Contacts of the helix formed by residues 364 - 371 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355B PHE* 5.3 11.4 - - + +
360B LYS 4.1 3.1 - - - +
361B LEU* 2.8 49.6 - - + +
363B GLU* 1.3 77.8 - - - +
365B LEU* 1.3 63.9 + - - +
367B TYR* 3.9 11.3 - - + +
368B LEU* 3.1 32.9 + - + +
381B ILE* 4.2 19.7 - - + -
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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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361B LEU 3.9 6.0 + - - +
362B GLN* 3.7 8.1 + - - +
364B VAL* 1.3 79.2 - - - +
366B ASP* 1.3 62.1 + - - +
367B TYR 3.0 2.3 + - - -
368B LEU* 3.1 5.9 + - + +
369B THR* 2.8 44.2 + - - +
379B PRO* 4.5 20.6 - - + +
380B ALA* 5.3 0.7 - - - +
381B ILE* 4.8 15.7 - - + +
393B TYR* 2.9 38.6 - - + +
395B GLN* 4.1 24.9 - - - +
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Residues in contact with ASP 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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362B GLN* 2.8 25.7 + - - +
363B GLU* 5.1 3.1 - - - -
365B LEU* 1.3 86.6 - - - +
367B TYR* 1.3 57.4 + - - +
369B THR* 4.0 4.8 - - - -
370B ASN* 3.0 48.4 + - - +
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Residues in contact with TYR 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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351B GLN* 5.6 4.9 + - + +
353B ILE* 3.9 21.2 - - + +
355B PHE* 4.2 43.7 - + + -
363B GLU 3.8 20.9 + - - +
364B VAL* 3.9 11.5 - - + +
365B LEU 3.0 0.8 - - - -
366B ASP* 1.3 76.8 - - - +
368B LEU* 1.3 70.9 + - + +
371B SER* 2.8 60.8 + - - +
373B SER* 4.8 4.0 + - - -
374B LEU* 3.9 21.2 - - + +
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Residues in contact with LEU 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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364B VAL* 3.1 21.1 - - + +
365B LEU* 3.1 8.6 + - + +
367B TYR* 1.3 89.9 - - + +
369B THR* 1.3 62.0 + - - +
374B LEU* 3.3 36.9 - - + +
375B GLN 3.6 1.4 + - - -
376B MET* 3.3 33.8 + - - +
379B PRO* 4.5 15.3 - - + -
381B ILE* 4.3 18.4 - - + -
904B VAL* 4.1 26.5 - - + -
916B PHE* 5.7 9.4 - - + -
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Residues in contact with THR 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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365B LEU* 2.8 32.3 + - - +
366B ASP* 4.3 5.8 - - - +
368B LEU* 1.3 75.3 - - - +
370B ASN* 1.3 69.7 + - - +
375B GLN* 3.9 9.2 - - - +
376B MET 3.6 22.4 - - - +
377B LYS* 5.5 0.4 - - - -
378B SER 5.3 3.4 - - - +
379B PRO* 3.6 22.2 - - + +
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Residues in contact with ASN 370 (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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366B ASP* 3.0 41.8 + - - +
369B THR* 1.3 91.1 - - - +
371B SER* 1.3 68.4 + - - +
372B ALA* 2.8 7.4 + - - +
375B GLN* 4.9 3.0 - - - +
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Residues in contact with SER 371 (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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366B ASP 4.1 0.2 + - - -
367B TYR* 2.8 54.5 + - - +
369B THR 3.9 0.2 - - - -
370B ASN* 1.3 67.6 - - - +
372B ALA* 1.3 53.3 + - - +
373B SER* 2.4 40.0 + - - -
374B LEU* 2.8 21.1 + - - -
375B GLN 3.1 9.2 + - - -
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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