Contacts of the helix formed by residues 365 - 376 (chain A) in PDB entry 2ODP
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 PRO 365 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A THR* 4.0 18.8 - - + -
320A TYR* 4.0 17.0 - - + +
323A LEU* 3.9 12.1 - - + +
359A SER* 4.7 7.2 - - - +
363A GLY 3.4 5.6 - - - +
364A SER* 1.3 85.2 - - - +
366A LYS* 1.3 64.0 + - - +
368A ALA* 3.0 15.1 + - - +
369A VAL* 3.0 15.0 + - - +
402A GLU* 3.6 23.6 - - - +
405A GLU* 4.7 9.4 - - - +
406A LEU* 3.7 22.2 - - + -
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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
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364A SER* 3.1 15.5 + - - +
365A PRO* 1.3 78.1 - - - +
367A THR* 1.3 58.0 + - - +
369A VAL* 3.2 10.8 + - + +
370A ASP* 2.7 64.4 + - - +
405A GLU* 5.7 5.5 + - + +
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Residues in contact with THR 367 (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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320A TYR* 3.9 14.4 - - + +
364A SER* 3.4 18.0 + - - -
365A PRO 3.1 1.0 - - - -
366A LYS* 1.3 77.6 - - - +
368A ALA* 1.3 57.6 + - - +
370A ASP* 3.8 5.3 - - - +
371A HIS* 3.0 53.3 + - + +
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Residues in contact with ALA 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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320A TYR* 3.6 26.7 - - + -
323A LEU* 3.7 25.1 - - + +
324A ASN* 3.8 15.9 - - + +
327A TYR* 5.0 1.5 - - + +
365A PRO 3.0 8.3 + - - +
367A THR* 1.3 76.8 - - - +
369A VAL* 1.3 66.1 + - - +
371A HIS* 3.3 8.5 + - - +
372A ILE* 3.0 29.7 + - - +
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Residues in contact with VAL 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LEU* 4.1 18.2 - - + -
365A PRO* 3.0 16.5 + - + +
366A LYS* 3.2 12.8 + - + +
368A ALA* 1.3 76.3 - - - +
370A ASP* 1.3 59.7 + - - +
372A ILE* 3.2 10.7 + - - +
373A ARG* 2.9 43.7 + - + +
388A ILE* 3.9 29.8 - - + -
405A GLU 6.1 0.4 - - - +
406A LEU* 4.9 12.3 - - + +
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Residues in contact with ASP 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A LYS* 2.7 59.1 + - - +
367A THR* 3.8 5.7 - - - +
369A VAL* 1.3 70.8 - - - +
371A HIS* 1.3 69.1 + - + +
373A ARG* 3.4 21.9 + - - +
374A GLU* 3.1 24.1 + - - +
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Residues in contact with HIS 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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320A TYR* 4.8 8.6 + - - -
324A ASN* 5.0 6.0 + - - +
327A TYR* 3.5 36.6 - + + -
367A THR* 3.0 40.7 + - + +
368A ALA* 3.3 11.0 + - - +
370A ASP* 1.3 75.5 - - + +
372A ILE* 1.3 57.8 + - - +
374A GLU* 3.2 21.5 + - - +
375A ILE 3.0 24.3 + - - -
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Residues in contact with ILE 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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323A LEU* 3.7 28.5 - - + +
326A VAL* 4.1 2.2 - - + -
327A TYR* 3.9 21.1 - - + +
330A MET* 3.8 24.9 - - + -
351A ILE* 3.9 22.0 - - + -
368A ALA 3.0 20.7 + - - +
369A VAL* 3.4 9.4 - - - +
371A HIS* 1.3 74.1 - - - +
373A ARG* 1.3 65.7 + - - +
375A ILE* 3.4 6.9 - - - +
376A LEU* 3.1 37.0 + - + +
386A LEU* 3.9 18.8 - - + -
388A ILE* 5.4 2.2 - - + -
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Residues in contact with ARG 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 VAL* 2.9 27.0 + - + +
370A ASP* 3.7 24.2 + - - +
372A ILE* 1.3 76.5 - - - +
374A GLU* 1.3 60.2 + - - +
377A ASN* 3.2 2.4 + - - -
378A ILE* 3.0 73.6 + - + +
379A ASN 6.1 0.4 - - - -
383A ASN* 4.6 7.5 + - - -
386A LEU* 3.8 19.5 - - + +
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Residues in contact with GLU 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 ASP 3.1 11.3 + - - +
371A HIS* 3.4 30.9 - - - +
372A ILE 3.1 0.2 - - - -
373A ARG* 1.3 75.8 - - - +
375A ILE* 1.3 66.0 + - - +
377A ASN* 3.1 15.3 + - - +
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Residues in contact with ILE 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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327A TYR* 3.9 23.1 - - + +
330A MET* 4.1 10.1 - - + -
331A ASN* 3.5 49.6 - - + +
334A MET* 3.7 36.9 - - + +
344A TRP* 4.2 9.7 + - + -
371A HIS 3.0 15.9 + - - +
372A ILE* 3.4 15.3 - - - +
374A GLU* 1.3 75.8 - - - +
376A LEU* 1.3 75.2 + - + +
377A ASN* 3.3 2.6 + - - +
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Residues in contact with LEU 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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330A MET* 3.8 22.2 - - + -
344A TRP* 3.7 22.9 - - + +
349A HIS* 3.4 51.6 - - + +
372A ILE* 3.1 29.4 + - + +
375A ILE* 1.3 78.5 - - + +
377A ASN* 1.3 67.6 + - - +
378A ILE* 3.3 14.7 + - + +
382A ARG* 2.7 33.7 + - - +
385A TYR* 4.1 5.8 - - + +
386A LEU* 3.9 12.6 - - + -
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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