Contacts of the helix formed by residues 361 - 367 (chain N) in PDB entry 1OCR
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 SER 361 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293N PHE* 3.6 35.3 - - - +
302N ARG* 4.2 8.1 - - - -
306N THR* 3.0 25.3 - - - +
359N ALA 3.1 6.1 + - - -
360N ASN* 1.3 71.0 - - - +
362N SER* 1.3 62.5 + - - +
364N ASP* 3.2 8.3 + - - +
365N ILE* 3.3 17.9 + - - +
80O SER* 4.6 1.5 + - - -
81O LEU* 5.2 0.2 - - - +
84O LEU* 3.1 32.2 - - - +
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Residues in contact with SER 362 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360N ASN* 4.2 1.6 - - - +
361N SER* 1.3 82.8 + - - +
363N LEU* 1.3 66.4 + - - -
365N ILE* 3.3 19.8 + - - +
20O LEU* 4.1 15.4 - - - +
23O PHE* 4.3 5.5 - - - -
80O SER* 3.5 37.2 + - - -
83O ILE* 3.9 23.9 - - - +
84O LEU* 3.9 12.8 - - - -
87O MET* 4.2 11.1 - - - +
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Residues in contact with LEU 363 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357N VAL* 4.0 27.1 - - + +
360N ASN* 3.3 14.3 + - + +
362N SER* 1.3 81.6 + - - +
364N ASP* 1.3 63.5 + - - +
365N ILE 3.1 1.0 + - - -
366N VAL* 3.3 19.1 + - + +
367N LEU* 3.3 21.9 + - + +
9O PHE* 4.3 13.9 - - + -
20O LEU* 4.0 37.2 - - + +
23O PHE* 3.5 26.9 - - + -
24O HIS* 4.1 22.7 - - + -
27O THR* 5.1 2.7 - - - +
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Residues in contact with ASP 364 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290N HIS 4.2 2.1 - - - +
293N PHE* 3.3 33.6 + - + +
294N THR* 5.0 0.7 - - - -
357N VAL 5.3 0.2 + - - -
358N LEU* 3.7 22.9 - - - +
360N ASN 2.7 23.3 + - - +
361N SER 3.2 5.1 + - - +
363N LEU* 1.3 71.1 - - - +
365N ILE* 1.3 60.5 - - - +
366N VAL 3.2 0.2 - - - -
367N LEU* 3.6 5.6 - - - +
368N HIS* 2.6 47.8 + - - +
516N HEA 2.5 37.0 - - - +
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Residues in contact with ILE 365 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293N PHE* 3.9 22.0 - - + +
294N THR* 4.2 12.8 - - + -
302N ARG* 5.4 6.1 - - - +
361N SER 3.3 10.1 + - - +
362N SER 3.3 17.3 - - - +
363N LEU 3.1 0.2 - - - -
364N ASP* 1.3 76.5 - - - +
366N VAL* 1.3 54.2 + - + +
368N HIS* 4.2 0.2 - - - +
20O LEU* 5.6 1.6 - - + -
87O MET* 3.5 27.4 - - + -
169O GLY 3.8 18.6 - - - +
170O LEU* 4.1 1.8 - - - -
171O LYS* 2.7 73.1 + - + +
23U GLN* 5.7 4.0 - - - +
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Residues in contact with VAL 366 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363N LEU* 3.4 15.7 - - + +
365N ILE* 1.3 81.4 - - + +
367N LEU* 1.3 60.4 + - - +
370N THR* 3.6 10.2 - - - +
432N GLY 4.9 1.9 - - - +
433N LEU 5.5 1.3 - - - +
435N GLY* 5.9 0.7 - - - -
9O PHE* 4.0 33.9 - - + -
17O MET* 4.6 9.6 - - + -
20O LEU* 4.1 23.3 - - + -
166O PRO* 4.6 29.5 - - + +
169O GLY* 4.9 7.2 - - - -
170O LEU 5.5 2.0 - - - +
171O LYS* 3.3 13.9 + - - +
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Residues in contact with LEU 367 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357N VAL* 3.8 28.9 - - + -
358N LEU* 3.9 24.2 - - + -
363N LEU* 3.3 27.0 + - + +
364N ASP* 3.1 4.5 + - - +
366N VAL* 1.3 76.9 - - - +
368N HIS* 1.3 68.8 + - - +
370N THR* 2.6 25.7 + - - +
372N TYR* 4.0 22.9 - - + -
373N VAL* 3.5 7.3 - - - +
432N GLY 4.4 7.9 - - - +
433N LEU* 4.0 13.0 - - + -
9O PHE* 3.7 31.6 - - + -
24O HIS* 5.3 0.7 - - + -
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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