Contacts of the helix formed by residues 362 - 369 (chain B) in PDB entry 2JGZ
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 362 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B GLU* 2.8 28.2 + - + +
361B TRP* 1.3 76.6 - - - +
363B PRO* 1.3 71.4 - - + +
364B THR* 3.7 13.1 + - - -
365B LEU* 3.2 28.5 + - - +
366B GLN* 3.1 24.3 + - - +
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Residues in contact with PRO 363 (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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360B GLU* 6.1 1.1 - - + -
361B TRP 4.5 1.1 - - - +
362B THR* 1.3 92.0 - - + +
364B THR* 1.3 60.4 + - + +
366B GLN* 3.2 21.7 - - + +
367B HIS* 2.9 27.3 + - - +
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Residues in contact with THR 364 (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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312B ILE* 5.2 10.2 - - - +
362B THR* 3.3 12.1 + - - -
363B PRO* 1.3 78.3 - - + +
365B LEU* 1.3 65.3 + - - +
367B HIS* 4.0 7.0 - - - -
368B TYR* 3.0 48.6 + - + +
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Residues in contact with LEU 365 (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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309B ALA 4.3 9.4 - - - +
312B ILE* 3.7 37.0 - - + +
349B PHE* 4.1 23.3 - - + -
353B LEU* 4.1 18.8 - - + -
360B GLU 4.6 1.1 - - - +
361B TRP* 4.1 18.2 - - + -
362B THR* 3.2 31.2 + - - +
364B THR* 1.3 84.7 + - - +
366B GLN* 1.3 57.0 + - - +
368B TYR* 5.2 0.4 - - - -
369B LEU* 3.2 46.3 + - + +
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Residues in contact with GLN 366 (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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361B TRP* 3.5 22.2 + - - +
362B THR 3.1 8.3 + - - +
363B PRO* 3.2 30.6 - - + +
365B LEU* 1.3 75.1 - - - +
367B HIS* 1.3 57.4 + - - +
370B SER* 3.2 23.9 + - - -
371B TYR 3.1 28.2 + - - +
372B THR* 4.3 18.0 + - - +
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Residues in contact with HIS 367 (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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172B LYS* 6.3 2.3 - - - -
363B PRO 2.9 17.2 + - - +
364B THR* 3.4 11.0 - - - +
365B LEU 3.2 0.4 - - - -
366B GLN* 1.3 80.9 - - - +
368B TYR* 1.3 78.9 + + + +
369B LEU 3.6 0.3 + - - -
370B SER* 3.7 11.4 + - - -
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Residues in contact with TYR 368 (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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172B LYS* 5.7 13.2 - - + -
179B ARG* 6.1 0.9 - - - -
308B ARG* 2.8 51.2 + - - +
312B ILE* 3.8 33.0 - - + -
364B THR* 3.0 40.7 + - + +
365B LEU 4.7 0.7 - - - +
367B HIS* 1.3 92.3 - + + +
369B LEU* 1.3 64.0 + - + +
370B SER* 4.6 2.2 + - - -
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Residues in contact with LEU 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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179B ARG* 3.5 11.7 + - - +
305B PHE* 4.9 7.6 - - + +
308B ARG* 3.9 26.5 - - + +
309B ALA* 3.7 32.1 - - + +
312B ILE* 5.0 2.0 - - + -
346B ALA* 4.3 12.6 - - + +
361B TRP* 3.8 29.2 - - + -
365B LEU* 3.2 23.5 + - + +
368B TYR* 1.3 87.9 - - + +
370B SER* 1.3 71.8 + - - +
371B TYR* 3.2 19.5 - - + -
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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