Contacts of the helix formed by residues 180 - 195 (chain B) in PDB entry 6G2T
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 ALA 180 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155B GLY 3.5 6.5 - - - +
156B ASP 3.0 16.2 - - - +
157B GLY 2.9 32.3 - - - +
159B THR* 4.6 1.1 - - - -
179B LEU* 1.3 76.1 - - - +
181B GLY* 1.3 62.7 + - - +
182B ARG* 3.2 1.8 - - + +
183B ASP* 3.1 20.4 + - - +
184B LEU* 3.0 28.3 + - - +
260B LEU* 4.4 3.6 - - - +
302B THR* 4.9 2.2 - - - -
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Residues in contact with GLY 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B GLY 3.1 12.6 + - - -
156B ASP* 4.4 5.6 - - - -
180B ALA* 1.3 72.7 - - - +
182B ARG* 1.3 61.4 + - - +
184B LEU* 3.0 14.7 + - - +
185B THR 2.9 11.3 + - - -
212B LYS* 2.6 32.3 + - - -
302B THR* 4.1 16.2 - - - +
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Residues in contact with ARG 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B SER* 5.8 0.7 - - - -
68B TYR* 4.2 16.3 - - + -
70B ILE 5.6 1.3 - - - -
71B GLU* 3.0 43.3 + - - -
72B HIS* 5.2 5.6 + - - +
156B ASP* 3.4 41.5 + - - +
180B ALA* 3.2 1.0 - - + -
181B GLY* 1.3 76.0 - - - +
183B ASP* 1.3 71.2 + - - +
185B THR* 3.1 19.1 + - - -
186B ASP* 3.2 23.9 + - - -
205B ARG* 3.3 46.9 - - - +
209B ARG* 6.4 0.4 - - - +
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Residues in contact with ASP 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B HIS* 3.5 28.3 + - - -
178B ASP 3.3 23.0 - - - +
179B LEU* 3.9 1.5 - - - -
180B ALA* 3.1 27.5 + - - +
182B ARG* 1.3 84.6 + - - +
184B LEU* 1.3 62.3 + - + +
186B ASP* 3.2 15.3 + - - +
187B TYR* 3.2 19.8 + - - +
266B LEU* 4.4 18.9 - - + +
268B MET* 5.5 2.6 - - + +
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Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LEU* 6.3 0.2 - - + -
180B ALA 3.0 18.2 + - - +
181B GLY* 3.0 10.3 + - - +
183B ASP* 1.3 78.5 - - - +
185B THR* 1.3 50.8 + - - +
187B TYR* 3.1 8.9 + - + +
188B LEU* 2.7 35.4 + - - +
212B LYS* 4.2 11.0 - - + -
256B CYS* 3.1 33.0 - - + +
257B PRO* 5.0 2.5 - - + -
259B ALA* 4.0 15.0 - - + -
260B LEU* 3.8 31.2 - - + -
266B LEU* 5.3 5.6 - - + -
302B THR* 3.7 23.1 - - - +
305B TYR* 4.1 14.4 - - + +
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Residues in contact with THR 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B GLY 2.9 5.1 + - - -
182B ARG* 3.1 14.6 + - - -
184B LEU* 1.3 76.6 - - - +
186B ASP* 1.3 56.3 + - - +
188B LEU* 3.2 7.5 + - - +
189B MET* 2.8 28.4 + - - +
205B ARG* 3.7 31.2 - - + +
208B VAL* 3.6 25.1 - - + +
209B ARG* 4.1 14.8 - - + +
212B LYS* 2.8 31.3 + - - +
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Residues in contact with ASP 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ARG* 3.2 17.1 + - - +
183B ASP* 3.2 13.8 + - - +
185B THR* 1.3 76.1 - - - +
187B TYR* 1.3 62.6 + - - +
189B MET* 3.1 29.7 - - - +
190B LYS* 3.2 11.9 + - - +
205B ARG* 2.9 38.7 + - - -
283C LYS* 5.5 8.4 + - - +
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Residues in contact with TYR 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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183B ASP 3.2 3.7 + - - +
184B LEU* 3.1 11.8 + - - +
186B ASP* 1.3 80.2 - - - +
188B LEU* 1.3 55.8 + - - +
190B LYS* 3.3 35.9 + - - +
191B ILE* 2.9 41.8 + - + +
255B ARG* 4.3 19.3 + - + +
256B CYS* 3.4 41.3 - - + -
259B ALA* 4.8 4.3 - - + -
265B PHE* 3.7 49.4 - + + +
266B LEU* 3.7 31.2 - - + -
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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
----------------------------------------------------------
184B LEU 2.7 20.4 + - - +
185B THR* 3.4 7.0 - - - +
187B TYR* 1.3 70.8 - - - +
