Contacts of the strand formed by residues 334 - 343 (chain A) in PDB entry 2ABJ
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 VAL 334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A LYS* 5.6 2.9 - - - +
288A THR* 3.4 15.2 - - + +
329A SER* 3.4 17.5 - - - -
330A GLY 2.8 17.4 + - - -
331A THR* 3.7 5.9 + - - +
332A ALA 3.6 2.1 - - - +
333A CYS* 1.3 81.1 - - - +
335A VAL* 1.3 70.6 + - + +
364A LEU* 3.7 29.2 - - + -
367A LEU* 3.6 36.3 - - + -
368A THR* 4.7 4.7 - - + -
371A GLN* 4.5 23.1 - - - +
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Residues in contact with VAL 335 (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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191A TYR* 6.0 0.7 - - - +
197A PHE* 3.4 40.6 - - + -
292A ILE* 4.2 5.4 - - + -
327A PHE* 3.6 32.1 - - + -
328A SER 3.4 4.0 - - - +
333A CYS* 2.7 19.5 + - - +
334A VAL* 1.3 87.4 - - + +
336A CYS* 1.3 62.9 + - - +
337A PRO* 4.6 1.1 - - + -
360A ALA* 3.8 26.2 - - + +
363A ILE* 4.0 23.1 - - + -
364A LEU* 4.8 3.1 - - + +
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Residues in contact with CYS 336 (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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191A TYR* 6.3 0.9 - - - -
197A PHE* 5.2 0.2 - - - -
198A ASN 4.3 7.4 - - - -
200A VAL* 3.7 35.4 - - - -
259A MET* 3.8 15.9 - - + -
327A PHE* 3.3 1.9 - - - -
328A SER* 2.8 37.2 + - - -
333A CYS* 3.6 17.9 - - + -
335A VAL* 1.3 75.3 - - - +
337A PRO* 1.3 72.4 - - - +
338A VAL* 4.0 0.2 - - - +
1401A CBC 3.9 17.0 - - - -
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Residues in contact with PRO 337 (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 PHE* 3.5 49.8 - - + -
198A ASN 5.0 1.6 - - - +
199A PRO* 3.3 11.0 - - + +
200A VAL* 3.0 25.3 + - - +
326A MET 3.6 5.8 - - - +
327A PHE* 3.9 5.8 - - + -
335A VAL* 4.6 1.6 - - + -
336A CYS* 1.3 90.3 - - + +
338A VAL* 1.3 60.5 + - - +
352A THR* 3.7 20.9 - - + -
353A MET* 3.8 17.3 - - - -
357A PRO* 4.6 4.5 - - + -
360A ALA* 5.2 1.3 - - + -
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Residues in contact with VAL 338 (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 PRO* 4.9 0.7 - - - -
200A VAL* 3.6 12.6 - - + +
202A LEU* 3.7 34.3 - - + -
256A VAL* 4.6 1.6 - - + -
326A MET* 2.7 41.9 + - + +
327A PHE* 4.4 0.9 - - - -
328A SER* 3.8 21.8 - - - +
336A CYS 4.0 0.7 - - - +
337A PRO* 1.3 76.4 - - - +
339A SER* 1.3 60.8 + - - +
340A ASP 3.8 17.5 - - - +
341A ILE* 4.3 1.3 - - + -
350A ILE* 3.5 12.3 - - + +
352A THR* 2.6 28.6 + - - -
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Residues in contact with SER 339 (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 PRO* 3.8 25.5 - - - +
200A VAL 3.1 14.0 + - - -
201A SER* 4.2 2.1 + - - -
337A PRO 4.1 1.0 + - - -
338A VAL* 1.3 73.7 - - - +
340A ASP* 1.3 79.6 + - - +
349A HIS* 3.2 10.0 + - - -
350A ILE* 2.7 40.4 + - - +
352A THR* 5.1 1.3 - - - -
353A MET* 4.7 8.1 - - - -
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Residues in contact with ASP 340 (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 3.7 1.0 + - - -
201A SER* 3.4 21.0 + - - +
202A LEU 2.8 28.8 + - - -
338A VAL* 3.7 5.5 - - - +
339A SER* 1.3 100.6 + - - +
341A ILE* 1.3 64.0 + - - +
342A LEU* 4.3 2.5 - - + -
347A THR* 4.0 22.0 - - + +
348A ILE 3.3 6.8 - - - +
349A HIS* 3.0 33.1 + - - +
350A ILE* 4.3 0.9 - - - -
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Residues in contact with ILE 341 (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 LEU* 3.4 16.6 - - + +
204A ALA* 3.8 26.7 - - + -
244A LEU* 3.9 19.5 - - + -
311A MET* 4.3 5.4 - - + -
314A LEU* 3.6 30.5 - - + -
326A MET* 4.0 13.2 - - - -
338A VAL* 4.3 4.0 - - + -
340A ASP* 1.3 79.6 - - - +
342A LEU* 1.3 66.3 + - - +
343A TYR* 3.6 11.1 + - + -
348A ILE* 2.9 43.3 + - + +
350A ILE* 3.8 17.7 - - + -
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Residues in contact with LEU 342 (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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201A SER* 5.0 3.6 - - - -
202A LEU 2.7 13.3 + - - +
203A TRP* 3.6 33.0 - - + -
204A ALA* 2.9 31.5 + - - +
238A ASN* 4.7 10.5 - - + +
240A CYS* 3.7 22.0 - - - -
340A ASP* 4.8 6.3 - - + -
341A ILE* 1.3 73.2 - - - +
343A TYR* 1.3 58.9 + - - +
345A GLY* 5.7 4.5 - - - +
346A GLU 3.3 9.2 - - - +
347A THR* 3.7 39.9 - - + +
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Residues in contact with TYR 343 (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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204A ALA* 3.4 24.7 - - + -
206A PRO* 4.4 10.8 - - + +
246A LEU* 3.8 20.4 - - + -
251A HIS* 3.5 29.3 + - - -
311A MET* 3.5 37.4 - - + +
312A ASP* 5.5 3.6 + - - -
315A THR* 5.3 4.3 - - + -
341A ILE* 3.6 9.1 + - + -
342A LEU* 1.3 74.2 - - - +
344A LYS* 1.3 100.0 + - + +
345A GLY 3.3 2.3 - - - +
346A GLU* 2.9 25.2 + - - +
348A ILE* 3.9 23.4 - - + +
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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