Contacts of the helix formed by residues 176 - 188 (chain B) in PDB entry 3OFN
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 GLY 176 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174B GLN* 3.7 1.2 - - - +
175B THR* 1.3 79.5 - - - +
177B LYS* 1.3 66.7 + - - +
178B THR 3.5 2.0 - - - -
179B ALA* 3.3 17.2 - - - +
180B VAL* 3.3 25.3 + - - +
354B LEU* 3.7 2.5 - - - -
359B PHE* 3.6 13.7 - - - -
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Residues in contact with LYS 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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169B ILE* 4.0 15.1 - - + +
170B ILE 4.0 2.7 - - - -
171B GLY* 3.5 28.4 + - - +
172B ASP 2.6 29.7 + - - -
173B ARG* 4.0 6.3 - - - +
174B GLN 4.4 4.0 - - - +
175B THR* 3.4 13.4 + - - +
176B GLY* 1.3 76.0 - - - +
178B THR* 1.3 65.6 + - - +
180B VAL* 3.2 15.8 + - - +
181B ALA* 3.4 9.8 + - - +
272B ASP* 5.2 1.6 - - - -
328B VAL* 3.6 33.0 - - + -
329B ILE 3.8 12.8 - - - +
330B GLU* 4.1 16.0 + - - +
354B LEU* 3.6 16.4 - - + +
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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
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176B GLY 3.5 0.2 - - - -
177B LYS* 1.3 77.1 - - - +
179B ALA* 1.3 52.8 + - - +
181B ALA* 3.0 8.4 + - + +
182B LEU* 2.7 37.3 + - + +
205B TYR* 3.7 17.9 - - + +
210B GLN* 5.8 0.2 - - - +
218B LEU* 3.9 22.7 - - + -
271B ASP* 3.0 32.2 + - - +
328B VAL* 5.4 1.5 - - - +
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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
----------------------------------------------------------
152B LEU* 6.1 0.2 - - - -
176B GLY* 3.3 23.2 + - - +
177B LYS 3.1 0.4 - - - -
178B THR* 1.3 77.7 - - - +
180B VAL* 1.3 57.4 + - + +
182B LEU* 3.2 2.8 + - - +
183B ASP* 2.9 37.5 + - - +
434B GLN* 3.6 38.4 - - + +
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Residues in contact with VAL 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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150B THR* 5.9 0.4 - - + -
152B LEU* 3.8 27.8 - - + +
155B VAL* 4.3 14.4 - - + -
169B ILE* 4.4 21.1 - - + -
176B GLY 3.3 14.8 - - - +
177B LYS 3.2 8.0 + - - +
179B ALA* 1.3 73.2 - - + +
181B ALA* 1.3 63.7 + - - +
184B THR* 2.9 31.2 + - - +
326B LEU* 5.7 1.1 - - + +
352B ILE* 4.8 9.4 - - + -
354B LEU* 4.5 15.9 - - + -
365B PRO* 4.7 19.1 - - + -
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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
----------------------------------------------------------
169B ILE* 4.4 12.0 - - + +
177B LYS 3.4 5.6 + - - +
178B THR* 3.0 17.2 + - + +
180B VAL* 1.3 81.1 - - - +
182B LEU* 1.3 61.9 + - - +
184B THR* 3.4 7.2 + - - -
185B ILE* 3.1 28.4 + - - +
205B TYR* 5.0 3.6 - - + -
269B VAL* 3.5 36.4 - - + +
326B LEU* 5.0 3.1 - - + -
328B VAL* 5.4 1.8 - - + -
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Residues in contact with LEU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B THR* 2.7 23.9 + - + +
179B ALA* 3.7 5.8 - - - +
181B ALA* 1.3 71.2 - - - +
183B ASP* 1.3 60.7 + - - +
185B ILE* 3.2 11.5 + - + +
186B LEU* 2.9 42.0 + - + +
205B TYR* 6.2 0.6 - - + -
218B LEU* 4.1 33.0 - - + +
221B THR* 4.5 12.8 - - + -
222B LEU* 3.7 33.9 - - + +
434B GLN* 4.3 6.5 - - - +
435B TYR* 4.2 24.7 - - + +
