Contacts of the helix formed by residues 288 - 295 (chain A) in PDB entry 5JLH
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 288 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ILE 5.7 0.2 - - - -
165A TYR* 3.5 56.3 - - + -
170A LEU* 3.8 24.9 - - + -
284A CYS* 4.1 4.9 - - + -
285A ASP* 3.6 16.8 - - + +
287A ASP* 1.3 77.0 - - - +
289A ARG* 1.3 66.7 + - - +
290A LYS* 2.8 8.1 + - - +
291A ASP* 2.5 29.3 + - - +
292A LEU* 3.5 24.7 + - + +
62C GLY* 4.1 21.5 - - - -
63C ILE* 4.9 3.4 - - + -
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Residues in contact with ARG 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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281A ILE* 2.9 30.6 + - + +
282A MET* 2.7 52.1 + - - +
284A CYS* 2.8 18.6 + - + -
285A ASP 3.5 11.4 - - - +
286A VAL* 3.6 29.8 - - - +
287A ASP 3.4 1.4 - - - -
288A ILE* 1.3 77.9 - - - +
290A LYS* 1.3 64.2 + - - +
292A LEU* 3.0 11.3 + - + +
293A TYR* 2.9 34.6 + - + -
243C ASP* 2.7 52.2 + - - +
245C GLN* 5.2 1.4 + - - -
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Residues in contact with LYS 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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165A TYR* 5.3 6.7 + - - -
287A ASP* 3.6 31.3 + - - +
288A ILE* 2.8 10.6 + - - +
289A ARG* 1.3 77.4 - - - +
291A ASP* 1.3 76.8 + - + +
293A TYR* 3.6 4.9 + - - +
294A ALA* 3.4 18.2 + - - +
324A MET* 3.6 24.1 - - + +
325A LYS 5.0 1.0 - - - +
59C SER 5.2 5.7 + - - -
242C PRO* 3.7 28.2 + - + +
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Residues in contact with ASP 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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148A THR* 3.2 20.9 + - - +
165A TYR* 3.2 27.9 - - - -
288A ILE* 2.5 27.4 + - - +
290A LYS* 1.3 88.2 + - + +
292A LEU* 1.3 69.6 + - - +
294A ALA* 3.0 5.2 + - + +
295A ASN* 2.6 51.3 + - - +
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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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148A THR* 4.3 1.1 - - + -
149A GLY* 3.4 37.2 - - - +
150A ILE* 3.6 11.6 - - + +
163A PRO* 4.0 10.1 - - + -
164A ILE 3.7 14.8 - - - +
165A TYR* 5.5 0.2 - - - -
281A ILE* 4.2 22.0 - - + -
284A CYS* 3.8 22.7 - - + -
288A ILE* 3.8 31.4 - - + +
289A ARG* 3.0 11.5 + - - +
291A ASP* 1.3 88.8 + - - +
293A TYR* 1.3 63.5 + - - +
295A ASN* 3.1 10.2 + - - +
296A THR* 3.3 14.9 + - - -
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Residues in contact with TYR 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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278A PHE* 3.9 22.0 - + - -
281A ILE* 3.7 24.1 - - + +
282A MET* 3.2 26.9 - - - +
289A ARG* 2.9 42.7 + - + -
290A LYS 3.7 6.7 - - - +
292A LEU* 1.3 77.1 - - - +
294A ALA* 1.3 58.2 + - - +
295A ASN 3.7 0.2 + - - -
296A THR* 3.9 4.9 + - - -
316A ILE* 4.3 9.6 - - + -
320A ALA* 3.7 20.4 - - + -
321A PRO* 4.3 9.2 - - + +
324A MET* 3.5 20.0 - - - -
325A LYS 4.8 0.7 - - - +
326A ILE* 3.1 54.6 - - + +
327A LYS 3.3 7.1 - - - +
243C ASP* 4.0 10.8 + - - -
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Residues in contact with ALA 294 (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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290A LYS 3.4 9.7 + - - +
291A ASP* 3.0 10.1 + - - +
293A TYR* 1.3 78.7 - - - +
295A ASN* 1.3 70.1 + - - +
325A LYS 3.8 15.9 - - - +
327A LYS* 2.9 44.8 - - + +
329A ILE* 5.2 0.5 - - - +
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Residues in contact with ASN 295 (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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146A ARG* 2.9 31.4 - - - +
148A THR* 3.5 22.9 - - - +
149A GLY* 3.3 19.3 - - - -
291A ASP* 2.6 45.5 + - - +
292A LEU 3.1 4.7 + - - -
294A ALA* 1.3 94.2 + - - +
296A THR* 1.3 63.4 + - - +
297A VAL* 3.2 10.7 + - - +
327A LYS* 4.6 5.7 - - - +
329A ILE* 4.2 4.9 - - - -
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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