Contacts of the strand formed by residues 279 - 285 (chain B) in PDB entry 3H90
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 ASP 279 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242B THR* 5.1 2.9 - - - +
243B ARG 2.7 9.9 + - - +
244B PHE* 3.4 29.8 - - + -
245B ILE 2.8 24.8 + - - +
277B GLY 5.3 0.7 - - - +
278B SER* 1.3 72.9 - - - +
280B VAL* 1.3 73.4 + - - +
281B ILE* 5.3 1.4 - - - +
235D ARG* 2.9 43.1 + - - -
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Residues in contact with VAL 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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245B ILE* 3.0 25.1 - - + +
268B GLU* 3.2 47.7 + - + +
271B ILE* 3.7 31.6 - - + -
272B LEU* 3.9 17.8 - - + +
278B SER* 4.3 0.6 + - - -
279B ASP* 1.3 86.6 - - - +
281B ILE* 1.3 65.7 + - - +
282B ILE* 3.9 16.2 - - + -
235D ARG* 5.4 0.2 + - - -
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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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245B ILE* 2.8 15.6 + - - +
246B GLN* 3.3 21.5 - - + +
247B ILE 3.2 23.0 + - - +
279B ASP* 5.3 2.7 - - - +
280B VAL* 1.3 76.3 - - - +
282B ILE* 1.3 69.7 + - - +
235D ARG* 5.6 1.1 - - - +
246D GLN* 3.8 50.5 - - + +
247D ILE 4.6 2.9 - - - +
248D HIS* 4.2 16.4 - - + +
281D ILE* 4.5 16.9 - - + +
283D HIS* 3.9 26.5 - - + +
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Residues in contact with ILE 282 (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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245B ILE* 6.1 0.4 - - + -
247B ILE* 3.5 25.4 - - + +
249B LEU* 3.7 38.8 - - + -
264B ALA* 3.9 30.7 - - + +
267B VAL* 4.7 9.4 - - + -
268B GLU* 4.3 15.9 - - + +
271B ILE* 4.7 4.0 - - + -
280B VAL* 3.9 24.9 - - + -
281B ILE* 1.3 78.4 - - - +
283B HIS* 1.3 65.4 + - - +
284B GLN* 3.7 3.4 - - + +
283D HIS* 2.9 37.5 + - + +
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Residues in contact with HIS 283 (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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247B ILE 2.9 9.5 + - - -
248B HIS* 3.2 35.7 - + + -
249B LEU 2.8 25.3 + - - -
281B ILE 4.1 0.2 + - - -
282B ILE* 1.3 73.2 - - - +
284B GLN* 1.3 60.7 + - - +
285B ASP* 3.0 7.0 + - - -
292B ZN 2.1 36.7 - - - -
261D HIS* 3.5 17.5 - + - -
264D ALA* 4.9 7.0 - - + -
268D GLU* 5.9 2.5 - - - -
281D ILE* 3.8 23.0 - - + +
282D ILE* 2.9 31.3 + - + +
284D GLN* 3.6 11.1 + - - -
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Residues in contact with GLN 284 (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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249B LEU* 3.4 5.6 - - + +
251B MET* 3.6 29.2 - - + -
257B LEU* 4.1 3.8 - - - +
260B ALA* 3.8 3.7 + - + -
261B HIS* 3.3 36.4 - - - +
264B ALA* 3.9 8.4 - - - +
282B ILE* 3.7 4.1 - - + +
283B HIS* 1.3 76.8 + - - +
285B ASP* 1.3 57.9 + - - +
257D LEU* 3.6 25.9 - - + +
261D HIS* 3.7 5.7 - - - -
283D HIS* 3.6 21.7 + - - -
284D GLN* 3.4 48.4 + - + +
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Residues in contact with ASP 285 (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 HIS* 2.9 15.8 - - + -
248B HIS* 3.1 4.8 + - - +
249B LEU 2.8 11.6 + - - +
250B GLU* 3.2 2.1 - - + -
251B MET 3.0 19.8 + - - -
283B HIS* 3.6 4.2 + - - +
284B GLN* 1.3 72.8 - - - +
286B PRO* 1.4 71.8 - - + +
288B SER* 5.1 4.9 - - - +
289B VAL* 5.6 3.8 - - + -
292B ZN 2.1 33.7 - - - -
294B ZN 2.0 36.4 - - - -
257D LEU* 3.9 4.0 - - - +
261D HIS* 2.6 14.0 + - - -
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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