Contacts of the helix formed by residues 284 - 296 (chain A) in PDB entry 1LDJ
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 GLN 284 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272A GLN* 4.8 15.8 - - + +
275A VAL* 2.5 65.4 + - + +
276A GLN* 3.9 11.5 - - - +
279A LEU* 3.3 11.5 - - - +
281A GLU* 3.4 21.4 + - - +
283A THR* 1.3 80.4 - - - +
285A ASP* 1.3 65.5 + - - +
287A LEU* 3.6 5.2 - - - +
288A ALA* 2.4 37.7 + - - +
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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 GLU 6.0 0.2 - - - -
282A SER* 4.5 12.4 - - - +
283A THR 4.1 1.6 - - - +
284A GLN* 1.3 85.1 - - - +
286A GLU* 1.4 58.2 + - + +
288A ALA* 3.9 6.3 - - - +
289A ARG* 2.3 42.0 + - + +
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Residues in contact with GLU 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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229A LYS* 3.6 14.9 + - - -
233A GLU* 2.5 29.5 - - - +
237A LEU* 4.5 13.1 - - + +
282A SER* 4.0 14.8 + - - +
283A THR* 4.3 6.9 - - - +
284A GLN 4.0 0.6 - - - +
285A ASP* 1.4 77.3 - - + +
287A LEU* 1.4 58.8 + - - +
289A ARG* 3.9 8.4 - - - +
290A LYS* 2.8 34.3 + - - +
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Residues in contact with LEU 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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236A PHE* 3.2 36.3 - - + -
237A LEU* 3.5 15.4 - - + +
240A THR* 4.3 8.1 - - + -
271A GLU* 3.4 35.7 - - + +
272A GLN* 5.6 0.4 - - - -
275A VAL* 4.3 7.9 - - + -
283A THR 1.8 37.3 + - - +
284A GLN* 3.6 4.3 - - - +
286A GLU* 1.4 74.7 - - - +
288A ALA* 1.3 60.6 + - + +
290A LYS* 3.0 9.0 - - + +
291A CYS* 3.0 51.3 + - - -
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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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268A LEU* 5.6 2.9 - - + -
284A GLN 2.4 30.4 + - - +
285A ASP* 3.4 6.5 - - - +
287A LEU* 1.3 76.1 - - + +
289A ARG* 1.3 65.5 + - - +
290A LYS 2.7 6.2 + - - -
291A CYS* 2.7 4.3 + - - +
292A GLU* 2.7 38.8 + - + +
328A ARG* 5.2 5.6 - - - +
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Residues in contact with ARG 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* 2.3 34.1 + - + +
286A GLU* 3.9 7.5 + - - +
288A ALA* 1.3 67.1 - - - +
290A LYS* 1.3 82.1 + - - +
292A GLU* 3.4 18.4 + - - +
293A GLN* 2.6 72.4 + - - +
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Residues in contact with LYS 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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237A LEU* 3.2 36.0 - - + +
238A ALA 5.0 0.2 - - - +
241A GLU* 3.1 36.0 + - + +
286A GLU* 2.8 21.3 - - - +
287A LEU* 3.0 14.3 + - + +
288A ALA 2.7 1.0 + - - -
289A ARG* 1.3 102.5 - - - +
291A CYS* 1.3 64.0 + - - +
292A GLU 3.0 1.7 + - - -
293A GLN* 3.2 11.3 + - - +
294A VAL* 3.1 27.4 + - - +
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Residues in contact with CYS 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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240A THR* 4.5 5.2 - - - -
241A GLU* 6.3 1.1 - - - +
244A TYR* 4.4 13.9 - - + -
268A LEU* 3.5 21.8 - - + -
271A GLU* 3.6 20.0 - - + -
287A LEU* 3.0 52.1 + - - +
288A ALA* 2.7 7.8 + - - +
290A LYS* 1.3 75.6 - - - +
292A GLU* 1.3 59.6 + - - +
294A VAL* 3.2 7.5 + - - -
295A LEU* 2.8 39.0 + - + +
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Residues in contact with GLU 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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268A LEU* 4.0 11.2 - - + +
288A ALA* 2.7 24.6 + - + +
289A ARG* 3.4 24.2 + - - +
291A CYS* 1.3 76.0 - - - +
293A GLN* 1.3 54.9 + - + +
294A VAL 3.1 0.2 + - - -
296A ILE* 2.3 47.6 + - + +
328A ARG* 2.5 61.7 + - + +
329A ILE* 4.0 14.6 - - + +
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Residues in contact with GLN 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 ARG* 2.6 51.5 + - - +
290A LYS* 3.2 14.9 + - - +
292A GLU* 1.3 79.2 - - + +
294A VAL* 1.3 61.2 + - + +
296A ILE 2.8 14.9 - - - +
297A GLU* 3.8 26.9 + - - +
298A LYS* 3.4 28.9 + - + +
329A ILE* 4.6 4.5 - - + -
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Residues in contact with VAL 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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241A GLU* 4.0 24.2 - - + +
244A TYR* 4.0 11.0 - - + -
245A THR* 3.1 47.6 - - + +
248A SER* 4.1 0.3 - - - -
290A LYS* 3.1 17.0 + - + +
291A CYS* 3.6 10.3 - - - +
292A GLU 3.0 1.2 - - - -
293A GLN* 1.3 80.6 - - + +
295A LEU* 1.3 58.5 + - + +
298A LYS* 5.0 7.2 - - + -
299A HIS* 2.7 34.6 + - + -
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Residues in contact with LEU 295 (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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244A TYR* 3.8 33.9 - - + -
248A SER* 4.8 4.0 - - - -
260A TYR* 3.4 23.4 + - - +
263A LYS* 6.4 0.2 - - - +
264A ALA* 3.1 40.6 - - + +
267A ARG* 4.7 6.5 - - + -
268A LEU* 3.3 25.1 - - + +
291A CYS* 2.8 23.4 + - + +
294A VAL* 1.3 77.7 - - + +
296A ILE* 1.3 73.8 + - + +
299A HIS* 3.2 25.8 - - - +
303A PHE* 4.1 5.2 - - - -
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Residues in contact with ILE 296 (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 TYR* 6.3 0.2 - - + -
264A ALA* 5.4 0.4 - - + -
268A LEU* 3.6 14.8 - - + -
292A GLU* 2.3 39.7 + - + +
293A GLN 2.8 16.6 - - - +
295A LEU* 1.3 91.2 - - + +
297A GLU* 1.4 63.1 + - - +
298A LYS 3.7 1.1 - - - -
300A LEU* 4.4 2.5 - - + -
303A PHE* 4.2 9.2 - - + -
325A LEU* 3.5 57.9 - - + +
326A VAL* 3.7 19.5 - - + +
328A ARG* 4.8 3.1 - - + -
329A ILE* 3.0 32.5 - - + -
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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