Contacts of the helix formed by residues 287 - 294 (chain A) in PDB entry 4JYI
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ARG* 4.1 9.0 - - - +
270A TYR* 4.3 3.8 + - - -
275A ASP* 2.8 52.3 + - - +
286A ASN* 1.3 75.6 - - - +
288A THR* 1.3 63.7 + - - +
290A MET* 3.3 2.6 + - - +
291A HIS* 3.0 21.8 + - - +
299A THR* 3.7 18.5 - - + +
300A ASP* 3.0 33.0 + - - +
303A PHE* 3.5 45.6 - - + +
304A THR* 5.4 0.8 + - - +
307A ASN* 4.6 5.1 + - - -
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Residues in contact with THR 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A SER 4.1 4.7 - - - +
207A ALA 4.0 9.3 + - - +
208A ASP 4.8 4.0 + - - -
209A HIS* 3.3 44.1 - - - +
210A ARG* 3.7 16.0 + - + +
286A ASN* 3.2 10.2 + - - -
287A ARG* 1.3 78.8 - - - +
289A GLN* 1.3 58.4 + - - +
291A HIS* 3.4 6.6 - - - +
292A ASN* 3.0 37.8 + - - +
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Residues in contact with GLN 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A THR* 6.0 0.3 - - - -
203A THR* 2.8 40.9 + - - +
205A SER 3.0 18.7 + - - +
206A SER 3.5 18.2 - - - +
207A ALA* 3.6 12.7 - - - +
217A LEU* 3.6 13.8 - - + +
284A THR 4.3 2.4 - - - +
285A LEU* 3.4 22.8 - - + +
286A ASN* 2.7 42.4 + - - +
288A THR* 1.3 71.6 - - - +
290A MET* 1.3 55.4 + - - +
292A ASN* 3.1 1.4 + - - -
293A ALA* 2.7 37.0 + - - +
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Residues in contact with MET 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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221A PHE* 4.5 3.6 - - + -
266A ILE* 4.4 6.1 - - + -
277A MET* 4.0 19.7 - - + -
279A PHE* 3.6 35.4 - - + -
285A LEU* 3.9 20.6 - - + +
286A ASN 3.0 18.7 + - - +
287A ARG 3.6 6.3 - - - +
289A GLN* 1.3 74.5 - - - +
291A HIS* 1.3 63.6 + - - +
293A ALA* 3.3 11.6 + - - +
294A GLY 3.3 1.4 + - - -
295A PHE* 3.1 63.2 + - + +
303A PHE* 4.0 25.4 - - + -
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Residues in contact with HIS 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ARG* 3.3 45.7 + - + +
211A VAL 3.1 17.4 + - - +
212A ARG* 5.1 5.1 + - - +
213A LEU* 5.8 0.2 - - - +
287A ARG 3.0 12.9 + - - +
288A THR 3.4 9.0 - - - +
290A MET* 1.3 78.2 - - - +
292A ASN* 1.3 84.7 + - - +
294A GLY* 3.2 5.2 + - - -
296A GLY* 3.1 53.1 + - - +
297A PRO* 4.5 1.6 - - + -
299A THR* 3.1 20.5 + - + +
387A ARG* 5.2 0.2 + - - -
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Residues in contact with ASN 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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206A SER* 3.1 37.6 + - - +
209A HIS 3.0 23.8 + - - -
210A ARG* 3.3 1.6 - - - -
211A VAL* 2.8 30.5 + - + +
213A LEU* 3.7 6.4 - - - +
214A ASP* 2.9 32.4 + - + +
217A LEU* 4.0 1.8 - - + -
288A THR* 3.0 16.3 + - - +
289A GLN 3.8 3.8 - - - +
291A HIS* 1.3 99.5 - - - +
293A ALA* 1.3 60.2 + - - +
294A GLY 3.5 0.2 + - - -
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Residues in contact with ALA 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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213A LEU* 4.0 1.5 - - - +
217A LEU* 3.8 21.7 - - + +
218A TRP* 3.5 30.3 - - - +
221A PHE* 3.7 30.3 - - + -
285A LEU* 4.5 9.0 - - + -
289A GLN 2.7 20.5 + - - +
290A MET* 3.6 9.6 - - - +
291A HIS 3.2 0.4 - - - -
292A ASN* 1.3 74.4 - - - +
294A GLY* 1.3 57.8 + - - +
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Residues in contact with GLY 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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213A LEU* 4.4 3.8 - - - -
218A TRP* 4.9 0.2 - - - -
221A PHE* 4.8 6.1 - - - -
291A HIS 3.2 4.5 + - - -
292A ASN 3.3 0.6 - - - -
293A ALA* 1.3 81.2 - - - +
295A PHE* 1.3 69.6 + - - +
296A GLY 3.1 2.7 - - - -
387A ARG* 2.9 25.2 + - - +
391A LEU* 3.7 28.3 - - - +
501A JYI 4.3 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