Contacts of the helix formed by residues 180 - 196 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C GLY 3.6 6.7 - - - +
156C ASP 2.9 15.9 - - - +
157C GLY 2.9 33.2 - - - +
159C THR* 4.6 1.1 - - - -
179C LEU* 1.3 76.6 - - - +
181C GLY* 1.3 64.5 + - - +
182C ARG* 3.2 1.6 - - + +
183C ASP* 3.1 18.9 + - - +
184C LEU* 3.0 28.2 + - - +
260C LEU* 4.4 3.8 - - - +
302C THR* 4.6 2.0 - - - -
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Residues in contact with GLY 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C GLY 3.4 11.1 + - - -
156C ASP* 4.4 4.9 - - - -
180C ALA* 1.3 74.7 - - - +
182C ARG* 1.3 55.8 + - - +
184C LEU* 3.0 7.1 + - - +
185C THR 2.9 18.0 + - - -
212C LYS* 2.7 31.4 + - - -
302C THR* 3.5 25.5 + - - -
305C TYR* 4.5 0.2 - - - -
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Residues in contact with ARG 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C SER* 5.8 0.9 - - - -
68C TYR* 4.0 15.9 - - + -
70C ILE 5.5 1.6 - - - -
71C GLU* 2.9 42.5 + - - -
72C HIS* 5.4 4.2 + - - -
156C ASP* 3.3 40.1 + - - +
157C GLY* 6.3 0.2 - - - -
180C ALA* 3.2 0.6 - - + -
181C GLY* 1.3 75.8 - - - +
183C ASP* 1.3 70.0 + - - +
185C THR* 3.1 19.1 + - - -
186C ASP* 3.2 22.9 + - - -
205C ARG* 3.2 47.2 + - - +
209C ARG* 6.4 0.7 - - - +
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Residues in contact with ASP 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C HIS* 3.7 26.0 + - - -
178C ASP 3.1 24.6 - - - +
179C LEU* 5.1 1.3 - - + -
180C ALA* 3.1 26.8 + - - +
182C ARG* 1.3 84.7 + - - +
184C LEU* 1.3 62.3 + - + +
186C ASP* 3.2 15.1 + - - +
187C TYR* 3.2 18.9 + - - +
266C LEU* 4.5 17.8 - - + +
268C MET* 6.0 3.1 - - + -
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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
----------------------------------------------------------
179C LEU* 6.1 0.2 - - + -
180C ALA 3.0 17.7 + - - +
181C GLY* 3.0 8.7 + - - +
183C ASP* 1.3 74.2 - - + +
185C THR* 1.3 54.5 + - - +
187C TYR* 3.1 5.5 + - + +
188C LEU* 2.7 30.7 + - - -
212C LYS* 4.3 9.2 - - + -
256C CYS* 3.1 41.2 - - - +
257C PRO* 4.9 2.0 - - + -
259C ALA* 4.1 13.5 - - + -
260C LEU* 3.7 35.9 - - + +
266C LEU* 5.2 6.3 - - + -
302C THR* 3.5 24.7 - - - +
305C TYR* 3.9 13.0 - - + +
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Residues in contact with THR 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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181C GLY 2.9 5.2 + - - -
182C ARG* 3.1 14.2 + - - -
184C LEU* 1.3 76.5 - - - +
186C ASP* 1.3 56.4 + - - +
188C LEU* 3.2 7.9 + - - +
189C MET* 2.8 28.8 + - - +
205C ARG* 3.7 29.6 - - + +
208C VAL* 3.5 26.0 - - + -
209C ARG* 4.1 14.2 - - + +
212C LYS* 2.8 32.1 + - - +
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Residues in contact with ASP 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C ARG* 3.2 16.4 + - - +
183C ASP* 3.2 14.0 + - - +
185C THR* 1.3 76.9 - - - +
187C TYR* 1.3 62.8 + - - +
189C MET* 3.0 29.7 - - - +
190C LYS* 3.1 11.6 + - - +
205C ARG* 2.9 38.3 + - - -
283D LYS* 5.5 8.8 + - - +
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Residues in contact with TYR 187 (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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183C ASP 3.2 4.8 + - - +
184C LEU* 3.1 11.6 + - + +
186C ASP* 1.3 79.8 - - - +
188C LEU* 1.3 55.2 + - - +
190C LYS* 3.2 31.9 + - - +
191C ILE* 2.9 48.0 + - + +
255C ARG* 4.4 13.8 + - + +
256C CYS* 3.5 38.6 - - + -
259C ALA* 4.8 5.6 - - + -
265C PHE* 3.8 47.3 - + + +
266C LEU* 3.6 32.3 - - + +
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Residues in contact with LEU 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C LEU 2.7 14.4 + - - +
185C THR* 3.2 6.0 + - - +
187C TYR* 1.3 70.6 - - - +
189C MET* 1.3 64.5 + - - +
191C ILE* 2.8 22.4 - - + +
192C LEU* 2.8 44.3 + - + +
208C VAL* 3.4 37.7 - - + +
211C ILE* 5.1 7.0 - - + -
