Contacts of the strand formed by residues 273 - 281 (chain B) in PDB entry 1ITB
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 SER 273 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233B VAL 3.6 0.2 - - - +
234B THR* 3.4 3.8 - - - -
235B GLY 2.7 38.7 + - - +
236B GLN 4.8 0.7 - - - -
237B LEU* 3.5 20.4 - - - +
264B VAL 3.3 15.7 - - - -
265B GLU* 3.8 3.6 - - - -
266B ASN* 3.0 20.5 + - - -
270B LYS* 2.9 20.8 + - - -
272B ARG* 1.3 74.6 - - - +
274B THR* 1.3 65.7 + - - +
275B LEU* 4.2 1.9 + - - +
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Residues in contact with THR 274 (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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232B ASN* 3.9 14.8 - - - +
233B VAL 3.1 9.9 - - - +
234B THR* 4.3 12.1 - - + +
263B SER* 3.5 2.3 - - - -
264B VAL* 3.1 45.3 + - - +
272B ARG 5.0 3.6 - - - +
273B SER* 1.3 80.2 - - - +
275B LEU* 1.3 64.6 + - - +
276B ILE* 4.0 9.8 + - - +
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Residues in contact with LEU 275 (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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4A ARG* 3.2 31.4 - - - +
231B CYS 3.5 2.0 - - - +
233B VAL* 2.9 54.6 + - + +
235B GLY 5.2 1.1 - - - +
236B GLN 3.8 13.2 - - - +
237B LEU* 4.3 4.3 - - + -
239B ASP* 3.1 38.8 - - + +
240B ILE* 4.2 7.6 - - - +
241B ALA* 4.1 12.1 - - + +
262B TYR 3.7 4.3 - - - +
263B SER* 3.4 10.3 - - - +
273B SER* 5.0 2.9 - - - +
274B THR* 1.3 77.9 - - - +
276B ILE* 1.3 67.1 + - - +
277B THR* 4.2 1.1 - - - -
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Residues in contact with ILE 276 (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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230B ILE* 3.9 21.8 - - + -
231B CYS 3.5 1.6 - - - +
232B ASN* 3.8 31.0 - - + +
260B ASP 3.7 1.0 - - - +
261B TYR* 3.7 1.6 - - - +
262B TYR* 2.8 53.3 + - + +
264B VAL* 5.3 7.0 - - + -
274B THR* 4.3 14.6 - - - +
275B LEU* 1.3 84.6 - - - +
277B THR* 1.3 63.2 + - - +
278B VAL* 4.0 14.6 - - + -
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Residues in contact with THR 277 (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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230B ILE* 3.7 0.3 - - - -
231B CYS* 3.0 34.1 + - - -
241B ALA* 2.7 44.3 + - - +
243B TRP* 3.2 17.9 + - + -
259B GLU* 3.4 26.5 - - + +
260B ASP 3.6 3.4 - - - +
261B TYR* 3.4 22.6 - - + +
275B LEU* 5.3 0.2 - - - +
276B ILE* 1.3 73.8 + - - +
278B VAL* 1.3 62.2 + - - +
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Residues in contact with VAL 278 (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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228B GLN* 3.7 36.6 - - + +
229B LEU 3.7 2.7 - - - -
230B ILE* 4.1 20.9 - - + +
243B TRP* 4.5 2.2 - - - -
258B GLY 3.3 2.1 - - - +
259B GLU* 3.1 7.9 - - - -
260B ASP* 2.9 48.1 + - + +
262B TYR* 4.5 11.7 - - + -
276B ILE* 4.0 19.5 - - + -
277B THR* 1.3 74.1 - - - +
279B LEU* 1.3 61.0 + - - +
280B ASN* 3.8 12.0 + - - +
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Residues in contact with LEU 279 (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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227B ILE 3.9 0.5 - - - +
228B GLN* 3.3 5.4 - - - +
229B LEU* 2.8 65.2 + - + +
243B TRP* 3.7 28.5 - - + +
250B ILE* 4.1 21.3 - - + -
257B LEU* 4.4 6.3 - - + -
258B GLY 3.5 21.8 - - - +
259B GLU* 4.6 3.1 - - + +
277B THR 3.8 0.4 + - - -
278B VAL* 1.3 71.2 - - - +
280B ASN* 1.3 67.5 - - - +
281B ILE* 3.9 12.9 + - + +
293B PHE* 3.7 34.1 - - + -
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Residues in contact with ASN 280 (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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226B GLN* 5.8 4.1 + - - +
227B ILE 3.8 3.8 - - - +
228B GLN* 3.0 36.5 + - - +
256B VAL 3.0 13.3 - - - +
257B LEU* 3.5 1.6 - - - -
258B GLY* 2.9 35.6 + - - +
259B GLU 4.9 0.2 - - - -
260B ASP* 4.4 11.5 + - - +
278B VAL* 3.8 16.8 + - - +
279B LEU* 1.3 74.3 - - - +
281B ILE* 1.3 61.3 + - - +
282B SER* 3.8 1.1 - - - +
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Residues in contact with ILE 281 (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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226B GLN* 3.0 8.5 + - - +
227B ILE* 3.0 63.3 + - + +
229B LEU* 4.2 4.7 - - + -
256B VAL 3.3 3.6 - - - +
257B LEU* 3.6 14.4 - - + -
279B LEU* 3.9 16.8 - - + +
280B ASN* 1.3 73.7 - - - +
282B SER* 1.3 61.4 + - - +
283B GLU 3.4 13.2 - - - +
284B ILE* 4.3 3.8 - - + -
288B PHE* 3.6 31.6 - - + -
293B PHE* 3.6 32.5 - - + -
310B LEU* 4.4 3.8 - - + -
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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