6 + - - +
195B LYS* 3.6 7.5 + - - +
196B GLU* 3.2 24.6 + - + +
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Residues in contact with ILE 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 3.8 25.1 - - + +
3B ILE* 3.4 30.7 - - + -
11B VAL* 3.7 31.9 - - + +
13B LEU* 3.9 40.4 - - + +
62B PHE* 4.7 1.8 - - + -
64B PHE* 3.8 22.9 - - + -
189B ALA 3.0 7.3 + - - +
190B ILE 3.8 3.1 - - - +
192B ARG* 1.3 73.5 - - - +
194B PHE* 1.3 65.5 + - - +
196B GLU* 3.0 4.0 + - - +
197B LYS* 3.0 25.3 + - + +
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Residues in contact with PHE 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B PHE* 3.6 25.1 - + - -
64B PHE* 5.3 0.4 - - - -
164B ALA* 4.1 20.4 - - + -
167B LEU* 4.3 14.8 - - + -
168B MET* 3.6 29.6 - - + -
171B LEU* 3.8 17.3 - - + -
190B ILE 2.9 17.6 + - - +
191B ALA* 3.6 4.3 - - - +
193B ILE* 1.3 75.8 - - - +
195B LYS* 1.3 52.9 + - - +
197B LYS 3.4 0.3 + - - -
198B CYS* 2.8 56.6 + - + +
201B THR* 3.7 24.0 - - + -
202B PHE* 3.6 26.0 - + - -
205B PHE* 4.6 2.5 - + - -
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Residues in contact with LYS 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B ALA 2.9 18.8 + - - +
192B ARG* 3.7 8.7 - - - +
194B PHE* 1.3 77.7 - - - +
196B GLU* 1.3 61.3 + - - +
199B PRO* 3.3 29.1 - - + +
202B PHE* 3.6 38.2 - - + -
203B GLU* 3.3 23.5 + - + +
206B LEU* 6.0 1.0 - - - +
219B GLN* 5.8 9.3 - - - +
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Residues in contact with GLU 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 4.0 34.5 - - + +
192B ARG* 3.2 12.7 + - + +
193B ILE 3.0 9.0 + - - +
195B LYS* 1.3 79.7 - - - +
197B LYS* 1.3 71.7 + - + +
199B PRO* 4.0 6.6 - - - +
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Residues in contact with LYS 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 4.7 13.6 - - - +
13B LEU* 3.4 34.8 - - + -
16B VAL* 4.1 18.8 - - + -
18B GLY 5.7 0.7 - - - +
19B ASN* 4.0 17.3 - - - +
62B PHE* 4.0 18.8 - - + -
193B ILE* 3.0 18.0 + - + +
194B PHE 4.1 0.2 - - - +
196B GLU* 1.3 90.9 + - + +
198B CYS* 1.3 62.4 + - - +
199B PRO* 3.5 6.7 - - - +
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Residues in contact with CYS 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B VAL* 5.6 0.2 - - - -
18B GLY 5.2 0.7 - - - -
19B ASN* 4.2 10.5 - - - -
20B ASP* 3.3 18.0 - - - +
60B ILE* 3.6 40.6 - - - -
62B PHE* 3.9 13.7 - - - -
194B PHE* 2.8 31.4 + - + +
197B LYS* 1.3 79.8 - - - +
199B PRO* 1.3 60.6 - - - +
200B TRP 3.4 0.2 + - - -
201B THR* 4.1 3.1 - - - -
202B PHE* 2.9 27.2 + - - +
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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
------------------------------------------------------------
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