Contacts of the helix formed by residues 374 - 385 (chain A) in PDB entry 2J2C
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 GLU 374 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A TRP* 3.6 32.9 - - + +
98A ARG* 2.7 58.6 + - - +
156A LEU* 3.4 17.8 - - + +
159A LEU* 5.3 1.4 - - + +
372A ILE* 3.7 2.4 - - - +
373A PRO* 1.3 75.7 - - - +
375A LEU* 1.3 65.6 + - - +
376A ALA 3.1 0.4 - - - -
377A GLN* 3.1 5.9 + - - +
378A GLU* 2.9 25.4 + - + +
440A LEU* 3.8 12.8 - - + +
1489A GOL 3.4 25.1 + - - +
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Residues in contact with LEU 375 (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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36A PHE* 4.3 8.3 - - + -
372A ILE* 2.9 25.8 + - + +
374A GLU* 1.3 77.7 - - - +
376A ALA* 1.3 62.6 + - - +
378A GLU* 4.2 8.7 - - + -
379A LEU* 2.9 59.8 + - + +
441A PHE* 3.7 27.6 - - + -
461A TYR* 3.9 27.1 - - + -
462A ALA* 3.8 8.1 - - - +
463A ALA* 3.6 24.0 - - - +
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Residues in contact with ALA 376 (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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5A TRP* 3.6 20.4 - - + +
8A ARG* 3.8 14.6 - - + +
9A LEU* 3.8 20.2 - - + -
32A TYR* 4.3 8.8 - - - -
373A PRO 3.2 16.1 + - - +
374A GLU 3.1 0.2 - - - -
375A LEU* 1.3 77.0 - - - +
377A GLN* 1.3 56.2 + - - +
379A LEU* 5.1 2.7 - - - -
380A HIS* 3.2 23.6 + - - -
463A ALA* 3.6 12.4 - - + +
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Residues in contact with GLN 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A THR* 3.7 24.8 + - - +
5A TRP* 3.7 29.3 - - + +
8A ARG* 2.5 44.9 + - - +
374A GLU 3.1 3.9 + - - +
376A ALA* 1.3 76.9 - - - +
378A GLU* 1.3 64.8 + - - +
379A LEU 3.2 1.8 - - - -
380A HIS* 3.0 19.9 + - - +
381A VAL* 3.1 26.4 + - + +
1489A GOL 6.1 0.9 - - - +
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Residues in contact with GLU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A GLU* 2.9 23.6 + - + +
375A LEU* 4.1 9.0 - - + +
377A GLN* 1.3 75.0 - - - +
379A LEU* 1.3 56.5 + - - +
381A VAL* 3.4 3.3 + - - +
382A TRP* 2.9 30.9 + - - +
434A TYR* 3.5 21.8 - - - -
439A SER* 2.6 25.7 + - - -
440A LEU* 2.9 19.8 + - - +
441A PHE* 3.3 17.8 - - + -
1489A GOL 2.7 44.9 + - - +
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Residues in contact with LEU 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ALA* 3.7 44.6 - - + +
32A TYR* 3.7 25.5 - - + +
36A PHE* 4.4 10.5 - - + -
375A LEU* 2.9 52.4 + - + +
376A ALA* 4.6 1.1 - - - +
378A GLU* 1.3 71.9 - - - +
380A HIS* 1.3 66.2 + - - +
382A TRP* 3.4 14.1 + - + +
383A THR* 3.1 26.2 + - - +
463A ALA* 5.0 4.3 - - + -
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Residues in contact with HIS 380 (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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8A ARG* 3.3 46.5 + - - +
32A TYR* 3.3 42.5 + + - -
376A ALA 3.2 25.5 + - - -
377A GLN* 3.0 20.6 + - - +
379A LEU* 1.3 77.4 - - - +
381A VAL* 1.3 56.0 + - - +
383A THR* 3.3 6.6 - - - +
384A ASP* 2.9 32.8 + - - +
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Residues in contact with VAL 381 (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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377A GLN* 3.1 29.7 + - + +
378A GLU 3.9 1.1 - - - +
380A HIS* 1.3 75.1 - - - +
382A TRP* 1.3 55.3 + - - +
384A ASP* 4.4 4.7 - - - -
385A LYS* 2.8 41.4 + - + +
433A CYS* 3.7 39.5 - - + +
434A TYR* 3.6 38.4 - - + +
1489A GOL 5.7 1.1 - - - +
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Residues in contact with TRP 382 (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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378A GLU 2.9 19.1 + - - +
379A LEU* 3.6 17.5 - - + +
380A HIS 3.3 0.2 - - - -
381A VAL* 1.3 76.3 - - - +
383A THR* 1.3 62.4 + - - +
385A LYS* 3.9 0.7 - - - -
386A SER* 3.2 32.2 + - - -
389A PHE* 3.6 51.1 - + + -
430A MET* 4.9 2.2 - - + -
434A TYR* 3.7 23.5 + - - +
442A ARG* 4.0 29.2 - - - -
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Residues in contact with THR 383 (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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32A TYR* 3.4 22.0 - - - +
379A LEU 3.1 16.7 + - - +
380A HIS* 3.3 11.9 - - - +
382A TRP* 1.3 80.2 - - - +
384A ASP* 1.3 68.6 + - + +
385A LYS 3.2 0.2 + - - -
386A SER* 3.1 23.2 + - - -
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Residues in contact with ASP 384 (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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380A HIS 2.9 24.6 + - - +
381A VAL* 4.0 4.7 - - - +
383A THR* 1.3 74.7 - - + +
385A LYS* 1.3 85.9 + - + +
386A SER* 3.5 0.7 + - - -
387A SER* 5.2 1.7 + - - -
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Residues in contact with LYS 385 (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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381A VAL* 2.8 32.1 + - + +
382A TRP 3.9 2.7 - - - -
384A ASP* 1.3 96.9 + - + +
386A SER* 1.3 63.9 + - - +
387A SER* 3.1 4.7 - - - -
388A LEU* 2.9 37.5 + - + +
389A PHE* 3.6 4.2 + - - +
430A MET* 5.6 6.4 - - + +
433A CYS* 3.6 35.1 - - + -
434A TYR* 5.9 0.9 - - + +
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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