Contacts of the helix formed by residues 364 - 379 (chain A) in PDB entry 2I88
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 364 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A LEU 3.9 0.3 - - - +
360A THR* 3.7 7.8 - - - -
363A TYR* 1.3 87.6 - - - +
365A GLU* 1.3 65.9 + - - -
366A LYS* 3.0 4.7 - - - -
367A TYR* 3.4 13.3 - - - +
368A SER 3.3 15.1 + - - -
519A VAL 4.4 11.0 + - - -
520A LEU* 5.2 2.2 - - - +
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Residues in contact with GLU 365 (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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357A GLN* 5.0 6.4 + - - +
360A THR* 3.7 32.6 + - + +
363A TYR 3.6 0.2 + - - -
364A GLY* 1.3 71.9 - - - -
366A LYS* 1.3 66.4 + - + +
368A SER* 3.2 11.1 + - - -
369A LYS* 3.2 38.8 + - - +
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Residues in contact with LYS 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A GLY* 4.8 2.2 - - - -
365A GLU* 1.3 83.5 - - + +
367A TYR* 1.3 62.1 + - - +
369A LYS* 3.5 8.2 + - - +
370A MET* 3.1 22.5 + - - +
518A GLU* 3.4 24.8 + - - +
519A VAL* 3.5 29.3 - - + +
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Residues in contact with TYR 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A LEU* 4.2 23.6 - - + -
363A TYR* 3.8 33.0 - + + -
364A GLY* 3.3 25.7 + - - +
365A GLU 3.1 0.4 - - - -
366A LYS* 1.3 79.4 - - - +
368A SER* 1.3 67.2 + - - +
370A MET* 3.0 21.5 + - + +
371A ALA* 3.0 18.8 + - + +
484A PHE* 5.7 1.7 - - - -
487A LEU* 4.5 15.4 - - + +
497A ILE* 3.7 15.7 - - + +
500A VAL* 5.7 0.5 - - - +
501A THR* 2.9 39.0 + - + +
504A LEU* 5.8 2.3 - - - +
516A ILE* 5.9 0.9 - - + -
519A VAL* 3.2 18.5 - - + +
520A LEU* 3.8 20.4 - - + -
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Residues in contact with SER 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A TYR* 2.7 35.8 + - - +
357A GLN* 5.5 0.2 + - - -
359A LEU* 3.5 11.8 - - - +
360A THR* 3.1 29.8 + - - -
364A GLY 3.3 2.7 + - - -
365A GLU 3.2 7.3 + - - -
367A TYR* 1.3 80.7 - - - +
369A LYS* 1.3 62.1 + - - +
371A ALA* 3.2 8.0 + - - +
372A GLN* 3.2 28.7 + - - +
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Residues in contact with LYS 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A GLU* 3.2 33.8 + - - +
366A LYS* 3.9 7.2 - - - +
367A TYR 3.3 0.6 - - - -
368A SER* 1.3 74.0 - - - +
370A MET* 1.3 61.7 + - - +
372A GLN* 3.3 21.8 + - - +
373A GLU* 2.9 39.4 + - + +
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Residues in contact with MET 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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366A LYS 3.1 12.9 + - - +
367A TYR* 3.0 15.5 + - + +
369A LYS* 1.3 77.0 - - - +
371A ALA* 1.3 64.5 + - - +
373A GLU* 3.2 15.8 + - - +
374A LEU* 3.0 36.8 + - + +
501A THR* 4.7 10.8 - - + -
505A CYS* 4.3 7.2 - - - -
512A LYS* 3.6 53.1 - - + +
515A THR* 4.2 5.8 - - + -
516A ILE* 4.1 20.9 - - + +
519A VAL* 3.7 32.1 - - + -
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Residues in contact with ALA 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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356A TYR* 4.4 2.7 - - + -
359A LEU* 3.8 25.4 - - + -
367A TYR* 3.0 20.1 + - + +
368A SER 3.3 10.8 - - - +
370A MET* 1.3 76.7 - - - +
372A GLN* 1.3 51.9 + - - +
374A LEU* 3.1 13.9 + - - +
375A ALA* 2.7 32.9 + - - +
484A PHE* 3.7 24.1 - - + -
