Contacts of the helix formed by residues 185 - 202 (chain B) in PDB entry 3E61
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 ILE 185 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B GOL 6.2 0.7 - - - -
67B PRO* 6.4 0.4 - - + -
99B ASN* 4.1 22.0 - - - +
122B THR* 6.5 1.3 - - - -
124B PHE* 4.4 22.9 - - + -
144B ASP* 5.8 3.1 - - - +
181B GLU* 5.1 1.8 - - - +
182B ASN* 3.5 29.4 - - + +
183B LEU 3.1 1.8 - - - +
184B LEU* 1.3 77.3 - - - +
186B ASP* 1.3 69.7 + - - +
187B ALA* 4.1 13.5 - - + +
188B PHE* 3.0 47.7 + - + +
189B HIS* 3.0 12.6 + - - +
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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
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123B ALA* 5.3 10.0 - - - +
144B ASP* 5.0 10.2 + - - +
183B LEU 5.3 0.2 - - - -
184B LEU 3.5 7.3 + - - +
185B ILE* 1.3 74.8 - - - +
187B ALA* 1.3 57.7 + - - +
189B HIS* 3.3 9.1 + - - +
190B GLN* 2.9 52.8 + - + +
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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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1B GOL 4.1 20.6 - - - +
144B ASP* 4.8 12.0 + - + -
157B HIS* 3.5 46.1 - - + +
185B ILE* 3.3 11.2 - - + +
186B ASP* 1.3 76.9 - - - +
188B PHE* 1.3 64.0 + - - +
190B GLN* 4.1 0.2 - - - +
191B ARG* 3.0 28.1 + - - +
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Residues in contact with PHE 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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1B GOL 3.5 33.7 - - - -
74B PHE* 6.2 0.4 - + - -
181B GLU* 3.4 38.6 - - + +
182B ASN 3.6 21.5 - - - +
183B LEU* 4.5 2.5 - - + -
185B ILE* 3.0 38.0 + - + +
187B ALA* 1.3 78.8 - - - +
189B HIS* 1.3 61.9 + - - +
191B ARG* 3.6 28.4 - - - +
192B VAL* 3.1 27.5 + - - +
235B SER* 3.7 29.5 + - - +
236B ASN* 4.3 3.8 - - - -
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Residues in contact with HIS 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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183B LEU* 3.4 44.9 + - - +
185B ILE 3.0 9.4 + - - +
186B ASP* 3.8 11.4 - - - +
188B PHE* 1.3 77.6 - - - +
190B GLN* 1.3 67.7 + - + +
192B VAL* 3.2 2.9 + - - +
193B GLN* 3.1 60.3 + - + +
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Residues in contact with GLN 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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144B ASP 5.5 2.6 + - - -
156B ASN* 4.4 9.4 + - - -
157B HIS* 3.8 32.8 + - + +
158B PHE* 3.5 21.7 + - + +
186B ASP* 2.9 41.2 + - + +
187B ALA 3.8 4.7 - - - +
189B HIS* 1.3 77.9 - - + +
191B ARG* 1.3 66.4 + - - +
193B GLN* 3.2 10.9 + - - +
194B GLY 3.0 17.7 + - - -
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Residues in contact with ARG 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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1B GOL 2.8 47.0 + - - -
157B HIS* 3.2 42.4 + - - +
161B GLY* 3.3 16.1 - - - +
164B GLN* 3.6 19.1 - - - +
187B ALA* 3.0 19.0 + - - +
188B PHE* 3.6 19.2 - - - +
190B GLN* 1.3 75.7 - - - +
192B VAL* 1.3 64.0 + - + +
194B GLY 3.1 2.6 + - - -
195B ILE* 3.0 21.1 + - + +
235B SER* 2.9 35.3 + - - +
263B TYR* 3.5 42.4 + - + -
281B GLN* 3.7 0.2 - - - +
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Residues in contact with VAL 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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178B ILE* 4.3 17.9 - - + -
180B HIS* 4.2 17.0 - - + -
183B LEU* 4.0 17.3 - - + -
188B PHE 3.1 15.4 + - - +
189B HIS 3.2 9.2 + - - +
191B ARG* 1.3 78.6 - - + +
193B GLN* 1.3 66.2 + - - +
195B ILE* 3.2 13.1 + - + +
196B LYS* 3.0 37.4 + - + +
208B MET* 3.7 26.7 - - + -
235B SER* 4.9 4.9 - - - +
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Residues in contact with GLN 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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158B PHE* 3.5 18.0 - - + -
183B LEU* 6.0 0.2 - - - +
189B HIS* 3.1 56.0 + - + +
190B GLN* 3.2 8.3 + - - +