189B MET* 1.3 64.9 + - - +
191B ILE* 2.9 12.9 - - + +
192B LEU* 2.8 43.2 + - + +
208B VAL* 3.4 38.8 - - + +
209B ARG 4.8 0.2 - - - +
211B ILE* 5.0 7.2 - - + -
212B LYS* 3.8 24.9 - - + +
216B CYS* 4.7 8.5 - - - -
249B ILE* 6.3 2.0 - - + -
252B GLU* 4.7 4.7 - - + +
253B ARG* 5.6 2.2 - - - -
256B CYS* 3.3 29.4 - - + -
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Residues in contact with MET 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B THR 2.8 15.8 + - - +
186B ASP* 3.1 42.2 - - - +
188B LEU* 1.3 74.1 - - - +
190B LYS* 1.3 62.3 + - + +
192B LEU* 3.4 17.6 + - - +
193B THR* 3.5 16.3 + - - +
199B PHE* 3.2 41.4 + - + +
200B THR* 4.7 8.3 - - - -
201B THR 5.6 0.4 - - - +
205B ARG* 4.4 25.8 - - + -
208B VAL* 4.6 16.1 - - + +
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Residues in contact with LYS 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ASP 3.2 8.9 + - - +
187B TYR* 3.4 46.9 + - - +
188B LEU 3.2 0.2 - - - -
189B MET* 1.3 84.8 - - + +
191B ILE* 1.3 59.1 + - - +
193B THR* 2.7 29.8 + - - -
194B GLU* 4.2 1.6 + - - +
265B PHE 5.4 4.3 - - - -
266B LEU* 5.5 1.0 - - - +
109C LEU* 4.6 24.2 - - + +
171C PRO* 4.7 18.4 - - - +
172C HIS* 5.1 12.8 - - - +
174C ILE 5.5 2.5 - - - +
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Residues in contact with ILE 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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187B TYR* 2.9 29.7 + - + +
188B LEU* 2.9 38.6 + - + +
190B LYS* 1.3 75.6 - - - +
192B LEU* 1.3 59.4 + - - +
194B GLU* 3.0 47.2 - - - +
252B GLU* 3.1 34.5 - - + +
255B ARG* 3.3 35.7 - - - +
256B CYS* 3.9 5.6 - - - -
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Residues in contact with LEU 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LEU* 2.8 51.1 + - + +
189B MET* 3.7 9.4 - - - +
190B LYS 3.3 0.4 - - - -
191B ILE* 1.3 76.6 - - - +
193B THR* 1.3 61.9 + - - +
195B ARG* 3.1 15.9 + - - +
197B TYR* 3.0 35.0 + - + +
198B SER* 5.6 0.2 - - - -
199B PHE* 3.6 35.9 - - + -
208B VAL* 3.9 9.0 - - + -
211B ILE* 5.3 6.3 - - + -
247B ILE* 5.1 11.9 - - + -
249B ILE* 5.4 7.6 - - + -
252B GLU* 3.0 28.4 + - - +
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Residues in contact with THR 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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189B MET 3.5 16.4 - - - +
190B LYS* 2.7 20.8 + - - +
192B LEU* 1.3 77.1 - - - +
194B GLU* 1.3 63.8 + - - +
196B GLY* 3.0 12.3 + - - -
197B TYR 3.1 10.3 + - - +
198B SER* 3.9 26.3 + - - +
199B PHE 5.1 3.1 - - - +
109C LEU* 3.5 38.1 + - + +
111C PRO* 3.5 16.5 - - - +
176C ARG* 5.1 4.5 - - - +
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Residues in contact with GLU 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B LYS 5.2 1.1 - - - +
191B ILE* 3.0 37.1 + - - +
193B THR* 1.3 83.8 + - - +
195B ARG* 1.3 61.4 + - + +
196B GLY 3.2 0.9 - - - -
251B ASN* 5.5 0.9 - - - +
252B GLU* 4.7 6.9 - - - +
255B ARG* 2.7 31.9 + - - -
109C LEU 5.0 0.4 - - - -
110C ASN 4.2 5.8 - - - +
111C PRO* 2.9 13.9 - - - +
112C LYS* 2.6 61.9 + - + +
113C ALA 4.5 0.9 + - - -
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Residues in contact with ARG 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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192B LEU* 3.1 11.2 + - - +
194B GLU* 1.3 84.2 + - + +
196B GLY* 1.3 58.4 + - - +
197B TYR* 3.7 23.7 - - + -
236B GLU* 4.8 10.3 + - - -
248B THR* 3.2 25.7 + - - +
249B ILE* 4.1 2.1 - - - +
250B GLY* 3.1 33.4 - - - +
251B ASN* 4.0 14.8 + - - -
252B GLU* 2.9 31.5 + - - +
111C PRO* 4.4 1.6 - - - -
112C LYS* 5.7 1.1 - - - -
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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