Contacts of the strand formed by residues 365 - 373 (chain A) in PDB entry 2JB3
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 GLY 365 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A HIS* 3.9 9.9 - - - -
326A ILE 3.7 0.5 - - - +
327A GLU* 4.2 3.1 - - - +
328A TYR* 2.9 29.8 + - - +
331A ARG* 3.6 14.8 - - - +
333A TRP* 3.7 16.1 - - - -
356A PRO* 4.9 0.7 - - - -
364A ARG* 1.3 80.3 - - - +
366A VAL* 1.3 64.1 + - - -
367A VAL 3.9 0.2 + - - -
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Residues in contact with VAL 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 4.0 42.6 - - + -
76A HIS* 4.1 21.2 - - + -
77A PHE 4.0 13.9 - - - +
78A TYR* 4.1 20.0 - - + -
325A GLY* 4.1 2.0 - - - -
326A ILE 3.2 16.2 - - - +
327A GLU* 4.2 5.8 - - + -
354A MET 4.7 0.2 - - - +
356A PRO* 3.4 28.0 - - - +
365A GLY* 1.3 74.1 - - - -
367A VAL* 1.3 73.6 + - - +
368A VAL* 4.2 1.6 + - + +
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Residues in contact with VAL 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A GLY* 3.2 1.2 - - - -
326A ILE* 2.8 32.4 + - + +
328A TYR* 3.9 19.7 - - + -
332A TRP* 4.9 0.7 - - + -
333A TRP* 3.6 42.2 - - + -
353A ILE* 3.5 31.4 - - + -
354A MET 3.6 8.1 - - - +
355A PHE* 3.9 17.0 - - + -
356A PRO* 4.3 1.1 - - + -
366A VAL* 1.3 77.2 - - - +
368A VAL* 1.3 67.0 + - - +
369A ALA* 3.1 6.6 + - + +
404A TYR* 4.1 8.1 - - + +
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Residues in contact with VAL 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A TYR* 3.8 32.8 - - + -
79A ASN 5.4 0.7 - - - +
323A LYS* 4.2 14.6 - - + -
324A LEU 3.5 7.4 - - - +
325A GLY* 4.2 0.4 - - - -
352A GLN 4.0 0.5 - - - +
353A ILE* 3.4 2.9 - - - -
354A MET* 2.9 71.4 + - + +
366A VAL* 4.2 1.7 + - + +
367A VAL* 1.3 72.2 - - - +
369A ALA* 1.3 59.9 + - - +
370A TYR 3.1 26.1 + - - +
371A TYR* 4.3 4.3 - - + -
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Residues in contact with ALA 369 (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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324A LEU* 2.7 22.2 + - + +
326A ILE* 3.5 30.5 - - + -
350A ILE* 3.7 14.4 - - - +
352A GLN 3.7 6.4 - - - +
353A ILE* 3.8 8.8 - - - +
367A VAL* 3.1 6.0 + - + +
368A VAL* 1.3 70.4 - - - +
370A TYR* 1.3 61.7 + - - +
392A ALA* 4.0 11.1 - - + +
404A TYR* 3.3 24.0 + - + +
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Residues in contact with TYR 370 (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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322A GLY 3.7 9.6 - - - -
323A LYS* 3.2 40.5 + - - -
324A LEU* 3.2 30.6 + - + +
350A ILE* 3.2 23.1 - - + +
352A GLN 3.4 6.7 - - - -
368A VAL* 3.1 18.7 - - - +
369A ALA* 1.3 80.1 - - - +
371A TYR* 1.3 61.5 + - - +
372A SER* 4.3 4.5 - - - -
377A GLN* 3.9 15.8 + - - -
380A PHE* 3.4 40.4 - + - +
388A ARG* 3.4 34.2 + - - +
392A ALA* 3.8 15.0 - - + -
413A SER* 4.1 3.8 - - - -
414A GLY 5.0 1.0 + - - -
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Residues in contact with TYR 371 (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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83A THR* 5.7 0.7 - - + -
84A ARG* 3.8 11.7 - - - -
321A SER* 3.2 22.0 - - - -
322A GLY 3.4 11.7 - - - -
323A LYS* 3.7 25.8 - - + -
350A ILE 3.4 3.6 + - - -
351A SER* 3.5 11.4 - - - -
352A GLN* 3.3 39.5 + - + +
354A MET* 3.8 25.4 - - - -
368A VAL* 4.3 1.6 - - + -
370A TYR* 1.3 75.5 - - - +
372A SER* 1.3 60.2 + - - +
373A SER* 4.0 8.1 - - - -
426A TRP* 3.9 8.0 - - - -
1489A FAD 3.5 21.5 - - + -
1490A BE2 2.9 45.2 + + - -
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Residues in contact with SER 372 (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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321A SER* 3.1 3.5 + - - -
322A GLY 3.0 31.1 + - - -
349A ASP 3.3 12.6 - - - -
350A ILE 4.1 2.2 - - - -
351A SER* 3.2 23.3 - - - -
370A TYR* 4.1 2.1 - - - -
371A TYR* 1.3 74.7 - - - +
373A SER* 1.3 66.6 + - - +
376A ARG* 2.9 20.1 + - - -
377A GLN* 2.8 24.8 + - - +
380A PHE* 3.7 7.6 - - - -
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Residues in contact with SER 373 (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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320A SER 3.3 13.5 - - - -
321A SER* 2.8 21.2 + - - -
351A SER* 4.8 0.6 + - - -
371A TYR* 4.0 6.4 - - - -
372A SER* 1.3 75.8 - - - +
374A GLY* 1.3 70.0 + - - +
375A LYS 3.4 0.3 + - - -
376A ARG* 3.3 16.9 + - - +
377A GLN* 3.7 2.7 - - - -
426A TRP* 3.7 18.6 - - - -
1490A BE2 5.8 1.2 - - - -
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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