Contacts of the strand formed by residues 260 - 271 (chain C) in PDB entry 2JIF
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 THR 260 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207C TRP* 3.6 43.5 - - + +
208C ILE 3.4 2.7 - - - -
209C SER* 4.4 1.2 + - - -
249C PRO* 3.4 3.5 - - - +
250C GLU* 2.8 39.5 + - + +
252C LYS* 3.3 26.2 - - + +
258C SER* 3.2 16.7 + - - -
259C SER* 1.3 74.9 + - - +
261C CYS* 1.3 58.7 + - - +
1433C FAD 3.7 26.6 - - + +
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Residues in contact with CYS 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C TRP 3.8 4.1 + - - -
208C ILE* 3.0 35.7 + - - +
211C ALA* 3.9 13.9 - - + -
212C GLU* 3.8 26.7 - - - -
246C ILE* 3.9 10.3 - - + -
247C GLY 3.5 24.0 - - - +
248C LYS 4.2 0.2 - - - -
249C PRO* 3.8 23.1 - - - -
250C GLU* 5.2 0.9 - - - -
259C SER* 4.3 0.2 - - - -
260C THR* 1.3 83.1 - - - +
262C PRO* 1.3 65.2 - - - +
263C LEU* 4.3 0.2 - - - +
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Residues in contact with PRO 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C LYS 3.7 8.7 - - - +
206C MET* 4.1 23.3 - - + -
247C GLY* 2.8 39.6 + - - -
248C LYS 3.3 19.3 - - - +
250C GLU* 4.0 14.6 - - - +
261C CYS* 1.3 87.0 - - + +
263C LEU* 1.3 63.6 + - - +
264C THR* 5.7 2.7 - - + -
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Residues in contact with LEU 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C CYS* 3.7 29.8 - - - -
204C SER* 3.2 4.2 - - - -
205C LYS* 2.9 35.2 + - + +
208C ILE* 3.9 16.2 - - + -
211C ALA* 4.0 17.9 - - + -
217C PHE* 3.8 12.3 - - + -
244C LEU* 4.6 4.0 - - + -
245C HIS 3.3 4.7 - - - +
246C ILE* 3.6 31.0 - - + -
261C CYS 3.8 1.5 + - - +
262C PRO* 1.3 83.9 - - - +
264C THR* 1.3 67.8 + - - +
265C PHE* 4.0 26.0 - - + -
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Residues in contact with THR 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C GLY 3.6 5.8 - - - -
204C SER* 4.3 11.7 - - - -
243C GLY 3.3 4.5 + - - +
244C LEU* 3.5 6.4 - - - +
245C HIS* 3.0 53.1 + - + +
262C PRO* 5.7 2.9 - - + -
263C LEU* 1.3 81.2 - - - +
265C PHE* 1.3 63.2 + - - +
266C GLU* 6.1 2.1 - - - +
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Residues in contact with PHE 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C THR* 4.7 5.8 - - + -
201C LEU* 3.7 26.7 - - + +
202C ASN* 3.4 6.9 - - - +
203C GLY 2.8 44.6 + - - +
204C SER* 4.5 2.5 - - - -
205C LYS* 3.9 24.0 - - + -
217C PHE* 5.5 0.7 - - + -
219C VAL* 3.8 38.6 - - + -
237C VAL* 4.8 2.2 - - + -
243C GLY 3.5 2.5 - - - -
244C LEU* 3.8 24.9 - - + -
263C LEU* 4.0 21.5 - - + -
264C THR* 1.3 76.5 - - - +
266C GLU* 1.3 61.3 + - - +
267C ASN 3.8 0.9 - - - -
268C VAL* 3.7 25.8 - - + -
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Residues in contact with GLU 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C ASN* 3.7 4.5 - - - +
242C PRO 4.6 0.2 - - - -
243C GLY* 2.8 34.6 + - - +
264C THR* 4.0 2.7 - - - +
265C PHE* 1.3 72.2 - - - +
267C ASN* 1.3 82.2 + - - +
268C VAL* 3.2 0.4 - - - +
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Residues in contact with ASN 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C VAL* 3.4 22.3 - - + +
201C LEU 3.3 2.3 + - - -
202C ASN* 2.8 39.2 + - - -
242C PRO* 4.1 5.7 - - - +
266C GLU* 1.3 84.9 + - - +
268C VAL* 1.3 64.0 + - - +
269C LYS* 3.5 21.7 + - - +
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Residues in contact with VAL 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C TYR 3.3 3.1 - - - +
200C VAL* 3.4 0.9 - - - -
201C LEU* 2.7 41.7 + - + +
237C VAL* 4.1 17.9 - - + -
241C THR* 3.7 22.2 - - + -
242C PRO 3.7 4.5 - - - +
243C GLY 3.3 36.8 - - - +
244C LEU* 3.5 7.0 - - + +
265C PHE* 3.7 32.5 - - + -
267C ASN* 1.3 75.5 - - - +
269C LYS* 1.3 62.2 + - - +
270C VAL* 3.8 9.8 + - + -
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Residues in contact with LYS 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C TYR* 3.6 39.2 + - + -
199C TYR 3.4 4.3 - - - -
200C VAL* 4.9 4.3 - - + -
237C VAL* 5.9 0.3 - - - +
241C THR* 4.0 16.0 + - - +
242C PRO* 4.7 3.1 + - - -
267C ASN* 3.6 21.8 - - - +
268C VAL* 1.3 74.0 - - - +
270C VAL* 1.3 62.7 + - - +
271C PRO* 4.1 5.4 - - - +
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Residues in contact with VAL 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C TYR* 3.3 3.2 - - - -
199C TYR* 2.8 41.0 + - + +
201C LEU* 4.0 23.6 - - + -
235C PHE* 4.0 22.7 - - + -
236C LEU 3.7 10.5 - - - +
237C VAL* 3.9 24.5 - - + -
268C VAL* 4.3 9.4 - - + -
269C LYS* 1.3 79.2 - - - +
271C PRO* 1.4 74.3 - - + +
274C ASN* 3.6 25.6 - - + -
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Residues in contact with PRO 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C ASP 3.9 7.9 - - - +
198C TYR* 4.1 4.2 - - + -
199C TYR* 5.1 0.2 - - - -
269C LYS 4.1 5.6 - - - +
270C VAL* 1.4 93.1 - - + +
272C GLU* 1.3 60.3 + - - +
273C ALA* 4.1 8.1 - - + +
274C ASN* 2.9 48.6 + - - +
275C ILE* 4.1 1.0 + - - +
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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