Contacts of the helix formed by residues 287 - 294 (chain A) in PDB entry 1NOZ
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 LEU 287 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ASP* 3.7 22.4 - - - +
213A TRP* 3.7 46.2 - - + +
286A SER* 1.3 71.8 - - - +
288A GLU* 1.3 64.8 + - - +
290A VAL* 3.8 0.6 - - - -
291A ALA* 2.6 42.7 + - + +
324A ASP* 4.0 31.4 - - + +
327A SER* 3.9 23.1 - - - +
328A VAL* 4.4 9.2 - - + -
331A ILE* 4.5 4.9 - - + -
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Residues in contact with GLU 288 (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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286A SER* 3.5 18.0 + - - +
287A LEU* 1.3 88.2 + - - +
289A SER* 1.3 52.4 + - - +
291A ALA* 3.5 3.6 - - - +
292A GLN* 2.6 40.1 + - - +
299A LYS* 3.7 30.3 + - + -
324A ASP* 4.3 4.6 - - - +
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Residues in contact with SER 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A LEU* 4.6 6.0 - - - +
283A PRO* 6.4 0.9 - - - -
284A SER* 3.4 36.9 - - - -
286A SER* 2.5 28.8 + - - -
288A GLU* 1.3 73.4 - - - +
290A VAL* 1.3 58.0 + - - +
292A GLN* 3.8 4.7 - - - +
293A HIS* 2.9 31.9 + - - +
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Residues in contact with VAL 290 (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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213A TRP* 3.3 41.1 - - + -
274A TYR* 3.6 28.0 - - + -
282A LEU* 4.4 6.3 - - + -
285A PHE* 3.5 29.4 - - + +
286A SER 2.9 25.3 + - - +
287A LEU 3.8 1.6 - - - +
289A SER* 1.3 75.9 - - - +
291A ALA* 1.3 52.6 + - - +
293A HIS* 3.0 7.7 + - - +
294A GLU* 2.7 37.2 + - - +
331A ILE* 3.7 13.0 - - + -
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Residues in contact with ALA 291 (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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287A LEU* 2.6 24.5 + - + +
288A GLU* 3.7 3.4 - - - +
290A VAL* 1.3 73.5 - - - +
292A GLN* 1.3 57.5 + - - +
295A THR* 2.8 42.2 + - + +
297A LYS 4.2 3.1 - - - +
327A SER* 3.7 29.8 - - - +
331A ILE* 3.9 15.7 - - + +
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Residues in contact with GLN 292 (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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288A GLU 2.6 23.9 + - - +
289A SER* 3.8 5.8 - - - +
291A ALA* 1.3 73.4 - - - +
293A HIS* 1.3 58.4 + - - +
296A LYS* 3.2 51.0 + - - +
297A LYS 3.6 16.1 + - - +
298A GLY* 3.9 13.3 - - - +
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Residues in contact with HIS 293 (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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274A TYR* 3.7 9.1 + - - -
280A THR* 4.7 6.1 - - + -
282A LEU* 4.1 28.6 - - + +
289A SER 2.9 20.3 + - - +
290A VAL* 3.3 4.9 - - - +
292A GLN* 1.3 79.9 - - - +
294A GLU* 1.3 83.5 + - - +
296A LYS* 3.6 26.2 + - - +
335A ARG* 5.1 5.4 - - - -
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Residues in contact with GLU 294 (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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274A TYR* 2.6 34.1 + - - -
290A VAL 2.7 18.6 + - - +
291A ALA 4.0 0.2 - - - +
293A HIS* 1.3 91.1 + - - +
295A THR* 1.3 64.1 + - - +
296A LYS* 3.3 7.8 + - - +
331A ILE* 3.9 31.0 - - + -
334A ILE* 3.7 33.6 - - + +
335A ARG* 2.9 32.5 + - + -
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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