Contacts of the helix formed by residues 267 - 270 (chain K) 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 ILE 267 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203K LEU* 4.1 12.6 - - + -
232K GLY* 5.3 0.7 - - - -
264K ILE* 3.3 31.9 - - + -
265K ASP 3.7 0.4 - - - -
266K GLU* 1.3 72.8 - - - +
268K ASP* 1.3 53.5 + - - +
269K ALA 3.1 0.7 - - - -
270K ILE* 2.8 10.5 + - + +
271K ALA* 2.7 35.1 + - + +
292K LEU* 5.3 2.5 - - + -
309K MET* 2.9 64.4 - - + -
311K THR* 3.1 21.5 - - + +
317K LEU* 4.3 11.2 - - + -
321K LEU* 4.1 19.7 - - + -
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Residues in contact with ASP 268 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266K GLU* 2.8 3.7 + - + -
267K ILE* 1.3 80.2 - - - +
269K ALA* 1.3 59.1 + - - +
270K ILE 3.0 1.2 + - - -
271K ALA 3.4 8.0 - - - +
272K THR* 2.6 44.2 - - - +
311K THR* 4.1 8.9 - - + +
312K ASN* 6.3 1.6 - - - +
313K ARG* 5.8 7.6 - - + +
316K THR* 2.7 29.1 + - - +
317K LEU* 4.4 8.6 - - + +
242L ARG* 4.1 15.1 + - - -
245L GLU* 5.1 0.9 - - - +
254L GLN* 4.8 4.3 - - - +
255L ARG* 5.9 0.3 - - - -
258L MET* 2.7 37.0 - - + +
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Residues in contact with ALA 269 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232K GLY 3.3 24.3 - - - +
233K SER* 3.4 24.2 - - - +
236K VAL* 5.7 2.6 - - - +
266K GLU* 3.2 7.6 + - + +
267K ILE 3.1 1.0 - - - -
268K ASP* 1.3 78.8 + - - +
270K ILE* 1.3 65.4 + - - +
272K THR* 5.0 0.2 - - - -
285K VAL* 4.1 4.9 - - - +
255L ARG* 3.1 39.8 + - + +
258L MET* 4.1 9.3 - - + +
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Residues in contact with ILE 270 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232K GLY* 2.9 33.9 - - - +
235K PHE* 3.4 39.7 - - + -
236K VAL* 5.0 2.9 - - + +
264K ILE* 5.6 2.5 - - + -
267K ILE* 2.8 11.8 + - + +
269K ALA* 1.3 83.7 - - - +
271K ALA* 1.3 62.8 + - + +
272K THR* 3.6 4.5 + - - -
275K PHE* 4.1 4.0 - - - -
285K VAL* 2.9 26.1 - - + +
288K ILE* 3.4 33.0 - - + +
289K LEU* 3.9 22.9 - - + +
292K LEU* 4.8 9.6 - - + -
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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