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Residues in contact with GLN 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A TYR* 3.4 48.7 - - + +
368A SER* 3.2 21.0 + - - +
369A LYS* 3.3 24.9 + - - +
371A ALA* 1.3 72.2 - - - +
373A GLU* 1.3 67.7 + - - +
375A ALA* 3.0 0.7 + - - +
376A ASP* 2.8 38.1 + - - +
434A TYR* 5.5 0.4 - - - +
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Residues in contact with GLU 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A LYS* 2.9 24.5 + - + +
370A MET* 3.4 15.6 + - - +
372A GLN* 1.3 75.8 - - - +
374A LEU* 1.3 59.2 + - + +
376A ASP* 3.5 8.5 - - - +
377A LYS* 2.9 34.7 + - - +
510A LYS* 4.0 16.8 + - - +
512A LYS* 3.9 28.4 + - - -
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Residues in contact with LEU 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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370A MET* 3.0 26.9 + - + +
371A ALA* 3.3 12.1 - - - +
373A GLU* 1.3 75.4 - - - +
375A ALA* 1.3 67.9 + - - +
377A LYS* 3.7 4.3 - - + +
378A SER* 3.2 19.6 + - - -
480A VAL* 5.3 0.9 - - + -
484A PHE* 5.4 2.9 - - + -
501A THR* 4.4 11.9 - - + -
504A LEU* 4.1 28.3 - - + -
505A CYS* 4.2 22.2 - - - -
508A ILE* 3.5 36.8 - - + +
510A LYS* 4.9 4.3 - - + +
512A LYS* 3.9 24.9 - - + -
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Residues in contact with ALA 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A TYR* 3.2 26.9 - - - +
371A ALA 2.7 14.5 + - - +
372A GLN 3.0 5.8 + - - +
374A LEU* 1.3 72.4 - - - +
376A ASP* 1.3 62.2 + - - +
378A SER* 2.6 23.8 + - - -
379A LYS* 3.7 9.4 + - - +
434A TYR* 4.0 14.6 - - + +
435A LEU* 3.8 10.8 - - + +
480A VAL* 4.5 8.1 - - - -
484A PHE* 4.0 12.5 - - + -
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Residues in contact with ASP 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A GLN* 2.8 30.6 + - - +
373A GLU* 3.5 7.5 - - - +
375A ALA* 1.3 74.3 - - - +
377A LYS* 1.3 65.9 + - - +
378A SER 2.9 2.1 + - - -
379A LYS* 3.0 38.5 + - - +
434A TYR* 3.6 16.6 + - - -
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Residues in contact with LYS 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 GLU 2.9 18.1 + - - +
374A LEU* 3.7 5.8 - - + +
376A ASP* 1.3 73.8 - - - +
378A SER* 1.3 58.6 + - - +
379A LYS 3.5 3.5 + - - +
381A LYS* 2.9 31.9 - - + +
508A ILE* 3.8 16.6 - - + -
509A ASP* 4.8 15.6 - - - +
510A LYS* 3.3 47.6 - - + +
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Residues in contact with SER 378 (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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374A LEU 3.2 10.2 + - - -
375A ALA 2.6 23.6 + - - -
376A ASP 3.1 0.2 - - - -
377A LYS* 1.3 76.4 - - - +
379A LYS* 1.3 68.2 + - - +
380A GLY 3.0 0.9 + - - -
381A LYS* 2.9 32.0 + - - +
435A LEU* 4.4 4.0 - - - +
476A VAL* 4.2 7.2 - - - -
477A SER* 4.0 14.7 + - - -
480A VAL* 3.8 15.3 - - - +
508A ILE* 3.6 22.0 - - - +
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Residues in contact with LYS 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ALA 3.7 5.2 - - - +
376A ASP* 3.0 35.2 + - - +
377A LYS 3.9 5.9 - - - +
378A SER* 1.3 79.8 + - - +
380A GLY* 1.3 58.5 + - - +
381A LYS* 3.4 4.2 + - - +
434A TYR* 4.0 44.8 + - - -
435A LEU* 4.1 24.7 - - + +
436A LYS* 5.9 1.8 - - + -
477A SER* 4.6 6.1 - - - -
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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