Contacts of the helix formed by residues 279 - 294 (chain A) in PDB entry 3LMK
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 GLU 279 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLN* 5.1 0.7 - - - +
100A TRP* 2.9 46.5 + - + -
151A SER* 3.9 9.7 + - - -
219A THR* 3.0 24.6 + - + +
220A GLU 5.8 0.2 - - - -
223A TYR* 4.0 18.4 - - + +
250A SER* 2.7 37.3 + - - +
278A CYS* 1.3 77.0 - - - +
280A GLY* 1.3 65.7 + - - +
281A MET* 3.3 2.9 - - + +
282A THR* 3.1 12.1 + - - -
283A VAL* 3.1 11.2 + - - +
306A GLY* 4.0 6.5 - - - -
310A ARG* 5.3 1.1 - - - +
506A GLU* 5.2 3.8 - - + +
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Residues in contact with GLY 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A GLU* 1.3 72.6 - - - +
281A MET* 1.3 52.3 + - - +
283A VAL* 3.1 8.1 + - - +
284A ARG* 2.7 35.3 + - - +
306A GLY 3.4 13.2 + - - -
307A TRP 4.4 0.9 - - - -
310A ARG* 3.0 28.5 - - - +
313A VAL* 3.6 17.9 - - - +
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Residues in contact with MET 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A HIS* 4.5 30.5 - - + +
61A ARG* 5.3 2.0 - - - +
250A SER* 4.1 27.1 - - - +
257A PHE* 4.3 2.3 - - - -
279A GLU* 3.3 2.7 - - + +
280A GLY* 1.3 79.2 - - - +
282A THR* 1.3 52.3 + - - +
284A ARG* 3.6 30.3 - - + +
285A GLY* 2.7 31.5 + - - -
288A MET* 5.7 1.1 - - - +
310A ARG* 4.1 10.6 - - - +
312A ASP* 4.0 27.6 - - + +
313A VAL* 4.9 0.7 - - + -
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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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217A VAL* 4.6 4.9 - - + -
219A THR* 2.7 34.3 + - - +
248A ILE* 4.0 24.1 + - + +
250A SER* 3.1 22.8 + - - -
257A PHE* 3.3 12.9 - - + -
276A CYS* 4.5 2.2 - - - -
278A CYS* 3.8 20.2 - - - -
279A GLU 3.1 6.5 + - - -
281A MET* 1.3 75.5 - - - +
283A VAL* 1.3 64.4 + - - +
285A GLY 3.2 0.9 + - - -
286A LEU* 3.1 23.0 + - + +
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Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A CYS* 4.2 10.8 - - + +
278A CYS* 3.8 18.6 - - + +
279A GLU 3.1 11.0 + - - +
280A GLY* 3.1 8.2 + - - +
282A THR* 1.3 75.7 - - - +
284A ARG* 1.3 65.2 + - - +
286A LEU* 3.2 12.4 + - - +
287A LEU* 3.1 28.4 + - + +
301A LEU* 4.7 7.9 - - + -
303A GLY* 5.6 0.7 - - - -
304A SER 6.2 0.2 - - - +
307A TRP* 3.7 46.0 - - + -
313A VAL* 3.6 19.5 - - + -
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Residues in contact with ARG 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A GLY 2.7 19.5 + - - +
281A MET* 3.6 25.6 - - - +
283A VAL* 1.3 72.9 - - - +
285A GLY* 1.3 63.0 + - - +
287A LEU* 3.0 15.1 + - + +
288A MET* 2.9 45.0 + - + +
312A ASP 2.9 24.8 + - - -
313A VAL* 2.7 37.5 + - - +
314A THR 4.0 0.6 - - - -
315A ASP* 2.9 32.0 + - - +
317A TYR* 3.5 22.5 - - + -
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Residues in contact with GLY 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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257A PHE* 3.4 29.8 - - - +
281A MET 2.7 20.8 + - - -
282A THR 3.2 3.3 + - - -
284A ARG* 1.3 71.6 - - - +
286A LEU* 1.3 60.3 + - - +
288A MET* 3.4 15.6 + - - +
289A ALA* 3.1 22.0 + - - +
292A ARG* 4.6 1.4 + - - -
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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
----------------------------------------------------------
217A VAL* 4.5 13.5 - - + -
257A PHE* 3.5 10.5 - - + +
260A LEU* 4.1 19.1 - - + -
261A LEU* 4.3 17.9 - - + +
264A LEU* 3.9 27.1 - - + -
274A VAL* 5.8 0.2 - - + -
276A CYS* 4.3 23.1 - - - -
282A THR* 3.1 17.2 + - + +
