Contacts of the helix formed by residues 167 - 184 (chain B) in PDB entry 3G1Q
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 LEU 167 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B TRP* 4.4 8.1 - - + -
165B ILE* 3.7 18.9 + - + -
166B ASN* 1.3 69.8 - - - +
168B LEU* 1.3 61.5 + - - +
170B ASP* 4.4 3.4 - - + -
171B CYS* 2.8 38.4 + - - -
301B THR* 4.0 11.2 - - + +
304B MET* 3.8 43.3 - - + -
305B LEU* 3.8 18.4 - - + -
308B MET* 3.7 27.6 - - + -
445B PHE* 5.2 0.2 - - + -
469B CYS* 3.0 19.0 + - + +
471B VAL* 4.1 12.6 - - + -
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Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ASN* 3.1 8.3 + - - +
167B LEU* 1.3 78.8 - - - +
169B GLU* 1.3 58.5 + - + +
171B CYS* 3.5 1.6 + - - +
172B SER* 2.9 39.2 + - - +
297B SER* 4.7 1.6 - - - +
298B ILE* 4.3 17.0 - - + +
301B THR* 3.5 34.0 - - + +
463B GLY* 5.7 0.9 - - - -
464B PRO* 3.7 35.9 - - + +
466B ALA* 3.8 23.8 - - + -
469B CYS* 4.1 9.0 - - + +
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Residues in contact with GLU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ASN* 3.1 40.8 + - - +
168B LEU* 1.3 75.8 - - + +
170B ASP* 1.3 63.9 + - - +
172B SER* 3.4 8.1 + - - -
173B THR* 2.9 32.5 + - - +
466B ALA* 5.9 3.5 - - + +
470B ARG* 5.3 3.2 + - - -
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Residues in contact with ASP 170 (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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153B PHE* 3.5 25.6 - - + -
157B ASN* 4.9 2.8 - - - +
158B TRP* 2.8 37.5 + - + -
165B ILE* 3.6 16.3 - - + +
166B ASN 3.0 20.7 + - - +
167B LEU* 3.8 5.4 - - + +
168B LEU 3.2 0.2 - - - -
169B GLU* 1.3 80.5 - - - +
171B CYS* 1.3 60.1 + - - +
173B THR* 3.3 5.2 + - - -
174B MET* 2.9 33.6 + - - +
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Residues in contact with CYS 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B LEU* 2.8 39.8 + - - +
168B LEU 3.8 0.9 - - - +
170B ASP* 1.3 68.8 - - - +
172B SER* 1.3 61.8 + - - +
174B MET* 3.1 14.8 + - - +
175B ILE* 2.9 34.7 + - - +
297B SER* 3.8 11.2 - - - +
300B THR* 3.8 28.3 - - + -
301B THR* 3.2 28.3 - - - +
304B MET* 4.0 7.6 - - - -
435B ILE* 5.7 0.2 - - - -
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Residues in contact with SER 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LEU* 2.9 24.3 + - - +
169B GLU* 3.5 7.7 - - - -
171B CYS* 1.3 76.1 - - - +
173B THR* 1.3 64.8 + - - +
176B ILE* 3.1 14.5 + - - +
293B GLN* 3.0 25.7 + - - +
294B HIS* 5.0 8.3 + - - -
297B SER* 3.3 23.3 + - - -
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Residues in contact with THR 173 (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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153B PHE* 3.7 26.0 - - + -
169B GLU* 2.9 16.1 + - - +
170B ASP* 3.7 8.8 + - - -
172B SER* 1.3 78.3 - - - +
174B MET* 1.4 60.9 + - - +
176B ILE* 3.5 11.5 + - + +
177B ASN* 3.0 39.7 + - - +
194B ALA* 5.4 5.4 - - + -
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Residues in contact with MET 174 (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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149B GLU 6.0 0.4 - - - -
150B VAL* 3.9 28.9 - - + -
153B PHE* 3.6 39.3 - - + -
154B MET* 4.3 6.7 - - - -
158B TRP* 4.4 20.0 - - + -
170B ASP 2.9 20.1 + - - +
171B CYS* 3.1 25.1 + - - +
173B THR* 1.4 75.9 - - - +
175B ILE* 1.3 59.4 + - - +
177B ASN* 3.2 6.8 + - - +
178B THR* 2.8 37.8 + - + +
304B MET* 5.3 0.4 - - - -
435B ILE* 4.0 32.3 - - + -
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Residues in contact with ILE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B CYS 2.9 18.8 + - - +
172B SER 3.9 3.8 - - - +
174B MET* 1.3 75.3 - - - +
176B ILE* 1.3 65.5 + - - +
178B THR* 3.4 2.0 - - - +
179B ALA* 2.9 32.1 + - + +
292B GLY 4.3 0.7 - - - +
293B GLN* 3.5 35.7 - - - +
296B SER* 4.0 18.8 - - - +
297B SER* 3.7 19.5 - - - +
300B THR* 4.3 6.1 - - - +
431B GLN* 3.7 38.8 - - + +
432B VAL 5.0 0.4 - - - +
435B ILE* 3.8 19.7 - - + -
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Residues in contact with ILE 176 (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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172B SER* 3.1 18.6 + - - +
