Contacts of the helix formed by residues 286 - 294 (chain G) in PDB entry 4P0S
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 GLU 286 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278G THR 5.2 7.5 - - - +
285G PRO* 1.3 75.8 - - - +
287G LEU* 1.3 68.5 + - - +
288G LEU* 4.8 4.7 - - + +
289G ARG* 3.3 36.2 + - + +
290G GLU* 3.6 10.1 + - - +
405G ILE* 5.6 3.1 - - - -
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Residues in contact with LEU 287 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273G VAL* 4.3 11.9 - - + -
277G GLU 5.0 14.1 - - - +
278G THR* 6.1 2.5 - - - -
286G GLU* 1.3 74.5 - - - +
288G LEU* 1.3 66.7 - - + +
290G GLU* 3.0 6.1 + - + -
291G LEU* 3.0 48.6 + - + +
308G PHE* 4.2 27.6 - - + -
334G ARG* 6.5 0.2 - - - -
405G ILE* 4.5 19.3 - - + +
408G SER* 6.2 0.4 - - - -
409G ALA* 3.9 23.1 - - + +
412G LEU* 4.6 5.6 - - + -
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Residues in contact with LEU 288 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286G GLU* 3.4 6.0 - - + +
287G LEU* 1.3 79.3 - - + +
289G ARG* 1.3 58.2 + - - +
291G LEU* 4.3 10.3 - - + -
292G GLN* 2.8 53.5 + - - +
298G HIS* 3.3 34.8 - - + +
300G VAL* 5.4 13.7 - - + -
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Residues in contact with ARG 289 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285G PRO* 5.4 4.5 - - + -
286G GLU* 3.3 33.4 + - + +
287G LEU 3.2 1.2 - - - -
288G LEU* 1.3 78.9 - - - +
290G GLU* 1.3 62.4 + - + +
292G GLN* 4.3 18.3 + - - +
293G ARG* 3.1 25.1 + - - +
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Residues in contact with GLU 290 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285G PRO* 5.5 13.8 - - + +
286G GLU 3.6 7.7 + - - +
287G LEU* 3.0 7.4 + - + +
289G ARG* 1.3 79.9 - - + +
291G LEU* 1.3 61.3 + - - +
293G ARG* 3.1 33.6 + - - +
294G LEU* 2.7 42.0 + - - +
405G ILE* 5.9 3.8 - - + -
406G LYS* 3.5 37.2 + - + +
409G ALA* 3.6 22.7 - - + -
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Residues in contact with LEU 291 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271G LEU* 4.4 16.8 - - + -
273G VAL* 4.6 5.2 - - + -
287G LEU* 3.0 53.9 + - + +
288G LEU* 3.8 10.3 - - + +
290G GLU* 1.3 75.1 - - - +
292G GLN* 1.3 63.4 + - - +
294G LEU* 3.1 5.5 + - - -
296G VAL* 3.1 48.6 + - + +
298G HIS* 4.4 24.7 - - + +
409G ALA* 3.9 24.2 - - + +
412G LEU* 4.3 11.0 - - + -
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Residues in contact with GLN 292 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288G LEU* 2.8 39.9 + - - +
289G ARG* 4.3 20.6 + - - +
291G LEU* 1.3 72.5 - - - +
293G ARG* 1.3 63.1 + - - +
295G HIS* 3.2 17.0 + - - +
296G VAL 4.9 2.0 - - - +
298G HIS* 3.7 29.6 + - + -
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Residues in contact with ARG 293 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289G ARG 3.1 19.8 + - - +
290G GLU* 3.1 27.9 + - - +
292G GLN* 1.3 81.9 - - - +
294G LEU* 1.3 85.7 + - - +
295G HIS* 3.5 15.9 + - - -
406G LYS* 2.9 37.7 - - - +
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Residues in contact with LEU 294 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290G GLU* 2.7 35.8 + - - +
291G LEU 3.1 0.6 + - - +
292G GLN 3.1 0.4 - - - -
293G ARG* 1.3 106.0 - - - +
295G HIS* 1.3 74.8 + - - +
296G VAL* 3.2 20.4 + - + +
406G LYS* 4.8 2.7 - - - +
409G ALA* 4.1 6.3 - - + -
410G ALA* 4.0 34.8 - - + +
413G ALA* 4.4 8.2 - - + +
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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