Contacts of the strand formed by residues 293 - 299 (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 PHE 293 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229B LEU* 3.9 18.6 - - + -
243B TRP* 3.3 21.5 - + + -
244B LYS 3.9 4.0 - - - -
245B TRP* 3.3 40.6 - + + -
250B ILE* 5.4 2.0 - - + -
257B LEU* 4.1 14.8 - - + -
279B LEU* 3.7 21.1 - - + -
281B ILE* 3.6 23.8 - - + -
288B PHE* 3.7 28.3 - + + -
291B HIS 4.7 1.8 - - - -
292B PRO* 1.3 70.5 - - - +
294B THR* 1.3 59.1 + - - +
307B TYR* 3.3 0.8 - - - -
308B ILE 2.9 33.4 + - - +
310B LEU* 3.8 24.7 - - + -
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Residues in contact with THR 294 (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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242B TYR 4.0 0.2 - - - +
243B TRP* 3.1 8.8 - - - -
244B LYS 2.9 34.7 + - - +
246B ASN 5.5 1.2 + - - -
292B PRO* 3.8 12.1 + - - +
293B PHE* 1.3 74.1 - - - +
295B CYS* 1.3 62.0 + - - +
296B PHE* 4.0 20.8 - - + -
305B ALA* 4.1 13.7 - - + -
306B ALA 3.5 26.2 - - - +
307B TYR* 3.8 12.1 - - + +
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Residues in contact with CYS 295 (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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211B ILE* 3.2 19.7 - - + +
214B PRO* 4.0 4.7 - - + -
231B CYS* 2.0 50.0 - - + -
233B VAL* 5.0 0.2 - - - -
241B ALA* 4.7 1.8 - - - -
242B TYR 3.5 15.7 - - - -
243B TRP* 3.8 16.2 - - + -
294B THR* 1.3 74.5 - - - +
296B PHE* 1.3 72.8 + - - +
305B ALA* 3.5 2.8 - - - -
306B ALA 2.8 26.2 + - - +
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Residues in contact with PHE 296 (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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240B ILE 3.5 1.4 - - - +
241B ALA* 3.2 7.3 - - - -
242B TYR* 2.8 65.1 + + + +
244B LYS* 3.4 53.4 - - + -
294B THR* 4.0 24.5 - - + -
295B CYS* 1.3 77.0 - - - +
297B ALA* 1.3 59.5 + - - +
298B LYS 3.9 0.2 - - - -
303B ILE* 3.9 19.7 - - + -
304B ASP 3.2 12.8 - - - +
305B ALA* 3.7 20.6 - - + -
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Residues in contact with ALA 297 (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 PRO* 3.3 30.6 - - + +
211B ILE* 3.6 25.7 - - + +
233B VAL* 4.1 13.5 - - + -
240B ILE 3.4 6.7 - - - -
296B PHE* 1.3 72.0 - - - +
298B LYS* 1.3 58.2 + - - +
303B ILE* 3.2 5.3 - - - -
304B ASP* 2.8 39.8 + - + +
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Residues in contact with LYS 298 (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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51A GLU* 3.1 38.2 + - - +
53A ASN* 4.5 12.7 - - - +
55A LYS 4.5 2.2 + - - -
56A ILE* 4.1 23.8 - - + +
209B PRO* 4.1 1.7 - - - +
238B SER 4.6 0.5 - - - +
239B ASP* 3.6 2.9 - - - +
240B ILE* 3.0 55.9 + - + +
242B TYR* 3.1 32.8 + - + -
296B PHE 3.9 0.8 - - - -
297B ALA* 1.3 76.1 - - - +
299B ASN* 1.3 78.4 + - - +
302B GLY 4.1 2.7 - - - -
303B ILE* 3.9 34.0 - - + +
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Residues in contact with ASN 299 (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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53A ASN* 4.6 4.9 + - - +
56A ILE* 4.3 11.3 - - - +
207B THR 3.0 27.5 + - - +
208B ARG* 4.0 0.9 - - - +
209B PRO* 3.7 8.1 - - - +
236B GLN* 6.1 0.8 - - - +
238B SER 4.8 5.6 - - - +
239B ASP* 3.0 31.5 + - - +
298B LYS* 1.3 82.6 - - - +
300B THR* 1.3 63.8 + - - +
301B HIS* 2.9 28.2 + - - +
302B GLY 3.2 21.9 + - - +
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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