Contacts of the strand formed by residues 352 - 359 (chain A) in PDB entry 3OPY
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 352 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A LYS* 5.3 6.7 + - - +
306A ASP 3.6 18.4 + - - -
307A ALA* 3.3 2.7 - - + -
308A LEU* 2.9 26.7 + - - +
350A ASN* 3.5 8.7 + - - +
351A LEU* 1.3 75.5 + - - +
353A ILE* 1.3 58.7 + - - +
354A VAL* 5.4 2.2 - - + -
518A ALA 5.1 0.2 - - - +
519A VAL* 3.7 48.2 - - + +
522A SER* 4.0 20.1 + - - -
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Residues in contact with ILE 353 (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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308A LEU* 3.4 35.2 - - + +
310A VAL* 4.1 3.4 - - + -
320A ALA* 3.8 37.9 - - + +
323A PHE* 4.5 10.3 - - + -
324A ARG* 3.6 24.9 - - + -
351A LEU* 3.8 13.8 + - + +
352A THR* 1.3 76.4 - - - +
354A VAL* 1.3 70.5 + - - +
528A SER* 3.2 42.6 + - - +
529A PRO* 3.6 8.7 - - - +
543A LEU* 4.9 5.5 - - + +
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Residues in contact with VAL 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LEU 3.0 6.5 + - - +
309A VAL* 3.4 15.3 - - + +
310A VAL* 3.1 26.2 + - - +
352A THR* 5.4 2.0 - - + -
353A ILE* 1.3 82.9 - - - +
355A GLY* 1.3 64.0 + - - +
515A ALA* 3.8 19.5 - - + +
518A ALA* 3.9 19.3 - - + +
519A VAL* 3.8 24.0 - - + +
529A PRO* 3.7 14.6 - - + +
531A ILE* 3.7 32.1 - - + -
543A LEU* 5.8 1.1 - - - -
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Residues in contact with GLY 355 (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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310A VAL* 3.5 7.2 - - - -
317A LEU* 4.0 16.4 - - - -
320A ALA* 6.2 0.4 - - - -
354A VAL* 1.3 76.1 - - - +
356A LEU* 1.3 60.5 + - - -
529A PRO 3.0 14.8 + - - -
530A VAL* 3.3 10.1 - - - +
531A ILE* 2.8 33.6 + - - +
543A LEU* 5.3 4.4 - - - +
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Residues in contact with LEU 356 (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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215A ILE* 4.8 0.9 - - + -
228A ALA* 4.3 14.1 - - + -
232A VAL* 4.1 18.2 - - + -
309A VAL* 3.9 22.9 - - + -
310A VAL 2.8 7.3 + - - +
311A CYS* 4.0 24.7 - - + -
312A GLY 3.1 26.5 + - - +
317A LEU* 4.1 3.4 - - - +
354A VAL 4.4 0.2 + - - -
355A GLY* 1.3 74.4 - - - -
357A VAL* 1.3 61.8 + - - +
371A ILE* 4.5 5.8 - - + -
511A GLN* 3.5 45.8 - - + +
512A GLY* 4.2 2.0 - - - +
515A ALA* 4.0 6.3 - - + -
531A ILE* 3.9 16.4 - - + -
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Residues in contact with VAL 357 (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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312A GLY 3.4 11.9 - - - +
313A GLY* 4.5 4.3 - - - -
314A ASP* 6.0 0.2 - - - +
317A LEU* 3.8 13.7 - - + -
356A LEU* 1.3 70.0 - - - +
358A GLY* 1.3 54.0 + - - +
359A SER* 3.6 11.5 + - - -
364A MET* 3.7 24.2 - - + -
367A THR* 4.6 7.0 - - + -
370A THR* 3.6 28.4 - - + -
371A ILE* 2.8 38.9 + - - +
511A GLN* 4.6 4.1 + - - +
530A VAL* 3.7 28.7 - - + -
531A ILE 4.5 7.5 + - - +
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Residues in contact with GLY 358 (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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220A GLY 4.4 4.2 - - - +
222A ALA* 3.8 10.1 - - - +
225A MET* 3.8 14.1 - - - +
311A CYS* 4.0 18.7 - - - -
312A GLY* 3.0 29.0 + - - +
313A GLY* 3.2 3.8 + - - -
356A LEU 3.3 4.0 + - - -
357A VAL* 1.3 68.9 - - - +
359A SER* 1.4 58.0 + - - -
371A ILE* 3.5 12.1 - - - -
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Residues in contact with SER 359 (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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222A ALA* 3.8 2.2 - - - +
313A GLY* 4.0 17.9 - - - -
314A ASP* 4.7 4.3 + - - -
357A VAL* 3.6 12.5 + - - +
358A GLY* 1.4 75.4 - - - +
360A ILE* 1.3 59.5 + - - +
361A ASP* 3.4 12.9 - - - +
362A ASN* 3.3 18.7 + - - -
363A ASP 4.2 1.9 + - - -
364A MET 5.2 0.5 + - - -
370A THR* 2.6 31.8 + - - +
371A ILE 2.8 17.2 + - - +
373A ALA 3.4 4.5 + - - -
496A ARG* 5.5 2.9 - - - +
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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