Contacts of the helix formed by residues 293 - 301 (chain M) in PDB entry 1JH0
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 ASN 293 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192M VAL 5.2 2.0 + - - -
193M HIS 3.6 4.3 - - - -
194M GLY* 3.5 20.7 - - - +
291M VAL* 3.5 4.5 - - - +
292M ASP* 1.3 82.5 + - + +
294M TRP* 1.3 58.7 + - - +
295M TYR* 2.8 34.9 + - - +
296M VAL* 2.9 31.5 + - + +
297M TRP* 3.1 27.2 + - - +
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Residues in contact with TRP 294 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H ALA* 4.5 6.5 - - + -
193M HIS* 2.9 35.7 + - + +
195M ASN 4.1 4.7 - - - +
196M LEU* 4.3 6.3 - - + -
198M TYR* 3.1 29.8 - - + +
199M ASN* 3.3 45.9 - - + +
200M PRO* 3.5 23.6 - - + -
201M PHE* 5.1 2.0 - + - -
283M GLY 4.2 2.0 - - - -
286M LEU* 3.7 25.4 - - + -
287M SER* 2.8 24.9 + - - +
291M VAL* 3.6 38.2 + - + +
293M ASN* 1.3 70.9 - - - +
295M TYR* 1.3 60.8 - - - +
297M TRP* 4.0 27.5 - + - +
298M GLY* 3.1 20.0 + - - -
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Residues in contact with TYR 295 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194M GLY* 3.8 13.6 + - - +
198M TYR* 4.0 37.7 - + + -
293M ASN* 2.8 13.1 + - - +
294M TRP* 1.3 77.7 - - - +
296M VAL* 1.3 77.1 + - + +
298M GLY* 3.1 11.1 + - - -
299M GLN* 3.1 41.9 + - + +
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Residues in contact with VAL 296 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293M ASN* 2.9 33.7 + - + +
295M TYR* 1.3 83.0 - - + +
297M TRP* 1.3 57.8 + - - +
299M GLN* 2.6 36.5 + - + +
300M ASN* 3.3 20.1 + - - +
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Residues in contact with TRP 297 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H ASP* 3.5 28.9 + - - -
13H ALA* 3.6 22.0 - - + +
14H SER* 3.8 21.1 - - - -
17H ILE* 5.0 9.6 - - + -
198M TYR 4.6 3.4 - - - -
200M PRO* 4.1 30.3 - - + -
291M VAL* 3.8 23.6 - - + -
293M ASN 3.1 15.4 + - - +
294M TRP* 4.0 19.3 - + - +
296M VAL* 1.3 78.8 - - - +
298M GLY* 1.3 72.7 + - - +
299M GLN 2.7 8.7 + - - -
300M ASN* 2.8 4.9 + - - +
301M HIS* 2.5 65.9 + + + +
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Residues in contact with GLY 298 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198M TYR* 5.4 6.1 - - - -
294M TRP 3.1 12.2 + - - -
295M TYR* 3.1 10.9 + - - -
296M VAL 3.1 1.4 - - - -
297M TRP* 1.3 92.0 - - - +
299M GLN* 1.3 60.7 + - - +
301M HIS* 3.7 17.3 + - - -
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Residues in contact with GLN 299 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295M TYR* 3.1 43.6 + - + +
296M VAL* 2.6 22.6 + - + +
298M GLY* 1.3 79.2 - - - +
300M ASN* 1.3 64.8 + - - +
301M HIS* 4.1 6.6 + - - -
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Residues in contact with ASN 300 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296M VAL* 3.3 28.5 + - - +
297M TRP* 2.8 9.7 + - - +
299M GLN* 1.3 79.5 - - - +
301M HIS* 1.3 82.6 + - - +
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Residues in contact with HIS 301 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H ASP* 4.1 9.1 + - - +
14H SER* 3.0 25.8 + - - +
18H TYR* 6.1 3.1 - + + -
297M TRP* 2.5 66.3 + + + +
298M GLY* 3.7 19.9 + - - -
299M GLN 4.1 6.0 + - - -
300M ASN* 1.3 97.0 + - - +
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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