Contacts of the strand formed by residues 210 - 224 (chain B) in PDB entry 6C3P
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 210 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B ARG* 4.2 14.0 - - + +
181B LEU* 5.3 16.4 - - + -
204B ASP* 4.7 9.2 - - - +
208B SER 4.0 1.4 + - - -
209B MET* 1.3 87.4 - - - +
211B ILE* 1.3 62.0 + - - +
212B SER 4.2 0.5 + - - -
213B ALA* 3.6 25.5 + - + +
250B PHE* 5.7 2.9 - - - -
251B LEU* 4.8 18.7 + - + +
287B LEU* 5.9 4.9 - - + -
288B GLU 5.2 0.2 - - - -
289B GLY* 3.4 33.2 - - - +
290B VAL 3.2 19.5 - - - +
291B VAL* 3.8 6.1 - - + +
298B THR* 4.1 16.8 - - + -
288C GLU* 5.0 0.5 - - - +
299C GLN* 3.8 2.8 - - - +
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Residues in contact with ILE 211 (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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209B MET* 3.6 8.3 - - + +
210B ILE* 1.3 71.8 - - - +
212B SER* 1.3 78.3 + - - +
213B ALA 3.1 1.6 - - - -
289B GLY* 3.1 2.8 - - - -
290B VAL* 2.7 55.4 + - + +
291B VAL 4.0 2.5 - - - +
292B GLU* 3.5 32.3 - - + -
288C GLU* 3.5 23.3 - - + +
297C THR* 3.7 31.0 - - + +
298C THR* 4.8 1.1 - - - -
299C GLN* 3.4 33.7 - - + +
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Residues in contact with SER 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ILE 4.2 0.2 + - - -
211B ILE* 1.3 78.3 - - - +
213B ALA* 1.3 58.1 + - - +
214B THR* 2.7 26.9 + - - -
248B SER* 4.3 10.9 + - - -
249B ILE 5.2 2.2 + - - -
288B GLU 3.1 6.6 - - - +
289B GLY* 4.0 1.5 - - - -
290B VAL* 5.4 5.2 - - - -
216C HIS* 6.1 1.1 - - - -
288C GLU* 3.1 30.1 + - - -
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Residues in contact with ALA 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ILE* 3.6 28.9 + - + +
211B ILE 3.1 3.7 - - - -
212B SER* 1.3 72.5 - - - +
214B THR* 1.3 55.2 + - - +
248B SER* 3.2 2.6 - - - -
249B ILE* 2.6 63.9 + - + +
251B LEU* 5.1 3.4 - - + +
287B LEU* 4.2 12.8 - - + -
288B GLU 3.4 7.2 - - - -
289B GLY* 4.3 2.5 - - - -
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Residues in contact with THR 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B SER* 2.7 23.6 + - - -
213B ALA* 1.3 72.6 - - - +
215B ILE* 1.3 66.0 + - - +
216B HIS* 3.3 29.7 + - + -
247B ASN* 3.2 22.9 - - + +
248B SER* 3.5 13.0 + - - +
286B ILE 3.4 5.7 - - - +
287B LEU* 3.4 3.2 - - - +
288B GLU* 2.8 37.7 + - - +
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Residues in contact with ILE 215 (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 PHE* 5.7 1.1 - - + -
202B VAL* 5.3 5.4 - - + -
214B THR* 1.3 73.0 - - - +
216B HIS* 1.3 65.0 + - - +
217B MET* 3.8 27.1 - - + +
240B MET* 3.6 16.2 - - + -
247B ASN* 2.7 38.5 + - - +
249B ILE* 3.9 28.9 - - + -
257B ILE* 3.9 30.3 - - + -
285B VAL* 5.0 10.1 - - + -
286B ILE 3.3 8.1 - - - +
287B LEU* 3.6 29.4 - - + -
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Residues in contact with HIS 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A SER* 6.2 0.9 - - - -
244A VAL* 6.4 2.0 - - + -
248A SER* 4.0 29.3 + - - -
250A PHE* 6.4 0.9 - - + -
214B THR* 3.3 32.3 + - + +
215B ILE* 1.3 76.0 + - - +
217B MET* 1.3 66.6 + - - +
218B GLN* 4.1 4.4 - - - +
237B ASP* 5.5 12.6 - - + +
247B ASN* 4.5 13.6 + - - +
284B ILE 3.2 4.3 - - - +
286B ILE* 3.0 56.9 + - + +
288B GLU* 4.5 11.9 + - - -
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Residues in contact with MET 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B PHE* 4.5 14.4 - - - -
200B LEU* 3.9 16.2 - - - -
215B ILE* 3.8 15.1 - - + +
216B HIS* 1.3 75.3 - - - +