192B VAL* 1.3 84.9 - - - +
194B GLY* 1.3 57.1 + - - +
196B LYS* 3.7 23.0 + - - +
197B TYR* 2.8 35.9 + - - +
208B MET* 5.7 0.8 - - - +
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Residues in contact with GLY 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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158B PHE* 3.2 35.1 - - - -
162B GLN* 3.6 20.1 - - - +
190B GLN 3.0 10.7 + - - -
191B ARG 3.1 4.4 + - - -
193B GLN* 1.3 76.1 - - - +
195B ILE* 1.3 61.7 + - - +
197B TYR* 3.3 4.3 - - - +
198B ILE* 3.3 16.5 + - - +
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Residues in contact with ILE 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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161B GLY 3.4 19.9 + - - +
164B GLN* 3.6 13.2 - - - +
165B ALA* 3.7 5.2 - - + +
178B ILE* 3.7 29.8 - - + -
191B ARG* 3.0 19.6 + - + +
192B VAL* 3.2 17.5 + - + +
194B GLY* 1.3 74.6 - - - +
196B LYS* 1.3 58.6 + - - +
198B ILE 3.2 2.1 + - - -
199B LEU* 2.9 51.9 + - + +
233B ILE* 3.6 42.2 - - + -
234B CYS 6.2 0.9 - - - -
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Residues in contact with LYS 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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178B ILE* 4.6 4.9 - - + -
192B VAL* 3.0 27.6 + - + +
193B GLN* 3.7 26.3 + - - +
195B ILE* 1.3 74.6 - - - +
197B TYR* 1.3 59.9 + - - +
199B LEU 4.5 0.7 - - - +
200B ASP* 2.8 41.6 + - - +
206B TYR* 3.7 40.6 - - + +
208B MET* 3.5 33.6 - - - +
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Residues in contact with TYR 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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158B PHE* 3.8 22.4 - - + -
162B GLN* 4.8 5.4 - - + -
193B GLN 2.8 22.1 + - - +
194B GLY* 3.3 7.4 - - - +
196B LYS* 1.3 73.9 - - - +
198B ILE* 1.3 67.1 + - + +
200B ASP* 4.3 2.8 - - - +
201B GLN* 3.5 18.9 + - - +
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Residues in contact with ILE 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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162B GLN* 3.7 52.9 - - + +
165B ALA* 3.6 31.2 - - + +
166B GLU* 4.3 7.4 - - + +
169B ARG* 5.0 5.8 - - - +
194B GLY 3.7 2.2 - - - +
195B ILE 3.2 2.2 + - - -
197B TYR* 1.3 78.0 - - + +
199B LEU* 1.3 67.9 + - + +
201B GLN* 3.3 7.7 + - + +
202B GLN* 3.1 32.9 + - + +
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Residues in contact with LEU 199 (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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165B ALA* 4.1 22.4 - - + +
168B VAL* 4.7 4.0 - - + -
176B VAL* 4.0 21.8 - - + -
178B ILE* 4.6 0.2 - - + -
195B ILE* 2.9 44.4 + - + +
198B ILE* 1.3 73.2 - - + +
200B ASP* 1.3 57.6 + - - +
202B GLN* 3.3 3.1 + - - -
203B ARG* 3.0 7.4 + - - -
204B ILE* 3.0 61.7 + - + +
206B TYR* 3.7 40.8 - - + -
233B ILE* 4.5 0.7 - - + -
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Residues in contact with ASP 200 (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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196B LYS* 2.8 29.3 + - - +
197B TYR* 4.3 3.3 - - - +
199B LEU* 1.3 68.4 - - - +
201B GLN* 1.3 66.5 + - - +
203B ARG* 2.9 17.5 + - - +
204B ILE 5.3 0.8 - - - +
206B TYR* 2.8 35.0 + - - -
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Residues in contact with GLN 201 (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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197B TYR 3.5 11.8 + - - +
198B ILE* 3.3 13.1 + - + +
200B ASP* 1.3 77.0 - - - +
202B GLN* 1.3 67.4 + - - +
203B ARG* 3.4 1.9 + - - +
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Residues in contact with GLN 202 (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 ARG* 3.4 42.1 - - + +
198B ILE* 3.1 25.6 + - + +
199B LEU* 3.7 3.6 - - - +
200B ASP 3.1 0.2 - - - -
201B GLN* 1.3 81.3 - - + +
203B ARG* 1.3 68.9 + - - +
204B ILE* 3.2 26.7 + - + +
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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