Contacts of the strand formed by residues 365 - 373 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B HIS* 3.7 11.7 - - - -
326B ILE 3.6 1.2 - - - +
327B GLU* 4.1 3.1 - - - +
328B TYR 2.8 33.5 + - - +
331B ARG* 3.6 15.7 - - - +
333B TRP* 3.7 14.6 - - - -
364B ARG* 1.3 77.6 - - - +
366B VAL* 1.3 64.0 + - - -
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Residues in contact with VAL 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE* 4.0 23.8 - - + -
76B HIS* 4.1 23.7 - - + -
77B PHE 3.8 14.6 - - - +
78B TYR* 3.9 34.9 - - + +
325B GLY* 4.1 0.2 - - - -
326B ILE 3.2 10.5 - - - +
327B GLU* 3.9 18.4 - - + -
354B MET 4.7 0.5 - - - +
356B PRO* 3.3 30.0 - - + +
365B GLY* 1.3 73.5 - - - -
367B VAL* 1.3 70.5 + - - +
368B VAL* 4.2 2.1 + - - +
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Residues in contact with VAL 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B GLY* 3.2 1.7 - - - -
326B ILE* 2.8 37.1 + - + +
328B TYR* 3.8 21.8 - - + -
332B TRP* 4.8 0.4 - - + -
333B TRP* 3.4 43.3 - - + -
353B ILE* 3.5 30.3 - - + -
354B MET 3.7 8.3 - - - +
355B PHE* 4.1 14.6 - - + -
356B PRO* 4.5 0.7 - - + -
366B VAL* 1.3 74.0 - - - +
368B VAL* 1.3 65.1 + - - +
369B ALA* 3.1 5.3 + - + +
404B TYR* 4.1 8.7 - - + +
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Residues in contact with VAL 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B TYR* 3.8 33.2 - - + -
79B ASN 5.5 1.3 - - - +
323B LYS* 4.4 13.9 - - + +
324B LEU 3.4 6.3 - - - +
325B GLY* 4.3 0.4 - - - -
352B GLN 4.1 0.2 - - - +
353B ILE* 3.3 4.9 - - - +
354B MET* 2.8 61.3 + - + +
366B VAL* 5.3 2.0 - - + +
367B VAL* 1.3 69.9 - - - +
369B ALA* 1.3 62.1 + - - +
370B TYR 3.2 25.7 + - - +
371B TYR* 4.3 10.5 - - + -
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Residues in contact with ALA 369 (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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324B LEU* 2.8 15.7 + - + +
326B ILE* 3.5 30.7 - - + -
350B ILE* 3.8 11.3 - - - +
352B GLN 3.6 6.6 - - - +
353B ILE* 3.8 11.2 - - - +
367B VAL* 3.1 4.7 + - + +
368B VAL* 1.3 72.8 - - - +
370B TYR* 1.3 61.9 + - - +
392B ALA* 4.0 16.0 - - + +
404B TYR* 3.3 24.6 + - + +
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Residues in contact with TYR 370 (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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322B GLY 3.7 7.6 - - - -
323B LYS* 3.2 42.4 + - - -
324B LEU* 3.2 36.4 + - + +
350B ILE* 3.3 22.9 - - + +
352B GLN 3.4 7.6 - - - -
368B VAL* 3.2 11.5 - - - +
369B ALA* 1.3 78.9 - - - +
371B TYR* 1.3 61.1 + - - +
372B SER* 4.2 5.2 - - - -
377B GLN* 3.7 21.5 + - - -
380B PHE* 3.4 40.3 - + - +
388B ARG* 3.3 31.7 + - - +
392B ALA* 3.8 14.8 - - + -
413B SER* 4.1 3.5 - - - -
414B GLY 5.0 1.3 + - - -
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Residues in contact with TYR 371 (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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83B THR* 6.0 0.2 - - + -
84B ARG* 3.9 8.3 - - - -
321B SER* 3.1 22.4 - - - -
322B GLY 3.4 11.4 - - - -
323B LYS* 3.7 32.1 - - + -
350B ILE 3.5 3.6 + - - -
351B SER* 3.6 7.4 - - - -
352B GLN* 3.3 43.0 + - + +
354B MET* 3.8 25.8 - - + -
368B VAL* 4.3 2.7 - - + -
370B TYR* 1.3 75.5 - - - +
372B SER* 1.3 59.9 - - - +
373B SER* 4.0 5.8 - - - -
426B TRP* 4.0 5.9 - - - -
1489B FAD 3.5 14.9 - + + -
1490B BE2 3.1 49.4 + + - -
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Residues in contact with SER 372 (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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321B SER* 3.2 2.1 + - - -
322B GLY 3.0 29.9 + - - -
349B ASP 3.3 24.5 + - - -
350B ILE 3.9 2.9 - - - -
351B SER* 3.3 12.1 - - - -
370B TYR* 4.0 1.9 - - - -
371B TYR* 1.3 73.4 - - - +
373B SER* 1.3 67.3 + - - +
376B ARG 2.8 20.8 + - - -
377B GLN* 2.9 19.9 + - - +
380B PHE* 3.8 6.1 - - - -
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Residues in contact with SER 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B SER 3.4 11.9 - - - -
321B SER* 2.7 23.4 + - - -
351B SER* 4.8 1.0 + - - -
371B TYR* 4.0 6.8 - - - -
372B SER* 1.3 72.8 - - - +
374B GLY* 1.3 69.0 + - - +
375B LYS 3.4 0.9 + - - -
376B ARG* 3.3 17.0 + - - +
377B GLN* 3.6 1.3 + - - -
426B TRP* 3.8 17.1 - - - -
1490B BE2 5.7 1.4 - - - -
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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