Contacts of the helix formed by residues 325 - 338 (chain A) in PDB entry 2JI8
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 ASP 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A PRO 5.0 0.7 - - - +
195A ALA* 3.5 8.6 - - - +
196A GLN* 2.9 29.9 + - - +
307A ILE* 3.9 19.1 - - + +
324A GLY* 1.3 73.3 - - - -
326A ILE* 1.3 59.2 + - - +
327A LYS* 3.4 12.6 + - - +
328A SER* 2.6 45.0 + - - -
329A ALA* 3.0 24.1 + - - +
1568A ADP 3.4 13.5 - - - +
1570A PGE 4.4 17.4 + - - +
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Residues in contact with ILE 326 (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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223A GLY 3.5 30.7 - - - +
224A ALA* 3.7 5.2 - - - -
227A ALA* 4.1 7.0 - - + -
229A CYS* 3.8 16.4 - - - -
233A ILE* 4.2 7.0 - - + -
279A ILE* 3.7 23.1 - - + -
280A GLY* 3.8 11.9 - - - +
305A ILE* 3.9 20.9 - - + -
325A ASP* 1.3 68.7 - - - +
327A LYS* 1.3 60.7 + - - +
330A VAL* 2.8 45.4 + - + +
1568A ADP 3.0 43.4 + - + +
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Residues in contact with LYS 327 (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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227A ALA* 4.9 7.8 - - + +
228A GLN 4.2 11.6 + - - -
229A CYS* 3.8 35.9 - - + +
232A GLU* 4.5 14.4 - - + +
325A ASP* 3.3 10.2 + - - +
326A ILE* 1.3 77.7 - - - +
328A SER* 1.3 63.9 + - - +
330A VAL* 4.2 1.6 - - - +
331A SER* 3.1 27.2 + - - -
1570A PGE 6.5 1.3 - - - -
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Residues in contact with SER 328 (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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195A ALA* 3.7 10.6 - - - +
196A GLN 3.9 10.3 - - - -
197A ILE* 3.7 24.9 - - - +
198A PRO* 4.6 1.8 - - - -
325A ASP* 2.6 33.4 + - - -
327A LYS* 1.3 76.8 - - - +
329A ALA* 1.3 64.5 + - - +
331A SER* 3.6 4.8 - - - -
332A LEU* 3.3 27.5 + - - +
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Residues in contact with ALA 329 (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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198A PRO* 4.0 16.8 - - + +
203A ILE* 3.6 6.3 - - - +
305A ILE* 3.6 30.3 - - + -
322A VAL* 3.8 20.9 - - + -
324A GLY 5.1 2.2 - - - +
325A ASP 3.0 16.0 + - - +
326A ILE 3.9 0.4 - - - +
328A SER* 1.3 75.8 - - - +
330A VAL* 1.3 58.8 + - - +
332A LEU 3.3 1.4 + - - -
333A LEU* 2.9 29.4 + - - +
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Residues in contact with VAL 330 (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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229A CYS* 5.5 0.2 - - - -
232A GLU* 3.6 38.6 - - + +
233A ILE* 4.2 8.1 - - + +
236A LEU* 4.1 19.5 - - + -
279A ILE* 4.5 12.6 - - + -
305A ILE* 4.1 15.9 - - + -
326A ILE* 2.8 43.4 + - + +
327A LYS* 4.2 2.0 - - - +
329A ALA* 1.3 69.2 - - - +
331A SER* 1.3 61.3 + - - +
333A LEU* 3.2 6.9 + - - +
334A ARG* 2.9 30.8 + - - +
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Residues in contact with SER 331 (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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232A GLU* 3.5 25.5 + - - -
327A LYS* 3.1 21.3 + - - -
328A SER* 3.6 7.4 - - - -
330A VAL* 1.3 77.8 - - - +
332A LEU* 1.3 63.8 + - - +
334A ARG* 3.8 3.3 - - - +
335A LYS* 3.3 39.7 + - - +
