Contacts of the strand formed by residues 260 - 271 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207B TRP* 3.5 44.9 - - + +
208B ILE 3.4 3.6 - - - -
209B SER* 4.4 1.7 + - - -
249B PRO* 3.4 4.3 - - - +
250B GLU* 2.7 39.9 + - + +
252B LYS* 3.2 35.7 + - + +
258B SER* 3.4 3.7 + - - -
259B SER* 1.3 75.3 + - - +
261B CYS* 1.3 58.9 + - - +
1433B FAD 3.6 25.0 - - + +
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Residues in contact with CYS 261 (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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207B TRP 3.7 3.8 + - - -
208B ILE* 3.0 36.5 + - - +
211B ALA* 3.7 25.6 - - + -
212B GLU* 4.1 14.6 - - - -
246B ILE* 3.9 5.4 - - + -
247B GLY 3.6 24.5 - - - +
248B LYS 4.4 0.4 - - - -
249B PRO* 3.8 20.2 - - - -
250B GLU* 5.3 0.7 - - - -
259B SER* 4.3 3.1 - - - -
260B THR* 1.3 83.5 - - - +
262B PRO* 1.3 71.9 - - - +
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Residues in contact with PRO 262 (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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205B LYS 3.4 11.4 - - - +
206B MET* 4.1 19.5 - - + -
207B TRP 4.7 0.6 - - - -
247B GLY* 2.8 39.1 + - - -
248B LYS 3.5 19.1 - - - +
250B GLU* 4.1 16.8 - - - +
261B CYS* 1.3 88.1 - - + +
263B LEU* 1.3 65.2 + - - +
264B THR* 5.7 4.0 - - + -
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Residues in contact with LEU 263 (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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175B CYS* 3.7 29.4 - - - -
204B SER* 3.2 7.0 - - - -
205B LYS* 2.8 36.4 + - + +
208B ILE* 3.8 15.3 - - + -
211B ALA* 4.2 8.3 - - + -
217B PHE* 3.9 19.1 - - + -
244B LEU* 4.5 5.6 - - + -
245B HIS 3.3 4.0 - - - +
246B ILE* 3.9 33.4 - - + -
261B CYS 4.5 0.4 - - - +
262B PRO* 1.3 84.3 - - - +
264B THR* 1.3 64.2 + - - +
265B PHE* 3.8 29.8 - - + -
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Residues in contact with THR 264 (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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203B GLY 3.8 5.4 - - - -
204B SER* 4.6 8.1 - - - -
243B GLY 3.1 3.6 - - - +
244B LEU* 3.5 4.3 - - - +
245B HIS* 2.9 62.5 + - - +
262B PRO* 5.7 4.3 - - + -
263B LEU* 1.3 78.6 - - - +
265B PHE* 1.3 62.0 + - - +
266B GLU* 3.9 11.8 + - - +
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Residues in contact with PHE 265 (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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190B THR* 4.9 5.6 - - + -
201B LEU* 3.8 24.5 - - + +
202B ASN* 3.3 7.9 - - - +
203B GLY 2.8 45.5 + - - +
204B SER* 4.5 0.7 - - - -
205B LYS* 3.7 27.1 - - + -
217B PHE* 5.5 0.4 - - + -
219B VAL* 3.8 37.7 - - + -
237B VAL* 4.8 2.7 - - + -
243B GLY 3.6 2.9 - - - -
244B LEU* 3.7 24.0 - - + -
263B LEU* 3.8 23.1 - - + -
264B THR* 1.3 74.8 - - - +
266B GLU* 1.3 63.7 + - - +
267B ASN 3.7 0.7 - - - -
268B VAL* 3.6 28.7 - - + -
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Residues in contact with GLU 266 (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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202B ASN* 3.8 3.6 - - - -
243B GLY* 2.9 28.3 + - - +
245B HIS* 3.5 29.3 + - + +
264B THR* 4.3 10.1 + - - +
265B PHE* 1.3 73.0 - - - +
267B ASN* 1.3 75.8 + - - +
268B VAL 3.3 0.2 - - - -
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Residues in contact with ASN 267 (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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200B VAL* 3.5 21.6 - - + +
201B LEU 3.3 2.8 + - - -
202B ASN* 2.8 38.1 + - - -
242B PRO 4.0 5.7 - - - +
266B GLU* 1.3 78.2 - - - +
268B VAL* 1.3 62.9 + - - +
269B LYS* 3.6 20.3 + - - +
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Residues in contact with VAL 268 (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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199B TYR 3.4 2.6 - - - +
200B VAL* 3.4 0.3 - - - -
201B LEU* 2.7 38.6 + - + +
237B VAL* 4.0 26.5 - - + -
241B THR* 4.3 13.0 - - + -
242B PRO 3.8 4.7 - - - +
243B GLY 3.3 35.7 - - - +
244B LEU* 3.5 6.7 - - + +
265B PHE* 3.6 36.1 - - + -
266B GLU 3.9 0.2 - - - +
267B ASN* 1.3 74.5 - - - +
269B LYS* 1.3 61.8 + - - +
270B VAL* 3.8 8.8 + - + -
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Residues in contact with LYS 269 (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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198B TYR* 3.6 41.3 + - + -
199B TYR 3.3 3.8 - - - -
200B VAL* 4.6 6.1 - - + -
237B VAL* 5.9 0.2 - - - +
241B THR* 3.6 23.9 - - + +
242B PRO 4.6 0.8 + - - +
267B ASN* 3.6 22.6 + - - +
268B VAL* 1.3 74.3 - - - +
270B VAL* 1.3 61.9 + - - +
271B PRO* 4.1 5.2 - - - +
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Residues in contact with VAL 270 (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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198B TYR* 3.3 2.6 - - - -
199B TYR* 2.8 41.5 + - + +
201B LEU* 4.0 21.8 - - + -
235B PHE* 4.2 22.2 - - + -
236B LEU 3.5 24.7 - - - +
237B VAL* 3.7 26.2 - - + -
268B VAL* 4.3 8.7 - - + +
269B LYS* 1.3 77.2 - - - +
271B PRO* 1.4 70.7 - - + +
274B ASN* 3.5 18.2 - - + -
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Residues in contact with PRO 271 (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 ASP 3.8 9.0 - - - +
198B TYR* 4.1 4.0 - - + -
199B TYR* 5.2 0.3 - - - -
235B PHE* 5.6 0.2 - - - -
269B LYS 4.1 5.4 - - - +
270B VAL* 1.4 93.9 - - + +
272B GLU* 1.3 59.0 + - - +
273B ALA* 4.2 9.6 - - + +
274B ASN* 2.8 47.3 + - - +
275B ILE* 4.1 0.9 + - - +
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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