173B THR* 3.7 14.8 - - + +
175B ILE* 1.3 74.8 - - - +
177B ASN* 1.4 60.8 + - - +
179B ALA* 4.0 1.3 - - - +
180B CYS* 2.9 35.4 + - - -
194B ALA* 3.6 32.8 - - + +
197B PHE* 3.6 29.6 - - + -
198B ALA* 3.8 29.6 - - + -
201B LEU* 6.4 0.4 - - + -
293B GLN* 3.4 29.3 + - + +
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Residues in contact with ASN 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B GLU* 3.8 23.1 + - + +
153B PHE* 5.3 5.6 - - + -
173B THR* 3.0 28.0 + - - +
174B MET* 3.2 10.5 + - - +
176B ILE* 1.4 82.3 - - - +
178B THR* 1.3 57.8 - - - +
180B CYS* 4.8 0.4 - - - -
181B GLN* 2.8 31.2 + - - +
189B ARG* 3.2 25.1 + - - +
194B ALA* 3.8 26.8 - - - +
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Residues in contact with THR 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ILE* 3.8 30.5 - - + +
149B GLU* 4.0 9.4 - - + -
150B VAL* 3.8 29.8 - - + +
174B MET* 2.8 27.9 + - + +
175B ILE* 3.2 8.1 + - - +
177B ASN* 1.3 73.8 - - - +
179B ALA* 1.3 62.8 + - - +
181B GLN* 3.4 4.9 + - - +
182B CYS* 3.1 29.7 + - - -
431B GLN* 2.6 27.6 + - - +
435B ILE* 5.1 3.1 - - + -
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Residues in contact with ALA 179 (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 ILE* 2.9 22.1 + - + +
176B ILE* 4.0 2.7 - - - +
178B THR* 1.3 79.0 + - - +
180B CYS* 1.4 58.6 + - - +
182B CYS* 3.1 1.9 + - - +
183B LEU* 2.8 40.3 + - + +
197B PHE* 6.0 3.1 - - + -
293B GLN* 5.0 3.1 - - - +
427B PHE* 4.0 18.8 - - + -
431B GLN* 3.6 13.9 - - - +
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Residues in contact with CYS 180 (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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176B ILE* 2.9 28.5 + - + +
177B ASN* 4.2 0.9 - - - +
179B ALA* 1.4 74.5 - - - +
181B GLN* 1.3 67.7 + - - +
183B LEU* 5.0 0.2 - - - -
184B PHE* 2.8 69.8 + - + +
189B ARG* 3.7 18.7 - - + +
192B LEU 5.2 3.1 - - - +
193B ASP 6.2 0.2 - - - -
194B ALA* 6.0 0.4 - - - -
197B PHE* 3.7 27.4 - - - -
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Residues in contact with GLN 181 (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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145B ALA* 3.6 36.5 - - + +
146B ILE 4.7 0.2 - - - +
148B HIS* 6.0 1.8 - - - -
149B GLU* 2.9 39.9 - - + +
152B LYS* 4.9 0.7 + - - -
177B ASN 2.8 19.3 + - - +
178B THR 3.5 5.2 - - - +
180B CYS* 1.3 78.2 - - - +
182B CYS* 1.3 63.7 + - - +
184B PHE 4.1 6.6 - - - +
186B GLU* 3.7 12.1 + - - +
189B ARG* 3.1 19.9 + - - +
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Residues in contact with CYS 182 (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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142B PHE* 3.6 55.9 - - + -
145B ALA* 4.7 5.4 - - - -
146B ILE* 3.4 29.6 - - - -
178B THR 3.1 13.6 + - - +
179B ALA 3.1 8.1 + - - +
181B GLN* 1.3 85.7 - - - +
183B LEU* 1.3 62.2 + - + +
184B PHE 5.1 0.4 - - - -
260B ASP* 5.7 1.9 - - - +
427B PHE* 3.9 17.5 - - + -
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Residues in contact with LEU 183 (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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133B GLU 4.3 7.4 - - - +
134B LEU* 4.1 24.9 - - + -
142B PHE* 4.2 16.6 - - + -
179B ALA* 2.8 26.2 + - + +
182B CYS* 1.3 83.8 - - + +
184B PHE* 1.3 67.1 + - + +
260B ASP* 3.4 2.9 - - - +
261B LEU* 2.8 65.0 + - + +
288B ALA* 5.7 3.6 - - + -
427B PHE* 3.9 22.2 - - + -
480B HEM 5.0 6.5 - - + -
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Residues in contact with PHE 184 (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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180B CYS* 2.8 59.2 + - + +
181B GLN 4.1 7.3 - - - +
182B CYS 5.4 0.2 - - - -
183B LEU* 1.3 86.7 - - + +
185B GLY* 1.3 72.1 + - - +
186B GLU* 3.7 2.4 + - - +
188B LEU* 3.5 27.8 - - + -
189B ARG* 3.8 14.1 - - + +
192B LEU* 3.8 33.7 - - + -
197B PHE* 4.0 15.3 - + - -
240B LEU* 6.2 0.7 - - + -
260B ASP* 3.8 4.9 - - - -
261B LEU* 4.7 13.9 - - + -
262B LEU* 5.9 0.9 - - + -
285B ILE* 4.6 25.6 - - + -
289B MET* 5.5 1.3 - - + -
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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