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Residues in contact with LEU 332 (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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197A ILE* 3.4 33.4 - - + -
198A PRO* 3.7 16.6 - - + +
199A ALA 5.7 0.4 - - - -
200A GLU* 6.0 1.8 - - - +
203A ILE* 3.8 21.6 - - + +
328A SER 3.3 12.4 + - - +
329A ALA 3.7 6.3 - - - +
330A VAL 3.2 0.4 - - - -
331A SER* 1.3 78.7 - - - +
333A LEU* 1.3 61.3 + - - +
334A ARG 3.2 1.8 - - - -
335A LYS* 3.2 15.7 + - + +
336A ALA* 2.9 29.1 + - - +
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Residues in contact with LEU 333 (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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203A ILE* 3.9 21.6 - - + +
206A ALA* 4.2 9.9 - - + -
207A ALA* 4.1 23.8 - - + +
210A ILE* 4.1 18.8 - - + -
236A LEU* 4.2 20.9 - - + -
277A VAL* 5.0 7.2 - - + -
303A VAL* 5.4 0.9 - - + -
305A ILE* 4.4 18.8 - - + -
322A VAL* 6.2 0.9 - - + -
329A ALA 2.9 17.4 + - - +
330A VAL* 3.7 6.1 - - - +
332A LEU* 1.3 75.8 - - - +
334A ARG* 1.3 57.0 + - - +
336A ALA* 3.4 0.5 + - - +
337A LEU* 3.0 55.4 + - + +
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Residues in contact with ARG 334 (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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231A ASP 5.2 0.4 - - - -
232A GLU* 2.9 57.2 + - - +
235A ALA* 3.4 19.0 - - - +
236A LEU* 3.9 24.9 - - + +
239A GLU* 2.9 39.7 + - - +
330A VAL 2.9 16.2 + - - +
331A SER* 3.8 5.4 - - - +
333A LEU* 1.3 76.0 - - - +
335A LYS* 1.3 61.0 + - + +
337A LEU* 3.2 4.2 + - - +
338A LYS* 2.9 47.7 + - - +
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Residues in contact with LYS 335 (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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331A SER* 3.3 27.8 + - - +
332A LEU* 3.2 18.7 + - + +
334A ARG* 1.3 76.3 - - + +
336A ALA* 1.3 60.3 + - - +
338A LYS* 3.4 26.6 + - - +
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Residues in contact with ALA 336 (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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203A ILE* 3.6 22.2 - - + -
204A ALA* 5.5 1.6 - - - +
207A ALA* 4.0 16.8 - - + +
211A LYS* 4.0 18.5 + - - -
332A LEU 2.9 17.1 + - - +
333A LEU 3.6 6.1 - - - +
334A ARG 3.2 0.2 - - - -
335A LYS* 1.3 76.8 - - - +
337A LEU* 1.3 57.9 + - - +
338A LYS 3.5 0.6 - - - +
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Residues in contact with LEU 337 (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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207A ALA* 3.8 28.3 - - + +
210A ILE* 3.8 30.3 - - + -
211A LYS* 4.1 12.3 - - + +
236A LEU* 3.9 7.4 - - + -
240A THR* 3.6 31.0 - - + -
333A LEU* 3.0 41.3 + - + +
334A ARG* 3.6 3.8 - - - +
336A ALA* 1.3 76.5 - - - +
338A LYS* 1.3 67.5 + - - +
339A GLY 3.3 0.5 + - - -
340A ALA* 3.0 27.9 + - + +
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Residues in contact with LYS 338 (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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239A GLU* 3.6 37.0 + - + +
334A ARG* 2.9 35.8 + - - +
335A LYS* 3.4 21.8 + - - +
336A ALA 3.5 1.1 - - - +
337A LEU* 1.3 77.1 - - - +
339A GLY* 1.3 61.1 + - - +
340A ALA* 3.5 2.1 + - - +
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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