Contacts of the helix formed by residues 367 - 377 (chain A) in PDB entry 2JG3
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 ASP 367 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A LEU* 1.3 73.4 - - - +
368A PRO* 1.4 67.5 - - - +
369A SER* 3.4 10.7 + - - -
370A SER* 3.0 34.7 + - - +
371A LEU* 3.0 21.6 + - - +
408A GLU 4.1 10.7 - - - +
409A TYR 3.0 12.6 + - - +
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Residues in contact with PRO 368 (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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345A TRP* 3.8 52.3 - - + +
366A LEU* 3.5 21.3 - - + +
367A ASP* 1.4 86.5 - - - +
369A SER* 1.3 57.4 + - - +
371A LEU* 3.8 5.7 - - + +
372A VAL* 2.9 37.8 + - + +
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Residues in contact with SER 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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367A ASP* 3.3 9.0 + - - -
368A PRO* 1.3 79.4 - - - +
370A SER* 1.3 62.0 + - - +
372A VAL* 3.8 5.2 + - - +
373A GLN* 3.2 31.7 + - - +
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Residues in contact with SER 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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367A ASP* 3.0 33.8 + - - +
369A SER* 1.3 78.9 - - - +
371A LEU* 1.3 62.2 + - - +
373A GLN* 3.3 11.6 + - - +
374A TRP* 2.9 23.7 + - - +
408A GLU 4.0 2.0 + - - -
409A TYR* 3.4 33.7 - - - -
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Residues in contact with LEU 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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260A LEU* 4.6 0.9 - - + -
264A PHE* 3.6 35.2 - - + -
331A LEU* 3.9 13.7 - - + -
366A LEU* 4.8 10.3 - - + -
367A ASP 3.0 17.2 + - - +
368A PRO* 3.8 4.7 - - + +
370A SER* 1.3 78.8 + - - +
372A VAL* 1.3 62.6 + - + +
374A TRP* 3.2 8.2 + - + +
375A LEU* 2.9 44.2 + - + +
405A VAL* 3.7 39.3 - - + -
409A TYR* 3.8 20.6 - - + +
410A GLY* 5.7 1.6 - - - -
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Residues in contact with VAL 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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301A GLY* 4.0 14.4 - - - +
331A LEU* 3.8 26.5 - - + -
343A ALA* 3.6 13.7 - - - +
344A ALA* 4.1 2.7 - - - -
345A TRP* 4.1 22.0 - - + +
368A PRO* 2.9 24.2 + - + +
369A SER* 4.0 4.7 - - - +
371A LEU* 1.3 74.2 - - + +
373A GLN* 1.3 64.3 + - - +
375A LEU* 3.2 8.4 + - - +
376A ASN* 3.0 45.7 + - - +
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Residues in contact with GLN 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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369A SER* 3.2 23.9 + - - +
370A SER* 3.5 13.7 - - - +
372A VAL* 1.3 78.1 - - - +
374A TRP* 1.3 63.2 + - - +
376A ASN* 3.4 5.4 + - - +
377A SER* 3.1 22.5 + - - -
409A TYR* 6.1 0.2 - - + -
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Residues in contact with TRP 374 (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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253A LEU* 3.9 37.9 - - + -
370A SER 2.9 11.7 + - - +
371A LEU* 3.6 13.5 - - + +
373A GLN* 1.3 75.4 - - - +
375A LEU* 1.3 72.5 + - + +
377A SER* 2.6 48.7 + - - -
379A ALA* 3.9 18.8 - - + -
380A MET* 3.4 28.5 - - + +
404A PRO* 2.8 28.6 + - + -
405A VAL* 4.3 3.9 - - + +
406A ARG* 5.7 1.8 - - + -
409A TYR* 3.5 48.4 - + + -
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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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260A LEU* 4.1 24.7 - - + -
331A LEU* 3.9 26.7 - - + -
333A VAL* 4.7 7.0 - - + -
341A VAL* 3.3 19.8 - - + +
343A ALA* 3.9 26.0 - - + -
371A LEU* 2.9 34.5 + - + +
372A VAL 3.2 3.8 + - - +
374A TRP* 1.3 82.1 - - + +
376A ASN* 1.3 59.1 + - - +
377A SER 3.3 0.2 - - - -
380A MET* 3.4 28.4 - - + +
381A GLN* 3.1 16.1 + - - -
403A LEU* 4.2 9.6 - - + -
405A VAL* 5.2 1.6 - - + -
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Residues in contact with ASN 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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300A PRO* 3.7 19.0 - - + +
301A GLY* 3.3 14.1 - - - +
341A VAL 3.3 8.7 - - - +
342A VAL* 3.3 2.8 - - - -
343A ALA* 2.8 47.6 + - - -
372A VAL* 3.0 27.9 + - - +
373A GLN* 3.7 5.1 - - - +
374A TRP 3.2 0.2 - - - -
375A LEU* 1.3 73.6 - - - +
377A SER* 1.3 65.1 + - - +
378A GLU* 3.9 1.0 + - - +
381A GLN* 3.3 13.6 + - - +
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Residues in contact with SER 377 (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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373A GLN 3.1 12.3 + - - -
374A TRP* 2.6 39.3 + - - -
375A LEU 3.3 0.2 - - - -
376A ASN* 1.3 78.8 - - - +
378A GLU* 1.3 65.2 + - - +
379A ALA* 3.7 3.4 + - - -
380A MET* 3.2 12.6 + - - +
381A GLN* 3.1 24.7 + - - +
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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