Contacts of the strand formed by residues 292 - 299 (chain B) in PDB entry 2A1A
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 292 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B LYS* 3.9 30.1 - - + -
284B ALA* 3.2 14.4 - - - +
285B LYS* 4.2 17.3 - - - +
290B GLY 5.1 0.3 + - - -
291B LYS* 1.3 89.5 - - - +
293B TYR* 1.3 68.0 + - - +
368B PHE* 4.0 28.0 + - + +
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Residues in contact with TYR 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B PHE* 4.4 3.1 - + + -
283B LYS* 3.7 3.5 - - - +
284B ALA 2.8 31.2 + - - +
286B HIS* 4.1 7.4 - - + -
289B ASP* 2.8 34.3 + - - -
291B LYS* 3.1 59.3 + - + +
292B THR* 1.3 78.4 - - - +
294B VAL* 1.3 63.6 + - - +
295B ILE* 3.9 6.8 - - + +
324B ASN* 3.3 41.8 + - + -
365B GLN* 3.3 36.8 - - + -
366B MET 3.5 5.6 - - - +
367B GLU* 5.3 0.7 - - - -
368B PHE* 4.2 6.1 - - - +
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Residues in contact with VAL 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ILE* 3.9 14.1 - - + -
281B VAL* 3.7 21.1 - - + -
282B PHE 3.2 9.9 - - - +
283B LYS* 4.8 0.7 - - - -
293B TYR* 1.3 76.0 - - - +
295B ILE* 1.3 65.0 + - - +
296B LYS 4.5 0.2 - - - +
364B ILE 3.7 0.2 - - - +
365B GLN* 3.4 2.6 - - - +
366B MET* 2.7 61.5 + - + +
367B GLU 4.1 10.3 - - - +
368B PHE* 3.7 33.9 - - + +
369B CYS 5.1 0.4 - - - +
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Residues in contact with ILE 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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263B PHE* 3.8 33.7 - - + -
267B PHE* 3.8 20.4 - - + -
282B PHE* 2.7 43.2 + - + +
284B ALA* 4.0 9.6 - - + +
293B TYR* 3.9 15.0 - - + +
294B VAL* 1.3 80.9 - - - +
296B LYS* 1.3 57.4 + - - +
327B TRP* 3.8 20.6 - - + -
363B PHE* 3.8 33.9 - - + -
364B ILE 3.3 7.6 - - - +
365B GLN* 4.2 12.6 - - + -
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Residues in contact with LYS 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B GLY* 5.4 2.7 - - - -
280B GLN 3.6 11.9 - - - +
281B VAL* 4.3 22.2 - - + +
294B VAL* 4.2 0.6 - - - +
295B ILE* 1.3 71.6 - - - +
297B ARG* 1.3 67.6 + - - +
298B VAL* 4.9 12.2 - - + +
308B GLU* 2.7 40.6 + - - -
362B LEU 3.3 4.5 - - - +
363B PHE* 3.5 1.3 - - - -
364B ILE* 2.8 50.2 + - + +
366B MET* 4.8 21.5 - - + -
431B GLY 5.8 0.2 - - - -
432B ASP* 2.9 32.6 + - - +
434B GLY* 4.2 4.0 - - - +
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Residues in contact with ARG 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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257B HIS* 2.6 30.1 + - - +
258B THR* 3.3 4.8 - - - +
279B GLY* 3.1 24.8 - - - -
280B GLN* 2.4 54.6 + - - +
282B PHE* 3.4 33.1 - - + -
295B ILE 3.9 2.2 + - - -
296B LYS* 1.3 70.7 - - - +
298B VAL* 1.3 61.5 + - - +
331B ASP* 2.9 36.4 + - - -
332B TYR* 3.8 25.5 + - - +
334B PRO* 3.9 6.4 - - - +
361B CYS* 4.0 10.8 - - + -
362B LEU 3.6 3.6 - - - -
363B PHE* 3.5 29.6 - - + -
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Residues in contact with VAL 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B PHE* 3.1 24.7 - - + +
279B GLY* 4.4 1.8 - - - -
296B LYS* 4.8 16.4 - - + +
297B ARG* 1.3 76.0 - - - +
299B LYS* 1.3 68.5 + - - +
300B TYR 3.3 0.2 + - - -
305B ALA* 4.3 11.2 - - + +
308B GLU* 5.0 14.8 - - - +
334B PRO* 3.7 6.5 - - - -
361B CYS* 3.3 4.0 - - - -
362B LEU* 2.7 54.7 + - + +
364B ILE* 5.1 2.5 - - + -
434B GLY* 6.3 1.6 - - - -
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Residues in contact with LYS 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B PHE 4.3 1.6 + - - -
298B VAL* 1.3 85.5 - - - +
300B TYR* 1.3 58.9 + - - +
301B ASN* 3.3 42.9 - - + +
305B ALA* 3.7 7.6 - - - +
333B ASP* 3.0 33.1 + - - +
334B PRO* 3.3 19.7 - - + +
335B GLU* 3.6 38.1 - - + +
359B THR* 3.7 29.5 + - - +
360B LYS 4.1 3.4 - - - +
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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