Contacts of the helix formed by residues 281 - 294 (chain A) in PDB entry 1JD7
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 GLY 281 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277A THR 4.3 0.4 + - - -
278A PHE 3.1 14.4 + - - -
279A GLU 3.3 3.2 + - - -
280A ASP* 1.3 75.7 - - - +
282A ARG* 1.3 62.0 + - - -
284A TYR* 3.0 16.6 + - - +
285A ASP* 3.1 11.4 + - - +
339A TRP* 3.9 15.0 - - - -
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Residues in contact with ARG 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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280A ASP 3.1 2.4 + - - -
281A GLY* 1.3 68.4 - - - -
283A LEU* 1.3 66.8 + - - +
285A ASP* 3.1 29.6 + - - +
286A LEU* 3.0 31.6 + - + +
341A TYR* 3.7 33.9 + - - -
436A TRP* 2.8 53.1 + - + +
437A ASP* 3.8 12.1 + - - +
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Residues in contact with LEU 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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233A PHE* 4.0 25.5 - - + +
234A ARG* 3.8 33.2 - - + +
276A ILE* 3.8 22.4 - - + -
280A ASP* 3.0 22.4 + - + +
282A ARG* 1.3 78.6 - - - +
284A TYR* 1.3 61.7 + - - +
286A LEU* 3.4 5.0 + - + +
287A ALA* 3.1 23.6 + - - +
383A LYS* 4.0 10.1 - - + -
436A TRP* 3.5 37.1 - - + -
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Residues in contact with TYR 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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260A VAL* 3.7 11.5 - - + +
261A ASP* 2.6 31.9 + - - -
276A ILE* 3.4 20.7 - - + +
277A THR* 3.0 37.0 - - - +
278A PHE* 4.1 6.7 - - - -
280A ASP 3.8 0.6 + - - -
281A GLY 3.0 13.6 + - - +
283A LEU* 1.3 78.1 - - - +
285A ASP* 1.3 63.4 + - - +
287A ALA* 3.4 1.7 + - - +
288A ASN* 2.7 56.9 + - - -
301A VAL* 5.7 0.2 - - - +
302A MET* 3.6 19.1 + - - +
336A GLU* 3.9 19.3 + - + -
339A TRP* 3.8 20.2 - + + -
342A ILE* 3.7 14.4 - - + -
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Residues in contact with ASP 285 (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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281A GLY 3.1 11.6 + - - +
282A ARG* 3.1 42.2 + - - +
284A TYR* 1.3 77.2 - - - +
286A LEU* 1.3 58.0 + - - +
288A ASN* 3.2 6.2 + - - +
289A VAL* 2.9 33.5 + - - +
339A TRP* 3.3 26.8 - - - +
341A TYR* 3.6 34.5 + - + +
342A ILE* 4.2 5.4 - - - +
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Residues in contact with LEU 286 (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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233A PHE* 3.5 26.8 - - + -
282A ARG* 3.0 21.4 + - - +
283A LEU* 3.7 5.4 - - - +
284A TYR 3.3 0.2 - - - -
285A ASP* 1.3 74.6 - - + +
287A ALA* 1.3 65.4 + - - +
289A VAL* 3.2 6.4 + - + +
290A PHE 2.9 18.4 + - - -
341A TYR* 5.2 4.3 - - + -
381A ILE* 3.7 18.1 - - + +
382A ASN 4.6 1.6 - - - +
383A LYS* 4.7 7.6 - - + -
436A TRP* 4.1 39.9 - - + +
437A ASP* 3.8 30.5 - - - +
438A ALA* 4.1 12.1 - - + -
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Residues in contact with ALA 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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229A LEU* 3.9 13.4 - - + +
233A PHE* 3.8 17.6 - - + -
260A VAL* 4.1 24.2 - - + -
276A ILE* 4.2 17.3 - - + -
283A LEU 3.1 15.9 + - - +
284A TYR* 3.9 4.7 - - - +
285A ASP 3.4 0.2 - - - -
286A LEU* 1.3 76.8 - - - +
288A ASN* 1.3 57.0 + - - +
290A PHE* 3.2 4.5 + - - +
291A MET* 3.0 27.7 + - - +
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Residues in contact with ASN 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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260A VAL* 3.8 12.3 - - - +