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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
----------------------------------------------------------
150B THR 3.5 3.9 - - - +
152B LEU* 3.7 32.5 - - + +
179B ALA 2.9 22.4 + - - +
182B LEU* 1.3 70.0 - - - +
184B THR* 1.3 61.0 + - - +
186B LEU* 3.4 9.8 + - - +
187B ASN* 2.8 31.4 + - - +
433B ASN 4.0 1.2 - - - +
434B GLN* 3.7 19.8 + - - +
435B TYR* 2.9 41.2 + - - -
436B SER 3.9 4.6 + - - -
437B PRO* 3.9 9.8 - - + +
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Residues in contact with THR 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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148B VAL* 4.4 13.2 - - + -
149B GLN 4.4 1.8 - - - +
150B THR* 3.3 43.9 + - + +
152B LEU* 4.5 0.4 - - - +
180B VAL* 2.9 16.5 + - - +
181B ALA* 3.5 11.2 - - - -
182B LEU 3.2 0.4 - - - -
183B ASP* 1.3 78.0 - - - +
185B ILE* 1.3 62.1 + - - +
187B ASN* 3.2 10.4 + - - +
188B GLN* 3.3 20.6 + - + +
267B LEU* 3.7 25.8 - - + -
326B LEU* 4.6 8.7 - - + +
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Residues in contact with ILE 185 (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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181B ALA 3.1 18.6 + - - +
182B LEU* 3.2 14.1 + - + +
184B THR* 1.3 71.4 - - - +
186B LEU* 1.3 54.3 + - - +
188B GLN* 3.6 2.6 + - - +
203B CYS* 3.7 39.3 - - + -
205B TYR* 4.2 27.4 - - + -
222B LEU* 3.8 25.6 - - + -
227B ALA* 4.3 0.6 - - + +
230B TYR* 2.5 35.2 + - + -
231B SER* 4.3 9.6 - - - +
267B LEU* 4.4 10.1 - - + -
269B VAL* 4.1 17.7 - - + -
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Residues in contact with LEU 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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182B LEU* 2.9 27.3 + - + +
183B ASP* 3.7 13.5 - - - +
185B ILE* 1.3 71.5 - - - +
187B ASN* 1.3 55.5 + - - +
188B GLN 2.8 16.4 + - - -
189B LYS* 2.8 22.5 + - - +
221B THR* 4.5 5.4 - - + +
222B LEU* 4.3 12.3 - - + -
225B HIS* 3.4 50.3 - - + +
227B ALA* 4.1 11.9 - - + -
230B TYR* 2.9 6.2 + - - -
435B TYR* 3.9 31.9 - - + -
437B PRO* 4.7 8.1 - - + -
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Residues in contact with ASN 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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149B GLN* 3.2 25.1 + - - +
150B THR 3.1 27.0 - - - +
151B GLY* 3.5 6.5 - - - +
183B ASP 2.8 13.6 + - - +
184B THR 3.2 5.1 + - - +
186B LEU* 1.3 71.8 - - - +
188B GLN* 1.3 60.8 + - - +
189B LYS 3.1 1.7 + - - -
190B ARG* 2.5 53.4 + - - +
191B TRP* 3.5 20.1 - - - -
437B PRO* 3.2 17.8 - - + +
438B LEU 3.9 1.5 + - - +
439B ALA* 6.1 0.2 - - - +
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Residues in contact with GLN 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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148B VAL* 5.2 0.2 - - - +
149B GLN* 2.7 32.1 + - - +
163B ARG* 3.8 8.5 + - - -
184B THR* 3.4 18.9 + - + +
185B ILE 3.7 1.1 - - - +
186B LEU 2.8 4.2 + - - -
187B ASN* 1.3 74.6 + - - +
189B LYS* 1.3 65.9 + - - +
190B ARG 3.0 3.5 + - - -
191B TRP* 3.1 20.4 + - - +
192B ASN* 2.8 41.3 + - - +
199B LYS 5.3 0.2 - - - +
201B LEU* 3.3 47.2 + - + +
203B CYS* 4.2 9.4 - - - -
230B TYR* 3.7 11.4 - - + -
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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