Contacts of the helix formed by residues 281 - 293 (chain A) in PDB entry 5JJA
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 LEU 281 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A LEU* 4.2 16.2 - - + -
244A LYS* 4.1 28.5 - - + -
247A LEU* 3.6 29.6 - - + -
248A LEU* 5.1 12.1 - - + -
274A PHE* 4.1 18.6 - - + +
275A LEU* 3.6 9.6 - - + -
278A ASP* 3.4 21.7 + - + +
279A SER 3.1 1.2 - - - -
280A THR* 1.3 79.6 + - - +
282A THR* 1.3 62.7 + - - +
283A GLU 3.4 1.1 + - - -
284A PRO* 3.7 14.2 - - + +
285A VAL* 3.3 23.2 + - - +
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Residues in contact with THR 282 (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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275A LEU* 3.7 23.6 - - + +
279A SER* 2.7 26.3 + - - -
280A THR 3.2 1.6 - - - -
281A LEU* 1.3 76.7 - - - +
283A GLU* 1.3 64.9 + - - +
285A VAL* 3.3 2.3 + - - +
286A VAL* 3.0 35.2 + - + +
311A ILE* 5.1 0.4 - - + -
315A ILE* 3.8 36.4 - - + +
316A GLU 5.6 0.3 + - - -
319A GLU* 3.9 19.0 - - + +
323A ILE* 4.7 5.2 - - + -
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Residues in contact with GLU 283 (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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280A THR 4.5 1.9 + - - +
282A THR* 1.3 78.3 - - - +
284A PRO* 1.3 74.0 - - + +
287A MET* 3.0 40.3 + - + +
319A GLU* 4.4 5.0 + - - +
322A LYS* 3.7 39.9 + - + +
323A ILE* 4.0 23.4 - - + +
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Residues in contact with PRO 284 (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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248A LEU* 4.0 26.0 - - + -
252A LEU* 4.1 2.5 - - - +
280A THR 4.3 5.8 - - - +
281A LEU* 3.7 22.9 - - + +
283A GLU* 1.3 97.7 - - + +
285A VAL* 1.3 60.9 + - - +
287A MET* 4.1 3.7 - - + +
288A ALA* 3.1 25.5 + - - +
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Residues in contact with VAL 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A LEU* 3.8 36.6 - - + -
248A LEU* 5.3 0.4 - - + -
252A LEU* 4.3 17.9 - - + +
271A VAL* 3.5 27.4 - - + -
275A LEU* 4.1 17.5 - - + -
281A LEU 3.3 17.8 + - - +
282A THR 3.3 3.5 + - - +
283A GLU 3.2 0.8 - - - -
284A PRO* 1.3 75.6 - - + +
286A VAL* 1.3 61.2 + - - +
288A ALA* 3.2 3.6 + - - +
289A LEU* 2.9 29.3 + - + +
311A ILE* 4.1 15.7 - - + -
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Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LEU* 5.5 0.2 - - + -
282A THR* 3.0 35.4 + - + +
283A GLU 4.2 1.6 - - - +
285A VAL* 1.3 75.4 - - + +
287A MET* 1.3 57.9 + - - +
289A LEU* 3.2 8.7 + - - +
290A LEU* 2.9 44.1 + - + +
308A LEU* 4.5 19.1 - - + -
311A ILE* 4.1 22.9 - - + -
315A ILE* 5.3 0.7 - - + -
323A ILE* 4.0 34.8 - - + -
327A LEU* 4.6 4.7 - - + -
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Residues in contact with MET 287 (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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283A GLU* 3.0 37.6 + - + +
284A PRO* 4.2 4.3 - - + +
286A VAL* 1.3 75.4 - - - +
288A ALA* 1.3 57.7 + - - +
290A LEU* 3.4 16.1 + - + +
291A LYS* 3.0 27.1 + - - +
322A LYS 6.0 0.2 - - - +
323A ILE* 4.1 16.6 - - + -
326A PRO* 4.1 30.7 - - + -
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Residues in contact with ALA 288 (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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252A LEU* 3.8 22.7 - - + -
284A PRO 3.1 20.5 + - - +
285A VAL 3.6 3.4 - - - +
287A MET* 1.3 73.2 - - - +
289A LEU* 1.3 67.0 + - - +
291A LYS* 3.1 18.4 + - - +
292A TYR* 3.0 44.6 + - + -
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Residues in contact with LEU 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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252A LEU* 5.5 2.3 - - + +
255A HIS* 3.9 13.0 - - + +
285A VAL* 2.9 15.3 + - + +
286A VAL* 3.5 9.9 - - - +
288A ALA* 1.3 75.0 - - - +
290A LEU* 1.3 58.6 + - + +
292A TYR* 3.3 5.9 + - - -
293A TRP* 3.0 33.8 + - + +
304A PHE* 3.5 32.3 - - + +
307A GLU* 3.4 28.0 - - + +
308A LEU* 3.9 42.0 - - + +
311A ILE* 4.1 18.2 - - + -
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Residues in contact with LEU 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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286A VAL* 2.9 29.3 + - + +
287A MET* 3.7 19.7 - - + +
288A ALA 3.2 0.2 - - - -
289A LEU* 1.3 75.7 - - + +
291A LYS* 1.3 62.7 + - - +
293A TRP* 3.4 28.8 - - + +
295A LYS* 5.4 1.9 + - - -
308A LEU* 5.3 4.3 - - + -
323A ILE 5.2 0.2 - - - +
326A PRO* 3.7 37.0 - - + +
327A LEU* 3.9 14.4 - - + +
330A GLN* 3.9 35.8 + - + +
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Residues in contact with LYS 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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287A MET 3.0 13.4 + - - +
288A ALA* 3.1 19.4 + - - +
290A LEU* 1.3 78.3 - - - +
292A TYR* 1.3 98.4 + - + +
293A TRP 3.6 0.5 + - - -
295A LYS* 3.8 25.2 + - - +
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Residues in contact with TYR 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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252A LEU* 3.3 30.7 - - + +
253A PRO* 3.8 24.5 - - + +
255A HIS* 3.9 27.1 - + + +
256A LYS* 3.7 34.6 - - + +
288A ALA* 3.0 38.1 + - + +
289A LEU* 3.3 4.0 + - - +
291A LYS* 1.3 102.9 + - + +
293A TRP* 1.3 66.0 + - - +
294A PRO* 3.4 3.3 - - - +
304A PHE* 3.6 14.2 - - + -
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Residues in contact with TRP 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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289A LEU* 3.0 19.3 + - + +
290A LEU* 3.4 25.4 - - + +
291A LYS 3.3 4.4 - - - +
292A TYR* 1.3 78.1 - - - +
294A PRO* 1.3 96.5 - - + +
295A LYS* 3.3 13.5 + - - +
301A GLU* 2.9 28.0 + - - +
304A PHE* 3.8 46.7 - + + -
305A LEU* 3.8 25.1 - - + -
308A LEU* 3.9 25.1 - - + -
330A GLN* 3.5 38.8 + - + +
334A CYS* 3.7 19.7 - - - -
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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