Contacts of the strand formed by residues 323 - 330 (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 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A LEU* 3.8 26.0 - - + -
265A TRP* 4.0 7.2 - - + -
314A LEU* 3.9 20.6 - - + -
317A ALA* 3.7 26.6 + - + -
318A LEU* 3.8 19.9 - - + +
321A ASN* 3.5 6.0 - - - +
322A ARG* 1.3 77.9 - - - +
324A ARG* 1.3 64.5 + - - +
325A GLU 4.1 5.4 - - - +
350A ILE* 4.0 24.9 - - + -
351A PRO* 3.4 19.5 - - + +
355A ASN* 3.9 2.6 + - - -
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Residues in contact with ARG 324 (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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264A TYR* 2.9 55.3 + - + +
265A TRP* 4.6 5.4 - - - +
266A ILE* 5.3 8.1 - - + +
272A GLU* 4.8 7.6 + - - -
322A ARG 3.7 6.3 + - - +
323A VAL* 1.3 78.6 - - - +
325A GLU* 1.3 68.4 + - - +
351A PRO* 3.5 11.1 - - - +
352A THR* 3.5 2.1 - - - -
355A ASN* 2.9 47.6 + - - +
358A LYS* 3.4 53.3 - - - +
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Residues in contact with GLU 325 (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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262A PHE 4.2 0.2 - - - +
263A LEU* 3.5 7.1 - - - +
264A TYR* 2.8 51.3 + - + +
323A VAL* 4.1 2.7 - - - +
324A ARG* 1.3 89.6 + - + +
326A MET* 1.3 60.4 + - - +
327A PHE* 4.4 7.4 - - + -
352A THR* 3.7 25.4 - - + +
355A ASN* 4.5 3.6 - - + -
357A PRO* 3.4 3.1 - - + +
358A LYS* 3.2 17.6 + - - +
359A LEU* 2.8 31.9 + - - +
360A ALA* 2.9 35.2 + - - +
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Residues in contact with MET 326 (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* 4.9 1.6 - - - -
244A LEU* 4.8 6.7 - - + -
253A ILE* 3.6 27.4 - - + -
261A LEU* 3.6 28.9 - - + -
262A PHE 3.4 15.3 - - - +
263A LEU* 4.3 10.5 - - + -
314A LEU* 4.2 16.6 - - + -
325A GLU* 1.3 74.5 - - - +
327A PHE* 1.3 59.2 + - - +
337A PRO* 3.6 1.7 - - - +
338A VAL* 2.7 55.2 + - + -
341A ILE* 4.0 16.6 - - + -
350A ILE* 3.9 20.2 - - + -
352A THR* 3.0 11.7 + - - +
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Residues in contact with PHE 327 (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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260A ASN 3.8 0.2 - - - +
261A LEU* 4.0 3.5 - - - +
262A PHE* 2.9 65.9 + + + +
264A TYR* 4.7 7.4 - - + -
274A LEU* 4.0 16.4 - - + -
292A ILE* 4.3 3.6 - - + -
325A GLU* 4.4 13.5 - - + -
326A MET* 1.3 80.3 - - - +
328A SER* 1.3 64.1 + - - +
335A VAL* 3.6 29.4 - - + -
336A CYS 3.3 19.1 - - - +
337A PRO* 3.9 4.3 - - + -
338A VAL* 4.3 3.1 - - - +
352A THR* 5.5 0.2 - - + -
359A LEU* 4.5 8.1 - - + -
360A ALA* 4.2 17.0 - - + -
363A ILE* 3.5 33.7 - - + -
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Residues in contact with SER 328 (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* 4.9 0.5 - - - +
256A VAL* 3.1 33.0 - - - +
259A MET* 3.3 37.7 - - - +
260A ASN 3.1 6.5 - - - -
327A PHE* 1.3 78.6 - - - +
329A SER* 1.3 60.7 + - - +
335A VAL* 3.4 5.2 - - - -
336A CYS* 2.8 36.5 + - - +
338A VAL* 3.8 5.0 - - - +
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Residues in contact with SER 329 (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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259A MET* 3.2 8.3 - - - -
260A ASN* 2.8 45.7 + - - +
262A PHE* 3.3 23.1 - - - -
288A THR* 3.9 4.9 - - - -
289A ARG 3.7 10.4 + - - -
292A ILE* 3.7 22.9 - - - -
328A SER* 1.3 74.7 - - - +
330A GLY* 1.3 59.2 + - - +
334A VAL 3.4 13.0 - - - -
335A VAL* 4.7 0.9 - - - -
420A PLP 3.9 4.7 - - - +
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Residues in contact with GLY 330 (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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259A MET* 4.2 0.6 - - - +
288A THR* 3.4 8.8 + - - -
329A SER* 1.3 75.9 - - - +
331A THR* 1.3 59.7 + - - -
332A ALA 3.4 2.2 - - - -
333A CYS* 4.7 1.2 - - - -
334A VAL* 2.8 35.2 + - - -
420A PLP 3.7 19.1 - - - -
1401A CBC 3.5 16.6 + - - -
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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