Contacts of the strand formed by residues 197 - 210 (chain B) in PDB entry 1O9T
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 197 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B TYR* 3.6 3.6 - - - -
190B VAL* 3.1 38.8 + - + +
191B GLN 5.0 0.7 - - - +
192B ASP* 3.5 40.8 - - + +
195B ALA 4.3 1.3 - - - +
196B VAL* 1.3 78.0 - - - +
198B PRO* 1.4 77.5 - - + +
199B VAL* 3.6 5.4 + - + +
235B LYS* 6.1 1.6 - - - +
313B ARG* 4.1 23.6 - - - +
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Residues in contact with PRO 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B GLU* 3.6 33.2 - - + +
153B LEU* 3.5 28.3 - - + -
187B VAL* 4.0 4.0 - - + -
188B GLN 4.0 2.0 - - - +
189B TYR* 3.6 23.8 - - + -
197B ILE* 1.4 95.8 - - + +
199B VAL* 1.3 60.5 + - - +
235B LYS* 4.2 7.8 + - - -
236B TYR* 3.9 25.1 - - + +
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Residues in contact with VAL 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B GLN* 2.8 23.0 + - + +
189B TYR 4.0 3.8 - - - +
190B VAL* 4.0 24.5 - - + -
197B ILE* 3.9 11.7 - - + +
198B PRO* 1.3 77.2 - - - +
200B ARG* 1.3 71.3 + - + +
235B LYS* 4.1 15.4 + - - +
236B TYR* 3.8 11.9 - - - -
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Residues in contact with ARG 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B VAL* 3.1 8.3 - - - +
188B GLN* 2.6 57.1 + - + +
199B VAL* 1.3 90.4 - - + +
201B VAL* 1.3 59.8 + - - +
202B HIS* 3.6 35.9 + - - +
235B LYS 5.1 1.3 - - - +
236B TYR* 3.6 19.5 - - - +
238B ASP* 3.1 43.8 + - - +
240B ASP* 3.7 15.5 + - - +
241B THR* 3.3 19.8 + - - +
242B ILE* 5.7 0.2 - - - +
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Residues in contact with VAL 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU* 4.0 15.5 - - + -
185B VAL* 4.4 5.8 - - + -
186B THR 3.9 6.3 - - - +
187B VAL* 4.0 9.2 - - + -
200B ARG* 1.3 73.5 + - - +
202B HIS* 1.3 63.8 + - - +
203B THR 4.0 8.5 - - - +
204B ILE* 3.4 37.2 - - + -
232B VAL* 3.9 17.5 - - + -
236B TYR* 3.0 32.4 + - + +
237B LEU* 4.6 2.2 - - + -
241B THR* 2.9 32.7 + - + +
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Residues in contact with HIS 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A LEU* 3.7 35.2 - - + +
20B MET* 3.7 16.9 - - + +
186B THR* 2.9 23.7 + - - +
188B GLN* 3.5 39.0 + - + -
200B ARG* 3.3 25.6 + - - +
201B VAL* 1.3 72.3 - - - +
203B THR* 1.3 67.6 + - + +
241B THR* 3.5 3.1 - - - -
242B ILE* 2.8 44.5 + - + +
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Residues in contact with THR 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLN* 3.5 20.3 - - - +
322A ALA* 5.8 0.4 - - + -
329A LEU* 4.7 2.7 - - + -
186B THR* 3.1 54.0 + - + +
201B VAL* 3.5 1.8 - - - +
202B HIS* 1.3 100.6 - - + +
204B ILE* 1.3 71.9 + - - +
205B VAL* 4.3 0.2 - - - +
241B THR* 4.6 0.2 - - - -
242B ILE* 3.0 26.1 + - + +
244B HIS* 3.7 19.8 - - - -
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Residues in contact with ILE 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LEU* 3.7 27.6 - - + -
184B GLN 3.6 6.3 - - - +
185B VAL* 4.7 8.7 - - + -
201B VAL* 3.4 31.2 - - + -
203B THR* 1.3 73.5 + - - +
