Contacts of the helix formed by residues 364 - 371 (chain H) in PDB entry 1R4N
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 VAL 364 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355H PHE* 5.3 12.6 - - + +
360H LYS 4.1 3.8 - - - +
361H LEU* 2.8 48.7 - - + +
363H GLU* 1.3 77.1 - - - +
365H LEU* 1.3 62.2 + - - +
366H ASP 3.6 0.2 - - - -
367H TYR* 3.9 12.1 - - + +
368H LEU* 3.1 33.6 + - + +
381H ILE* 4.2 19.1 - - + -
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Residues in contact with LEU 365 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361H LEU 3.9 5.8 + - - +
362H GLN* 3.7 8.4 + - - +
364H VAL* 1.3 77.9 - - - +
366H ASP* 1.3 60.3 + - - +
367H TYR 3.0 4.3 + - - -
368H LEU* 3.1 5.9 + - + +
369H THR* 2.8 47.4 + - - +
379H PRO* 4.6 17.7 - - + +
380H ALA* 5.7 0.7 - - - -
381H ILE* 4.8 16.4 - - + +
393H TYR* 3.0 38.4 - - + +
395H GLN* 4.1 25.1 - - - +
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Residues in contact with ASP 366 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362H GLN* 2.8 25.6 + - - +
363H GLU* 5.1 2.9 - - - -
365H LEU* 1.3 84.8 - - - +
367H TYR* 1.3 57.4 + - - +
369H THR* 4.4 4.8 - - - -
370H ASN* 3.0 48.3 + - - +
371H SER 4.1 0.2 + - - -
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Residues in contact with TYR 367 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351H GLN* 5.6 4.7 + - + +
353H ILE* 3.9 21.6 - - + +
355H PHE* 4.2 44.2 - + + -
363H GLU 3.7 20.8 + - - +
364H VAL* 3.9 10.9 - - + +
365H LEU 3.0 0.6 - - - -
366H ASP* 1.3 76.7 - - - +
368H LEU* 1.3 70.9 + - + +
371H SER* 2.8 61.2 + - - +
373H SER* 4.7 3.8 + - - -
374H LEU* 3.9 21.2 - - + +
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Residues in contact with LEU 368 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364H VAL* 3.1 21.5 + - + +
365H LEU* 3.1 7.8 + - + +
367H TYR* 1.3 89.4 - - + +
369H THR* 1.3 62.3 + - - +
374H LEU* 3.3 35.5 - - + +
375H GLN 3.6 1.2 + - - -
376H MET* 3.3 34.3 + - - +
379H PRO* 4.5 16.2 - - + -
381H ILE* 4.3 19.3 - - + -
904H VAL* 4.1 25.6 - - + -
916H PHE* 5.7 9.4 - - + -
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Residues in contact with THR 369 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365H LEU* 2.8 32.3 + - - +
366H ASP* 4.3 6.3 - - - +
368H LEU* 1.3 74.1 - - - +
370H ASN* 1.3 69.2 + - - +
375H GLN* 3.9 9.2 - - - -
376H MET 3.6 22.9 - - - +
377H LYS* 5.5 0.4 - - - -
378H SER* 5.3 3.4 - - - +
379H PRO* 3.6 21.7 - - + +
395H GLN* 5.5 0.2 + - - -
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Residues in contact with ASN 370 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366H ASP* 3.0 42.3 + - - +
369H THR* 1.3 92.0 - - - +
371H SER* 1.3 66.7 + - - +
372H ALA* 2.8 8.1 + - - +
375H GLN* 4.9 3.6 - - - +
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Residues in contact with SER 371 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366H ASP 4.1 0.4 + - - -
367H TYR* 2.8 53.8 + - - +
369H THR 3.9 0.2 - - - -
370H ASN* 1.3 68.3 - - - +
372H ALA* 1.3 53.1 + - - +
373H SER* 2.4 39.7 + - - -
374H LEU* 2.8 22.3 + - - -
375H GLN 3.1 8.7 + - - -
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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