Contacts of the strand formed by residues 260 - 271 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A TRP* 3.7 42.6 - - + +
208A ILE 3.4 4.3 - - - -
209A SER* 4.4 1.6 + - - -
249A PRO* 3.3 4.0 - - - +
250A GLU* 2.8 40.6 + - + +
252A LYS* 3.2 25.2 + - + +
258A SER* 3.2 15.8 + - - -
259A SER* 1.3 73.6 + - - +
261A CYS* 1.3 58.6 + - - +
1433A FAD 3.7 26.1 - - + +
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Residues in contact with CYS 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A TRP 3.7 3.3 + - - -
208A ILE* 3.0 36.6 + - - +
211A ALA* 3.8 25.4 - - + -
212A GLU* 4.1 11.9 - - - -
246A ILE* 3.9 7.4 - - + -
247A GLY 3.6 19.3 - - - +
248A LYS 4.2 0.2 - - - -
249A PRO* 3.9 21.1 - - - -
250A GLU* 5.7 0.7 - - - -
259A SER* 4.3 2.5 - - - -
260A THR* 1.3 83.6 - - - +
262A PRO* 1.3 76.4 - - + +
263A LEU* 4.5 0.2 - - - +
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Residues in contact with PRO 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A LYS 3.4 12.8 - - - +
206A MET* 4.0 24.2 - - + -
207A TRP 4.7 0.6 - - - -
246A ILE* 3.8 0.2 - - - -
247A GLY* 2.8 40.1 + - - -
248A LYS 3.2 21.5 - - - +
250A GLU* 4.8 10.5 - - - +
260A THR 4.5 1.1 - - - +
261A CYS* 1.3 87.7 - - + +
263A LEU* 1.3 63.9 + - - +
264A THR* 5.8 2.2 - - + -
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Residues in contact with LEU 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A CYS* 3.6 31.0 - - - -
204A SER* 3.2 6.8 - - - -
205A LYS* 2.9 35.3 + - + +
208A ILE* 3.8 16.8 - - + -
211A ALA* 4.2 7.6 - - + -
217A PHE* 3.8 19.3 - - + -
244A LEU* 4.3 5.6 - - + -
245A HIS 3.3 5.4 - - - +
246A ILE* 3.8 34.1 - - + -
261A CYS 4.6 0.4 - - - +
262A PRO* 1.3 84.0 - - - +
264A THR* 1.3 65.7 + - - +
265A PHE* 4.1 24.9 - - + -
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Residues in contact with THR 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A GLY 3.5 7.0 - - - -
204A SER* 4.2 10.3 - - - +
243A GLY 3.4 2.8 - - - +
244A LEU* 3.6 6.4 - - - +
245A HIS* 3.1 54.3 + - - +
262A PRO* 5.8 2.5 - - + -
263A LEU* 1.3 79.6 - - - +
265A PHE* 1.3 64.1 + - - +
266A GLU* 4.1 7.9 + - - +
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Residues in contact with PHE 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A THR* 4.5 6.7 - - + -
201A LEU* 3.8 26.0 - - + +
202A ASN* 3.3 7.2 - - - +
203A GLY 2.7 44.9 + - - +
204A SER* 4.3 2.0 - - - -
205A LYS* 3.8 24.9 - - + -
217A PHE* 5.7 0.2 - - + -
219A VAL* 3.6 39.0 - - + -
237A VAL* 4.8 4.7 - - + -
243A GLY 3.6 2.7 - - - -
244A LEU* 3.7 27.6 - - + -
263A LEU* 4.1 18.8 - - + -
264A THR* 1.3 73.2 - - - +
266A GLU* 1.3 63.4 + - - +
267A ASN 3.9 0.9 - - - -
268A VAL* 3.8 22.2 - - + -
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Residues in contact with GLU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ASN* 3.5 4.7 - - - -
243A GLY* 2.9 31.7 + - - +
245A HIS* 4.1 20.5 + - - +
264A THR* 5.1 6.4 + - - +
265A PHE* 1.3 76.1 - - - +
267A ASN* 1.3 75.2 + - - +
268A VAL* 3.1 1.1 + - - +
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Residues in contact with ASN 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A VAL* 3.5 22.5 - - + +
201A LEU 3.3 2.3 + - - -
202A ASN* 2.9 35.6 + - - +
242A PRO 4.3 4.0 - - - +
266A GLU* 1.3 75.6 - - - +
268A VAL* 1.3 63.0 + - - +
269A LYS* 3.3 14.2 + - + +
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Residues in contact with VAL 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A TYR 3.4 4.3 - - - +
200A VAL* 3.4 0.4 - - - -
201A LEU* 2.8 39.8 + - + +
237A VAL* 4.1 15.0 - - + -
241A THR* 3.6 21.8 - - + -
242A PRO 3.8 5.6 - - - +
243A GLY 3.3 36.1 - - - +
244A LEU* 3.5 5.8 - - - +
265A PHE* 3.8 28.7 - - + -
266A GLU 4.0 0.2 - - - +
267A ASN* 1.3 73.7 - - - +
269A LYS* 1.3 60.5 + - - +
270A VAL* 3.6 15.6 + - + +
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Residues in contact with LYS 269 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A TYR* 5.2 13.9 - - + -
199A TYR 3.5 4.7 - - - -
200A VAL* 4.4 15.9 - - + +
241A THR* 3.8 19.5 - - + +
242A PRO 4.6 1.2 + - - -
267A ASN* 3.3 13.6 + - + +
268A VAL* 1.3 72.0 - - - +
270A VAL* 1.3 60.4 + - - +
271A PRO* 4.2 4.6 - - - +
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Residues in contact with VAL 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A TYR* 3.2 4.7 - - - +
199A TYR* 2.7 44.1 + - + +
201A LEU* 3.7 26.7 - - + -
235A PHE* 4.2 16.6 - - + -
236A LEU 3.9 9.9 - - - +
237A VAL* 4.2 15.0 - - + -
241A THR* 5.5 0.4 - - + -
268A VAL* 3.8 16.6 - - + +
269A LYS* 1.3 77.2 - - - +
271A PRO* 1.3 70.6 - - + +
274A ASN* 3.3 31.9 - - + +
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Residues in contact with PRO 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A ASP 3.9 1.3 - - - +
198A TYR* 3.6 26.9 - - + -
199A TYR* 5.4 0.7 - - - -
235A PHE* 5.4 0.3 - - - -
269A LYS 4.2 4.5 - - - +
270A VAL* 1.3 94.0 - - + +
272A GLU* 1.3 60.4 + - - +
273A ALA* 4.2 7.9 - - + +
274A ASN* 2.9 46.6 + - - +
275A ILE* 4.2 1.4 + - - +
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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