Contacts of the helix formed by residues 287 - 293 (chain A) in PDB entry 4OWW
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 GLY 287 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A ILE 5.3 0.4 - - - -
278A PRO* 4.2 10.4 - - - +
285A PHE* 3.4 9.2 - - - -
286A THR* 1.3 83.2 + - - +
288A ILE* 1.3 63.1 + - - -
289A LEU* 2.9 9.8 + - - -
290A GLN* 3.1 23.9 + - - +
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Residues in contact with ILE 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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255A VAL* 4.1 20.0 - - + -
271A TRP* 3.7 24.9 - - + -
274A ILE* 3.9 23.8 + - + +
275A ILE* 5.3 5.2 - - + -
285A PHE* 3.8 13.1 - - + -
287A GLY* 1.3 71.0 - - - -
289A LEU* 1.3 60.6 + - - +
291A LEU* 3.0 8.0 + - + +
292A LEU* 2.9 40.4 + - + +
445A TYR* 4.2 16.4 - - + -
448A LEU* 4.1 12.3 - - + -
98C LEU* 3.6 27.1 - - + -
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Residues in contact with LEU 289 (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 GLY* 2.9 3.3 + - - +
288A ILE* 1.3 82.6 - - - +
290A GLN* 1.3 57.4 + - - +
292A LEU* 4.4 2.0 - - - -
293A GLN* 2.9 57.7 + - + +
401A PHE* 3.8 28.0 - - + -
448A LEU* 4.1 23.1 - - + -
451A HIS* 3.8 30.1 - - + +
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Residues in contact with GLN 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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245A MET* 5.0 0.8 - - - +
248A LEU* 3.7 22.7 - - + +
284A GLN 3.2 20.8 + - - +
285A PHE* 3.8 13.4 - - + +
286A THR* 2.9 36.7 + - - +
287A GLY 3.1 14.1 + - - +
289A LEU* 1.3 79.0 - - - +
291A LEU* 1.3 63.6 + - - +
293A GLN* 3.7 9.3 + - - +
294A SER* 3.5 19.9 + - - -
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Residues in contact with LEU 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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244A PHE* 4.7 8.1 - - + -
248A LEU* 3.6 43.5 - - + +
251A GLY* 3.4 31.6 - - - +
252A ARG* 3.4 9.1 + - - -
254A LEU* 4.0 19.1 - - + -
255A VAL* 3.7 25.1 - - + -
258A LEU* 5.7 2.9 - - + -
274A ILE* 6.2 1.6 - - + -
285A PHE* 4.4 10.5 - - + -
288A ILE* 3.0 14.2 + - + +
290A GLN* 1.3 80.6 - - - +
292A LEU* 1.3 63.2 + - - +
294A SER* 3.0 25.2 + - - +
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Residues in contact with LEU 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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252A ARG* 2.8 37.8 + - + -
255A VAL* 3.9 24.2 - - + -
288A ILE* 2.9 37.0 + - + +
289A LEU 3.2 4.5 + - - +
291A LEU* 1.3 75.7 - - - +
293A GLN* 1.3 57.6 + - - +
294A SER 3.3 0.7 - - - -
397A TYR* 4.5 6.1 - - + +
401A PHE* 3.6 51.9 - - + +
444A PHE* 4.0 21.3 - - + -
445A TYR* 5.5 0.2 - - + -
448A LEU* 3.8 18.4 - - + -
98C LEU* 4.7 2.0 - - + -
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Residues in contact with GLN 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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252A ARG* 3.7 7.5 + - - +
289A LEU* 2.9 49.0 + - + +
290A GLN* 4.1 8.1 - - - +
291A LEU 3.2 0.6 - - - -
292A LEU* 1.3 77.3 - - - +
294A SER* 1.3 59.0 + - - +
295A ARG 4.1 0.5 + - - -
401A PHE* 4.5 17.1 - - + +
406A LYS* 3.1 48.0 + - + +
451A HIS* 4.2 13.3 + - - -
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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