Contacts of the helix formed by residues 286 - 291 (chain L) in PDB entry 5GJQ
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 ASP 286 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313K ARG* 4.1 1.0 + - - -
239L GLY 4.0 9.0 + - - +
240L GLY 3.5 2.8 + - - -
241L ARG* 4.1 17.7 - - - +
242L ARG* 2.3 53.0 + - - +
257L LEU* 4.1 11.4 - - + +
261L LEU* 5.3 0.8 - - + +
285L LEU* 1.3 75.8 - - - +
287L PRO* 1.4 98.3 - - - +
288L ALA* 3.0 15.8 + - - +
289L LEU* 3.0 24.0 + - + +
290L LEU* 3.8 6.5 + - - +
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Residues in contact with PRO 287 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208K PRO* 4.1 21.6 - - + +
313K ARG* 4.2 8.7 - - - +
241L ARG* 3.9 31.4 - - - +
285L LEU 3.7 0.4 - - - +
286L ASP* 1.4 89.6 - - - +
288L ALA* 1.3 57.2 + - - +
289L LEU 2.8 6.9 + - - -
290L LEU* 3.5 15.1 + - + +
291L ARG* 4.0 8.1 + - - +
389L VAL* 6.5 0.7 - - + -
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Residues in contact with ALA 288 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208K PRO* 3.7 15.3 - - + -
312K ASN* 3.6 24.2 - - - +
501K ADP 5.6 0.2 - - - +
242L ARG* 4.4 6.5 - - - +
261L LEU* 3.8 10.8 - - + -
286L ASP* 3.0 19.8 + - - +
287L PRO* 1.3 77.7 - - - +
289L LEU* 1.3 57.6 + - - +
291L ARG* 3.6 8.3 - - - +
294L ARG* 2.9 31.9 + - - +
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Residues in contact with LEU 289 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235L ILE* 4.9 10.8 - - + -
239L GLY 4.6 7.6 - - - +
257L LEU* 4.5 17.0 - - + -
260L LEU* 5.7 2.0 - - + -
261L LEU* 3.6 22.0 - - + +
264L MET* 4.1 14.1 - - + -
277L MET* 3.5 31.4 - - + -
285L LEU* 4.3 23.1 - - + -
286L ASP* 3.0 15.2 + - + +
287L PRO 2.8 1.4 + - - -
288L ALA* 1.3 78.1 - - - +
290L LEU* 1.3 68.8 + - + +
291L ARG 3.0 3.7 + - - -
294L ARG* 3.3 16.2 - - + +
295L LEU* 3.2 18.4 - - + +
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Residues in contact with LEU 290 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171L LEU* 4.4 10.1 - - + -
282L PRO* 4.9 5.2 - - + +
285L LEU* 3.9 37.9 - - + +
286L ASP 4.1 11.9 - - - +
287L PRO* 3.5 7.5 + - + +
289L LEU* 1.3 76.1 - - + +
291L ARG* 1.3 63.0 - - - +
292L PRO* 3.5 2.4 - - - +
295L LEU* 3.1 37.9 - - + +
298L LYS* 4.1 23.8 + - + +
388L PRO* 4.6 14.4 - - + -
389L VAL* 3.5 33.0 - - + +
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Residues in contact with ARG 291 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208K PRO* 3.8 26.9 - - + +
209K GLY* 4.4 1.3 - - - -
213K THR* 6.3 0.4 - - - -
373K ALA* 3.7 24.9 - - - +
374K ASP* 4.1 5.8 - - - +
501K ADP 3.8 26.8 + - - -
265L ASP* 1.6 44.4 + - - +
287L PRO 4.0 7.6 + - - +
288L ALA 3.6 17.7 - - - +
289L LEU 3.0 2.2 - - - -
290L LEU* 1.3 77.8 - - - +
292L PRO* 1.3 110.4 + - + +
293L GLY* 3.6 5.7 + - - -
294L ARG* 2.7 42.9 + - - +
295L LEU 3.1 5.5 + - - -
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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