205B VAL* 1.3 66.0 + - - +
206B ILE* 4.1 6.2 + - + -
228B ILE* 3.6 44.2 - - + -
232B VAL* 4.4 13.0 - - + -
237B LEU* 4.6 3.6 - - + -
241B THR* 4.8 1.1 - - + -
242B ILE 2.7 11.6 + - - +
243B TYR* 3.5 12.2 - - + +
244B HIS* 2.8 26.7 + - - +
245B LEU* 4.6 0.7 - - - +
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Residues in contact with VAL 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLN* 3.2 35.4 - - + +
323A ILE* 4.7 6.7 - - + -
182B LYS* 4.7 0.6 - - + -
183B THR* 3.5 3.5 - - - +
184B GLN* 2.8 59.1 + - + +
203B THR* 4.3 0.7 - - - +
204B ILE* 1.3 74.3 - - - +
206B ILE* 1.3 66.1 + - - +
207B SER* 4.8 5.4 - - - +
244B HIS* 3.3 32.8 - - + +
247B PRO* 4.1 15.5 - - + -
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Residues in contact with ILE 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LEU* 4.7 10.8 - - + -
165B MET* 3.3 43.1 - - + -
182B LYS 3.4 8.1 - - - +
183B THR* 4.4 6.7 - - - +
204B ILE* 4.1 12.3 - - + -
205B VAL* 1.3 77.9 - - - +
207B SER* 1.3 67.9 + - - +
223B LEU* 3.7 18.1 - - + +
227B VAL* 4.1 13.5 - - + -
228B ILE* 4.2 4.5 - - + -
244B HIS 3.0 5.0 + - - +
245B LEU* 3.3 32.6 - - + -
246B GLN* 2.9 26.3 + - - +
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Residues in contact with SER 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B SER* 3.1 4.6 - - - -
182B LYS* 2.7 49.1 + - - +
205B VAL* 4.8 5.0 - - - +
206B ILE* 1.3 77.0 - - - +
208B VAL* 1.3 62.7 + - - +
246B GLN* 3.0 8.1 - - - -
247B PRO* 3.5 20.4 - - - +
248B SER* 5.0 5.8 + - - -
251B PHE* 4.4 14.3 - - - -
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Residues in contact with VAL 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B MET* 3.5 31.6 - - + -
176B TRP* 4.5 1.8 - - + -
177B LEU* 3.5 26.9 - - + -
178B ARG 3.6 13.7 - - - +
180B ASP 3.5 5.8 - - - +
181B SER* 3.8 9.4 - - - -
207B SER* 1.3 76.7 - - - +
209B GLN* 1.3 75.9 + - - +
210B HIS* 3.5 3.5 + - - -
219B MET* 4.3 4.7 - - + -
223B LEU* 4.5 5.2 - - + -
246B GLN* 2.7 49.5 + - - +
251B PHE* 3.5 9.3 - - - +
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Residues in contact with GLN 209 (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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93B TYR* 3.5 14.1 + - - -
98B LYS 2.8 25.7 + - - +
177B LEU* 4.0 1.2 - - - -
178B ARG* 3.1 41.0 + - + +
179B PRO 4.0 1.2 - - - -
180B ASP* 2.7 45.2 + - - +
208B VAL* 1.3 84.8 - - - +
210B HIS* 1.3 59.9 + - - +
251B PHE* 3.1 23.6 - - + +
252B VAL 3.1 29.5 - - - +
254B GLY 4.2 0.7 - - - -
255B GLY* 3.4 10.6 + - - -
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Residues in contact with HIS 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B TRP* 3.2 15.3 - - + +
178B ARG* 3.1 26.2 + - - +
208B VAL 3.5 8.1 + - - -
209B GLN* 1.3 77.3 - - - +
211B ASN* 1.3 82.8 + - - +
214B ILE* 4.4 1.8 - - + -
219B MET* 3.2 43.8 - - + +
246B GLN* 3.6 3.8 + - - -
249B GLY 4.4 2.0 - - - -
250B ARG* 3.6 24.4 + - - +
251B PHE* 2.9 37.4 + - + -
252B VAL* 3.3 33.8 - - + +
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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