284A TYR* 2.7 66.2 + - - +
285A ASP 3.4 4.3 - - - +
287A ALA* 1.3 75.1 - - - +
289A VAL* 1.3 59.8 + - - +
291A MET* 3.7 20.4 - - - +
292A LEU* 2.9 39.6 + - + +
301A VAL* 4.7 5.7 - - - +
302A MET 5.6 0.2 + - - -
342A ILE* 3.6 37.3 - - + +
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Residues in contact with VAL 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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285A ASP 2.9 22.8 + - - +
286A LEU* 3.5 10.8 - - - +
288A ASN* 1.3 75.3 - - - +
290A PHE* 1.3 63.8 + - - +
292A LEU* 4.0 5.0 - - - +
293A ALA* 3.1 24.6 + - + +
341A TYR* 4.1 23.8 - - + +
345A GLY* 5.3 3.4 - - - -
379A MET* 4.2 7.6 - - + -
381A ILE* 4.0 20.4 - - + -
405A LEU* 3.8 42.2 - - + -
438A ALA* 4.5 2.9 - - + -
439A MET 5.3 2.0 - - - +
440A ALA* 5.3 2.9 - - + -
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Residues in contact with PHE 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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225A TYR* 4.3 2.0 - - - -
229A LEU* 3.5 21.8 - - + -
233A PHE* 4.1 8.3 - + + -
241A LEU* 3.7 35.7 - - + -
244A PHE* 3.8 25.4 - + + -
286A LEU 2.9 13.1 + - - +
287A ALA 3.4 6.7 - - - +
289A VAL* 1.3 77.8 - - - +
291A MET* 1.3 58.6 + - - +
293A ALA* 3.1 1.6 + - - +
294A TYR* 2.7 77.9 + + + +
361A TRP* 4.3 3.6 - + - -
369A ILE* 4.0 21.8 - - + -
371A PHE* 4.2 14.4 - + - -
379A MET* 4.4 2.9 - - + -
381A ILE* 4.0 10.1 - - + +
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Residues in contact with MET 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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225A TYR* 3.0 34.7 + - + +
229A LEU* 4.4 2.2 - - + -
258A VAL* 4.3 2.0 - - + -
259A PHE* 3.5 33.9 - - - -
260A VAL* 3.8 15.7 - - + +
287A ALA 3.0 15.2 + - - +
288A ASN* 3.7 24.5 - - - +
290A PHE* 1.3 78.1 - - - +
292A LEU* 1.3 75.8 + - + +
294A TYR* 3.1 9.4 - - - +
296A TYR 4.9 1.0 - - - +
299A PRO* 3.9 21.7 - - + +
300A ARG 4.5 8.3 - - - +
301A VAL* 4.7 7.2 - - + -
349A ARG* 3.0 18.2 + - - -
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Residues in contact with LEU 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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4A THR* 4.0 33.9 - - + +
288A ASN* 2.9 27.2 + - + +
289A VAL 4.3 0.7 - - - +
291A MET* 1.3 91.1 - - + +
293A ALA* 1.3 57.0 + - - +
299A PRO* 4.2 7.4 - - + -
301A VAL* 4.4 2.2 - - + -
342A ILE* 3.2 42.2 - - + +
345A GLY* 3.6 22.7 - - - +
346A VAL* 3.6 13.5 - - + +
349A ARG* 2.7 39.1 + - + +
373A ARG* 4.8 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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289A VAL* 3.1 22.0 + - + +
290A PHE 3.8 1.1 - - - +
292A LEU* 1.3 76.1 - - - +
294A TYR* 1.3 62.6 + - - +
295A PRO* 3.5 2.9 - - - +
345A GLY* 5.7 0.2 - - - -
348A PHE* 3.6 27.3 - - + -
371A PHE* 3.8 17.1 - - + -
373A ARG* 3.0 29.6 + - - -
379A MET* 4.0 16.8 - - + -
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Residues in contact with TYR 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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225A TYR* 4.7 2.5 - - - +
241A LEU 3.8 13.0 - - - -
242A SER 3.7 8.5 + - - -
243A ASN* 3.6 3.3 - - - -
244A PHE* 2.8 55.9 + + + -
290A PHE* 2.7 50.4 + + + +
291A MET* 3.1 8.3 - - - +
293A ALA* 1.3 73.2 - - - +
295A PRO* 1.3 65.9 - - + +
296A TYR* 3.0 36.5 + + + +
349A ARG* 2.6 27.6 + - - -
358A VAL* 3.8 20.8 - - + +
361A TRP* 4.4 7.4 - + - -
371A PHE* 3.9 11.6 - + - -
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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