218B GLN* 1.3 60.1 + - - +
237B ASP* 3.7 4.3 - - - +
238B ILE* 3.0 41.0 + - + +
239B PRO 4.4 0.4 - - - +
240B MET* 3.5 39.6 - - + +
247B ASN* 5.9 0.4 - - - +
257B ILE* 3.6 17.3 - - + -
258B TYR 3.8 8.1 - - - -
259B HIS* 3.7 25.4 - - + -
283B ILE* 4.5 4.5 - - + -
284B ILE 3.3 6.1 - - - +
285B VAL* 4.4 14.8 - - + +
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Residues in contact with GLN 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ILE* 5.6 0.4 - - - +
250A PHE* 3.1 38.2 - - - +
216B HIS* 4.1 5.6 - - - +
217B MET* 1.3 77.3 - - - +
219B VAL* 1.3 58.4 + - - +
220B VAL* 4.6 3.6 - - + -
235B GLN* 3.1 41.4 + - + +
236B VAL 3.4 17.3 - - - +
237B ASP* 3.0 26.4 + - - +
238B ILE* 3.6 1.4 - - - +
283B ILE* 4.0 2.6 - - - +
284B ILE* 2.2 52.4 + - + +
286B ILE* 4.0 4.9 - - - +
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Residues in contact with VAL 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B GLN* 1.3 72.5 - - - +
220B VAL* 1.3 67.2 + - - +
221B ARG* 4.5 8.3 - - - +
234B HIS* 3.9 0.7 - - - +
235B GLN* 3.6 0.2 - - - -
236B VAL* 2.9 52.2 + - + +
238B ILE* 3.9 9.9 - - + +
266B PRO* 4.2 12.8 - - + -
267B LEU* 3.9 25.8 - - + -
281B LEU* 4.0 17.5 - - + -
282B GLU 3.2 12.1 - - - +
283B ILE* 3.7 20.6 - - + +
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Residues in contact with VAL 220 (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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250A PHE* 6.5 0.2 - - + -
35B PHE* 4.7 10.1 - - + -
218B GLN* 4.0 4.9 - - + +
219B VAL* 1.3 82.7 - - - +
221B ARG* 1.3 62.4 + - - +
233B LEU* 5.2 11.7 - - + -
234B HIS 3.0 14.6 - - - +
235B GLN* 3.6 24.2 - - + +
281B LEU 3.8 1.0 - - - -
282B GLU* 2.5 62.1 + - + +
284B ILE* 3.6 31.0 - - + -
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Residues in contact with ARG 221 (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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219B VAL* 4.5 11.7 - - - +
220B VAL* 1.3 75.2 - - - +
222B LYS* 1.3 62.7 + - - +
223B THR* 3.8 28.0 - - + +
232B PRO 3.4 5.8 - - - -
233B LEU* 4.7 3.8 - - - +
234B HIS* 2.8 35.8 + - + +
266B PRO* 4.2 27.4 + - - +
267B LEU* 4.8 5.5 - - - +
270B LEU* 5.7 3.2 - - - +
280B ASP* 3.2 30.8 + - - +
281B LEU* 3.4 28.1 - - - +
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Residues in contact with LYS 222 (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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221B ARG* 1.3 73.3 - - - +
223B THR* 1.3 60.0 + - - +
224B THR* 4.6 1.0 + - - -
230B VAL* 3.5 32.8 - - + +
231B VAL 3.4 9.0 - - - +
232B PRO* 3.0 28.0 + - + +
280B ASP* 2.7 23.7 + - - +
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Residues in contact with THR 223 (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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221B ARG* 3.3 22.7 + - + +
222B LYS* 1.3 73.5 - - - +
224B THR* 1.3 77.9 + - - +
229B GLU 4.1 0.5 - - - +
230B VAL* 3.2 15.1 - - - +
231B VAL* 3.3 15.0 + - + +
234B HIS* 3.3 42.2 - - + +
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Residues in contact with THR 224 (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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193A HIS* 5.8 0.5 + - - -
222B LYS 4.6 1.0 + - - -
223B THR* 1.3 90.8 + - - +
225B SER* 1.3 75.2 + - - +
226B PRO* 4.6 1.0 - - - +
228B GLY* 3.1 30.7 - - - +
229B GLU 3.3 6.1 - - - +
230B VAL* 3.2 18.5 - - + +
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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