Contacts of the helix formed by residues 167 - 182 (chain B) in PDB entry 6B3I
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 ASP 167 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B ASP 4.2 0.4 + - - -
166B VAL* 1.3 71.4 - - - +
168B LYS* 1.3 57.8 + - - +
169B ASP* 3.2 10.4 + - - +
170B LEU* 3.1 34.7 + - + +
171B ALA* 2.9 24.4 + - - +
204B GLN* 2.9 19.8 + - - +
195C GLU* 2.8 28.8 - - - +
199C LYS* 3.9 14.3 - - - +
200C ARG* 5.0 0.3 + - - -
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Residues in contact with LYS 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B VAL* 3.7 21.0 + - + +
167B ASP* 1.3 73.9 + - - +
169B ASP* 1.3 62.7 + - - +
171B ALA* 3.4 6.1 + - + +
172B GLY* 3.1 23.0 + - - -
207B ALA* 4.0 12.8 - - + +
210B GLN* 3.4 27.3 - - - +
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Residues in contact with ASP 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ASP* 3.2 4.7 + - - +
168B LYS* 1.3 79.1 + - - +
170B LEU* 1.3 60.2 + - - +
172B GLY* 3.3 1.8 + - - -
173B GLN* 3.0 27.5 + - - +
191C LEU* 5.4 11.9 - - - +
195C GLU* 3.5 29.1 - - + +
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Residues in contact with LEU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ASN* 6.1 0.9 - - - +
167B ASP* 3.1 30.4 + - + +
169B ASP* 1.3 74.5 - - - +
171B ALA* 1.3 58.9 + - - +
173B GLN* 3.3 6.8 + - + +
174B ASP* 2.9 51.5 + - - +
200B ARG* 4.0 23.8 - - - +
204B GLN* 3.7 19.1 - - + +
170C LEU* 5.3 0.2 - - + -
195C GLU* 3.7 9.8 - - - +
200C ARG* 3.7 30.1 - - - +
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Residues in contact with ALA 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ASP 2.9 12.0 + - - +
168B LYS* 3.7 7.6 - - + +
170B LEU* 1.3 75.3 - - - +
172B GLY* 1.3 61.0 + - - +
174B ASP* 4.6 0.4 - - - -
175B ALA* 3.1 24.6 + - - +
204B GLN* 3.2 18.9 - - - +
207B ALA* 3.8 17.0 - - + +
208B THR* 3.6 35.6 - - - +
211B ALA* 4.2 3.7 - - + +
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Residues in contact with GLY 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LYS 3.1 14.7 + - - -
169B ASP* 3.3 3.5 + - - -
170B LEU 3.2 0.2 - - - -
171B ALA* 1.3 75.4 - - - +
173B GLN* 1.3 63.0 + - - +
175B ALA* 3.4 6.1 + - - +
176B LYS* 3.1 36.3 + - - +
211B ALA* 4.6 9.6 - - - +
215B LEU* 4.1 4.5 - - - +
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Residues in contact with GLN 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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169B ASP 3.0 16.3 + - - +
170B LEU* 3.3 9.8 + - + +
172B GLY* 1.3 73.6 - - - +
174B ASP* 1.3 61.3 + - - +
176B LYS* 3.2 22.8 + - - +
177B ASP* 2.8 57.0 + - - +
185B ARG* 5.8 0.4 - - - +
174C ASP* 5.8 1.6 - - - +
177C ASP* 3.4 33.4 + - + +
186C TRP* 5.8 2.4 - - - -
192C ALA* 4.5 16.9 - - + +
195C GLU* 5.7 5.8 - - + -
200C ARG* 6.1 2.2 - - - +
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Residues in contact with ASP 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU* 2.9 31.5 + - - +
173B GLN* 1.3 77.3 - - - +
175B ALA* 1.3 57.8 + - - +
177B ASP* 3.2 11.7 + - - +
178B LEU* 2.8 34.5 + - - +
196B VAL* 3.8 19.4 - - + +
200B ARG* 2.8 47.8 + - - +
204B GLN* 4.8 0.5 + - - -
208B THR* 3.8 23.5 + - + -
173C GLN* 6.0 0.7 - - - +
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Residues in contact with ALA 175 (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 ALA 3.1 19.8 + - - +
172B GLY 3.7 4.5 - - - +
173B GLN 3.2 0.2 - - - -
