Contacts of the helix formed by residues 287 - 294 (chain B) in PDB entry 4JYH
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 ARG 287 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B ARG* 3.9 17.5 - - - +
270B TYR* 4.1 4.2 + - - -
275B ASP* 2.9 49.6 + - - +
286B ASN* 1.3 74.3 - - - +
288B THR* 1.3 57.6 + - - +
290B MET* 3.2 4.0 + - - +
291B HIS 3.0 22.9 + - - -
299B THR* 3.6 21.9 - - + +
300B ASP* 3.7 27.0 + - - +
303B PHE* 3.4 49.4 - - + +
304B THR* 5.4 1.0 + - - +
307B ASN* 4.5 5.5 + - - -
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Residues in contact with THR 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B SER 4.3 8.3 - - - +
207B ALA 4.3 8.5 - - - +
208B ASP 4.6 2.7 + - - +
209B HIS* 3.7 10.8 - - - +
210B ARG* 3.5 47.1 + - + +
286B ASN* 2.9 16.7 + - - +
287B ARG* 1.3 80.7 - - - +
289B GLN* 1.3 58.1 + - - +
291B HIS* 3.2 6.7 - - - +
292B ASN* 2.9 32.2 + - - +
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Residues in contact with GLN 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B THR* 5.9 0.5 - - - -
203B THR* 3.1 40.0 + - - +
205B SER 2.9 28.1 + - - +
206B SER 3.9 2.2 - - - +
207B ALA* 3.3 22.0 - - - +
217B LEU* 3.6 15.0 - - + +
284B THR 4.3 2.1 - - - +
285B LEU* 3.5 22.0 - - + +
286B ASN* 2.7 43.4 + - - +
288B THR* 1.3 70.7 - - - +
290B MET* 1.3 59.2 + - - +
291B HIS 3.2 0.2 - - - -
292B ASN* 3.2 2.2 + - - -
293B ALA* 2.8 30.5 + - - +
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Residues in contact with MET 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B PHE* 4.8 0.9 - - + -
266B ILE* 4.1 7.2 - - + -
277B MET* 3.8 22.4 - - + -
279B PHE* 4.0 23.3 - - + -
285B LEU* 3.9 31.2 - - + +
286B ASN 3.0 11.0 + - - +
287B ARG 3.4 7.9 - - - +
289B GLN* 1.3 73.2 - - - +
291B HIS* 1.3 65.4 + - - +
293B ALA* 3.3 9.3 + - - +
294B GLY 3.4 1.6 + - - -
295B PHE* 3.1 68.2 + - + +
299B THR* 4.9 0.2 - - + -
303B PHE* 3.7 29.6 - - + -
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Residues in contact with HIS 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ARG* 2.9 43.9 + - + +
211B VAL 3.1 21.9 + - - -
212B ARG* 4.7 5.4 + - - +
287B ARG 3.0 12.0 + - - +
288B THR* 3.2 13.5 - - - +
290B MET* 1.3 76.7 - - - +
292B ASN* 1.3 78.1 + - - +
294B GLY* 3.3 2.3 + - - -
295B PHE* 3.2 18.0 + - - -
296B GLY* 3.3 37.7 + - - +
297B PRO* 4.8 0.7 - - + -
299B THR* 3.2 17.8 + - + +
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Residues in contact with ASN 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B SER* 3.2 24.0 + - - -
209B HIS 3.2 23.0 + - - -
210B ARG* 3.5 2.4 - - - -
211B VAL* 3.1 33.6 + - + +
213B LEU* 3.8 5.4 - - - +
214B ASP* 2.8 34.3 + - + +
217B LEU* 3.8 16.8 - - + -
288B THR 2.9 16.3 + - - +
289B GLN 3.2 0.6 + - - -
291B HIS* 1.3 92.3 - - - +
293B ALA* 1.3 63.3 + - - +
294B GLY 3.2 1.3 + - - -
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Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B LEU* 3.9 1.5 - - - +
217B LEU* 3.9 17.3 - - + -
218B TRP* 3.3 32.3 - - - +
221B PHE* 3.8 33.9 - - + -
285B LEU* 4.4 9.0 - - + -
289B GLN 2.8 17.0 + - - +
290B MET* 3.6 11.0 - - - +
291B HIS 3.2 0.4 - - - -
292B ASN* 1.3 77.8 - - - +
294B GLY* 1.3 57.2 + - - +
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Residues in contact with GLY 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ARG 5.7 0.2 - - - -
213B LEU* 3.9 15.9 - - - -
218B TRP* 4.8 0.7 - - - -
221B PHE* 5.2 3.1 - - - -
291B HIS 3.8 2.7 - - - -
292B ASN 3.2 2.8 - - - -
293B ALA* 1.3 81.9 - - - +
295B PHE* 1.3 66.1 + - - +
296B GLY 3.4 2.2 - - - -
387B ARG* 3.0 27.6 + - - +
391B LEU* 3.8 19.8 - - - +
501B JYH 4.8 3.1 - - - -
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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