212C LYS* 3.9 23.8 - - + +
216C CYS* 4.6 10.5 - - - -
252C GLU* 4.9 5.8 - - - +
253C ARG* 5.2 2.7 - - + -
256C CYS* 3.3 27.3 - - + -
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Residues in contact with MET 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C THR 2.8 14.9 + - - +
186C ASP* 3.0 45.8 - - - +
188C LEU* 1.3 73.9 - - - +
190C LYS* 1.3 62.1 + - + +
192C LEU* 3.4 17.6 + - - +
193C THR* 3.4 17.0 + - - +
199C PHE* 3.2 40.5 + - + +
200C THR* 4.7 8.1 - - - -
201C THR 5.3 0.7 - - - +
205C ARG* 4.4 25.6 - - + -
208C VAL* 4.6 17.2 - - + +
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Residues in contact with LYS 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C ASP 3.1 9.5 + - - +
187C TYR* 3.3 41.0 + - - +
189C MET* 1.3 83.9 - - + +
191C ILE* 1.3 62.5 + - - +
193C THR* 2.7 29.4 + - - -
194C GLU* 4.1 1.7 + - - +
265C PHE 5.0 5.4 + - - -
266C LEU* 6.2 0.7 - - - +
109D LEU* 4.4 24.6 - - + +
171D PRO* 4.7 17.2 + - - +
172D HIS* 5.0 17.3 - - - +
174D ILE 5.5 2.0 - - - +
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Residues in contact with ILE 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C TYR* 2.9 33.8 + - + +
188C LEU* 2.8 40.3 + - + +
190C LYS* 1.3 80.5 - - - +
192C LEU* 1.3 61.5 + - - +
194C GLU* 2.9 59.9 - - - +
252C GLU* 2.9 35.8 - - + +
255C ARG* 3.6 22.2 - - - +
256C CYS* 5.2 0.2 - - - -
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Residues in contact with LEU 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C LEU* 2.8 53.5 + - + +
189C MET* 3.7 9.4 - - - +
190C LYS 3.4 0.2 - - - -
191C ILE* 1.3 78.6 - - - +
193C THR* 1.3 61.9 + - - +
195C ARG* 3.1 15.2 + - - +
196C GLY 3.3 0.5 + - - -
197C TYR* 3.1 36.9 + - + +
199C PHE* 3.6 33.4 - - + +
208C VAL* 3.9 11.4 - - + -
211C ILE* 5.3 6.3 - - + -
247C ILE* 5.3 8.5 - - + -
249C ILE* 5.2 5.8 - - + -
252C GLU* 3.3 23.8 - - - +
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Residues in contact with THR 193 (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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189C MET 3.4 16.6 - - - +
190C LYS* 2.7 20.8 + - - +
192C LEU* 1.3 77.6 - - - +
194C GLU* 1.3 62.8 + - - +
196C GLY* 3.1 10.9 + - - -
197C TYR 3.2 15.2 + - - +
198C SER* 4.1 19.8 + - - +
199C PHE 5.1 3.6 - - - +
109D LEU* 3.6 36.5 + - + +
111D PRO* 3.5 16.9 - - - +
176D ARG* 5.3 5.6 + - - -
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Residues in contact with GLU 194 (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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190C LYS 5.1 1.6 - - - +
191C ILE* 2.9 39.4 + - - +
193C THR* 1.3 82.3 + - - +
195C ARG* 1.3 62.3 + - - +
252C GLU* 3.7 8.6 - - - +
255C ARG* 2.6 32.2 + - - -
109D LEU 5.7 0.2 - - - -
110D ASN 4.2 5.8 - - - +
111D PRO* 2.9 13.0 - - - +
112D LYS* 2.6 61.0 + - + +
113D ALA 4.4 0.3 + - - -
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Residues in contact with ARG 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C LEU 3.1 10.8 + - - +
194C GLU* 1.3 84.2 - - + +
196C GLY* 1.3 57.0 + - - +
197C TYR* 3.6 22.3 - - + -
236C GLU* 4.6 12.7 + - - -
248C THR* 3.3 25.1 + - - +
249C ILE* 4.0 8.0 - - - +
250C GLY* 3.0 33.8 - - - +
251C ASN* 4.1 8.7 + - - -
252C GLU* 3.6 31.6 + - - +
111D PRO* 4.3 3.2 - - - +
112D LYS* 5.6 1.8 - - - -
113D ALA* 5.3 7.1 + - - +
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Residues in contact with GLY 196 (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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193C THR 3.1 12.4 + - - -
195C ARG* 1.3 79.3 - - - +
197C TYR* 1.3 72.8 + - - +
198C SER* 4.2 2.9 + - - -
111D PRO* 4.0 15.0 - - - -
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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
------------------------------------------------------------
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