174B ASP* 1.3 76.8 - - - +
176B LYS* 1.3 62.3 + - - +
178B LEU* 3.5 2.0 + - - -
179B TYR* 3.1 18.7 + - - +
208B THR* 3.7 23.0 - - - +
211B ALA* 4.2 2.0 - - + -
212B TYR* 3.4 37.4 - - + +
215B LEU* 4.1 11.9 - - + -
216B ILE* 5.2 0.7 - - - +
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Residues in contact with LYS 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B GLY* 3.1 21.6 + - - +
173B GLN* 3.2 25.6 + - - +
175B ALA* 1.3 76.1 - - - +
177B ASP* 1.3 63.9 + - - +
179B TYR* 3.3 4.0 + - - +
180B ASP* 3.0 28.9 + - - +
215B LEU* 3.8 26.9 - - + -
216B ILE* 5.9 0.2 - - - -
186C TRP* 3.5 60.6 + - + +
187C GLY 5.8 0.4 - - - +
188C THR 6.2 0.2 - - - +
191C LEU* 5.9 5.9 - - - +
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Residues in contact with ASP 177 (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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173B GLN* 2.8 34.9 + - - +
174B ASP* 3.2 12.3 + - - +
176B LYS* 1.3 78.6 - - - +
178B LEU* 1.3 58.1 + - + +
180B ASP* 3.3 2.3 + - - +
181B ALA* 2.9 30.5 + - - +
185B ARG* 2.6 36.5 + - - +
192B ALA* 4.4 7.8 - - + +
196B VAL* 5.7 3.4 - - + -
173C GLN* 3.6 16.9 - - + +
177C ASP* 2.9 29.1 - - - +
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Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ASP 2.8 23.9 + - - +
175B ALA* 3.9 5.4 - - - +
176B LYS 3.3 0.2 - - - -
177B ASP* 1.3 72.3 - - - +
179B TYR* 1.3 60.1 + - - +
181B ALA* 3.6 2.6 + - - -
182B GLY* 3.4 15.2 + - - -
192B ALA* 3.8 23.6 - - + +
193B PHE* 3.6 47.8 - - + +
196B VAL* 3.9 28.7 - - + -
197B LEU* 5.0 3.1 - - + -
208B THR* 4.3 11.4 - - + -
209B PHE* 5.2 0.4 - - + -
212B TYR* 4.2 11.9 + - + -
220B ILE* 3.6 28.7 - - + -
227B GLU* 4.6 0.9 - - - +
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Residues in contact with TYR 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 ALA 3.1 12.4 + - - +
176B LYS* 3.7 6.7 - - - +
177B ASP 3.3 0.2 - - - -
178B LEU* 1.3 74.8 - - - +
180B ASP* 1.3 80.4 + - - +
182B GLY* 3.1 12.2 + - - -
183B GLU* 3.4 41.5 + - + +
212B TYR* 3.7 15.8 - - + -
216B ILE* 3.5 44.2 - - + -
227B GLU* 5.2 2.6 - - - +
186C TRP* 3.7 22.0 - + - -
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Residues in contact with ASP 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 LYS 3.0 17.0 + - - +
177B ASP* 3.8 1.6 - - - +
179B TYR* 1.3 90.3 - - - +
181B ALA* 1.3 60.6 + - - +
183B GLU* 3.0 23.4 + - - +
184B GLY 3.2 8.5 + - - -
185B ARG* 3.3 54.0 + - + +
185C ARG* 4.0 14.8 - - - +
186C TRP* 3.4 22.4 + - - -
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Residues in contact with ALA 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ASP 2.9 17.4 + - - +
178B LEU 3.8 5.8 - - - +
179B TYR 3.3 0.2 - - - -
180B ASP* 1.3 75.7 - - - +
182B GLY* 1.3 60.2 + - - +
183B GLU 3.5 0.5 + - - -
184B GLY 3.5 5.8 + - - +
185B ARG* 4.2 7.5 - - - +
189B ASP* 3.2 40.9 - - - +
192B ALA* 3.6 25.1 - - + -
193B PHE* 4.1 13.7 - - + -
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Residues in contact with GLY 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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178B LEU 3.4 5.8 + - - -
179B TYR 3.1 8.4 + - - -
181B ALA* 1.3 77.7 - - - +
183B GLU* 1.3 67.0 + - - +
184B GLY 3.4 0.4 - - - -
189B ASP* 4.8 4.3 - - - +
193B PHE* 4.4 1.0 - - - -
227B GLU* 3.3 44.1 + - - +
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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