Contacts of the helix formed by residues 284 - 293 (chain O) in PDB entry 5C7O
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 284 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283O THR* 1.3 72.8 + - - +
285O ALA* 1.3 58.3 + - - +
286O ALA 3.3 2.7 - - - -
287O LYS* 3.2 11.9 + - - +
288O ALA* 2.8 31.9 + - - +
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Residues in contact with ALA 285 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223O SER* 3.8 7.6 - - - +
225O THR* 3.5 35.2 - - + -
226O THR* 2.9 30.6 + - - +
229O LEU* 5.2 0.4 - - - -
247O MET* 4.6 0.9 - - + -
283O THR* 3.1 20.9 + - + +
284O GLY* 1.3 78.8 - - - +
286O ALA* 1.3 61.2 + - - +
288O ALA* 3.4 1.1 + - - -
289O VAL* 3.3 18.2 + - - +
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Residues in contact with ALA 286 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229O LEU* 4.0 14.4 - - + -
247O MET* 4.0 23.2 - - + +
283O THR 4.8 1.4 + - - +
284O GLY 3.3 0.6 - - - -
285O ALA* 1.3 74.7 - - - +
287O LYS* 1.3 67.3 + - - +
289O VAL* 3.1 19.2 + - - +
290O THR 3.8 0.5 + - - -
300O LEU* 3.8 15.5 - - + +
301O THR* 3.3 37.0 - - - +
302O GLY* 3.7 4.7 - - - +
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Residues in contact with LYS 287 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284O GLY* 3.2 13.1 + - - +
286O ALA* 1.3 78.8 - - - +
288O ALA* 1.3 58.1 + - - +
290O THR* 2.6 37.8 + - - +
291O LYS* 3.7 16.4 + - - +
300O LEU 3.7 18.7 + - - +
301O THR* 4.2 13.5 + - - +
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Residues in contact with ALA 288 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195O PRO* 5.9 3.1 - - + -
201O MET* 4.0 27.1 - - + +
226O THR* 3.5 14.4 - - + +
284O GLY 2.8 17.7 + - - +
285O ALA* 3.5 8.3 - - - +
286O ALA 3.2 0.2 - - - -
287O LYS* 1.3 77.1 - - - +
289O VAL* 1.3 58.1 + - - +
291O LYS* 2.9 33.7 + - + +
292O VAL* 3.5 6.1 + - - +
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Residues in contact with VAL 289 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226O THR* 4.0 7.9 - - + +
229O LEU* 3.8 27.1 - - + -
230O ALA* 3.8 24.7 - - + +
233O ALA* 4.1 4.5 - - + -
285O ALA 3.5 14.1 - - - +
286O ALA 3.1 10.5 + - - +
287O LYS 3.1 0.6 - - - -
288O ALA* 1.3 77.0 - - - +
290O THR* 1.3 55.4 + - - +
291O LYS 3.1 0.2 - - - -
292O VAL* 3.3 10.1 + - - +
293O ILE* 2.8 47.5 + - + +
296O LEU* 4.5 1.8 - - + -
300O LEU* 3.7 21.5 - - + -
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Residues in contact with THR 290 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286O ALA 4.0 1.8 - - - +
287O LYS* 2.6 26.8 + - + +
289O VAL* 1.3 75.5 - - - +
291O LYS* 1.3 68.5 + - - +
293O ILE 3.4 18.6 - - - +
294O PRO* 3.4 12.5 - - - +
296O LEU* 3.1 35.4 - - + +
297O LYS* 3.8 14.8 + - - +
298O GLY 4.6 2.9 + - - +
300O LEU* 3.8 33.2 - - + +
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Residues in contact with LYS 291 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201O MET* 4.8 13.0 - - + -
207O ASN* 5.0 1.6 + - - -
287O LYS* 4.3 14.7 + - - +
288O ALA* 2.9 24.4 + - - +
290O THR* 1.3 88.7 + - - +
292O VAL* 1.3 64.2 + - + +
294O PRO* 4.2 11.6 - - - +
297O LYS* 6.0 5.3 - - - +
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Residues in contact with VAL 292 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201O MET* 3.8 30.3 - - + +
203O VAL* 4.1 13.2 - - + -
206O VAL* 3.7 24.1 - - + +
207O ASN* 3.5 44.5 - - - +
210O ASP* 5.3 0.3 - - - +
226O THR* 5.0 0.7 - - + -
230O ALA* 4.0 14.1 - - + -
288O ALA 4.1 4.3 - - - +
289O VAL* 3.3 23.1 - - - +
291O LYS* 1.3 78.3 - - + +
293O ILE* 1.3 62.2 + - + +
294O PRO* 3.7 7.5 - - - +
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Residues in contact with ILE 293 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206O VAL* 3.7 13.5 - - + -
230O ALA* 3.5 25.4 - - - +
233O ALA 4.2 0.4 - - - -
234O LYS* 3.7 26.0 - - + +
237O HIS* 4.7 8.3 - - + -
289O VAL* 2.8 26.8 + - + +
290O THR* 3.4 9.2 - - - +
292O VAL* 1.3 82.5 - - + +
294O PRO* 1.3 60.0 - - - +
295O GLU* 3.7 15.9 - - + +
296O LEU* 2.9 47.9 + - + +
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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