283A VAL* 3.2 10.7 + - - +
285A GLY* 1.3 76.4 - - - +
287A LEU* 1.3 56.8 + - + +
289A ALA* 3.1 7.3 + - - +
290A MET* 2.8 40.1 + - + +
301A LEU* 4.7 18.2 - - + -
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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
----------------------------------------------------------
283A VAL* 3.1 19.6 + - + +
284A ARG* 3.0 8.3 + - - +
286A LEU* 1.3 74.8 - - - +
288A MET* 1.3 57.1 + - - +
290A MET* 3.2 13.0 + - - +
291A ARG* 3.1 23.2 + - - +
301A LEU* 4.0 19.7 - - + -
313A VAL* 3.7 33.4 - - + +
314A THR* 4.4 4.7 - - + -
317A TYR* 4.0 20.9 - - + +
320A GLU* 3.6 15.6 - - + +
321A ALA* 3.6 45.5 - - + +
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Residues in contact with MET 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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281A MET* 5.7 1.1 - - - +
284A ARG* 2.9 38.9 + - + +
285A GLY* 3.6 15.7 - - - +
287A LEU* 1.3 72.7 - - - +
289A ALA* 1.3 64.5 + - - +
291A ARG* 3.4 4.0 + - - +
292A ARG* 3.2 45.9 + - - +
317A TYR* 3.6 46.1 - - + +
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Residues in contact with ALA 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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257A PHE* 3.9 23.3 - - + +
258A ASP* 4.2 5.6 - - - +
261A LEU* 3.4 20.9 - - + +
285A GLY 3.1 13.8 + - - +
286A LEU* 3.3 9.9 - - - +
288A MET* 1.3 76.2 - - - +
290A MET* 1.3 60.8 + - - +
292A ARG* 3.3 24.0 + - - +
293A LEU* 3.2 21.3 + - - +
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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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261A LEU* 3.6 23.3 - - + -
264A LEU* 6.5 0.2 - - + -
286A LEU* 2.8 21.2 + - + +
287A LEU* 3.2 18.6 + - + +
289A ALA* 1.3 77.0 - - - +
291A ARG* 1.3 51.8 + - - +
293A LEU* 4.9 0.2 - - - -
294A GLY* 2.7 34.1 + - - -
295A LEU* 3.4 10.0 + - + +
296A ALA* 4.2 13.3 + - - +
297A GLY 5.8 0.7 - - - -
299A PHE* 3.8 39.0 - - + -
301A LEU* 4.0 28.0 - - + -
320A GLU* 3.7 34.5 - - + +
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Residues in contact with ARG 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 LEU 3.1 5.4 + - - +
288A MET 3.6 9.4 - - - +
289A ALA 3.2 0.4 - - - -
290A MET* 1.3 75.5 - - - +
292A ARG* 1.3 66.0 + - + +
293A LEU 3.2 1.2 + - - -
294A GLY* 3.5 9.3 + - - -
316A GLY 2.5 31.2 + - - -
317A TYR* 3.4 33.5 - - + +
318A GLN 4.7 0.2 - - - +
319A ARG* 5.5 1.0 - - - +
320A GLU* 2.8 41.8 + - - +
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Residues in contact with ARG 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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254A GLU* 3.2 52.4 + - - +
257A PHE* 4.3 6.1 - - - +
258A ASP* 3.5 21.9 + - - +
285A GLY 4.6 2.0 + - - -
288A MET* 3.2 34.1 + - - +
289A ALA* 3.3 28.1 + - - +
291A ARG* 1.3 78.3 - - + +
293A LEU* 1.3 60.1 + - - +
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Residues in contact with LEU 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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258A ASP* 4.6 13.0 - - + +
261A LEU* 3.8 32.3 - - + -
262A LYS* 4.0 41.5 - - + +
265A THR* 5.4 5.6 - - + -
289A ALA 3.2 10.8 + - - +
290A MET 4.2 1.6 - - - +
291A ARG 4.1 0.4 - - - -
292A ARG* 1.3 81.0 - - - +
294A GLY* 1.3 58.9 + - - +
295A LEU* 3.4 11.0 - - + +
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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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290A MET 2.7 17.4 + - - -
291A ARG* 3.5 7.0 + - - -
293A LEU* 1.3 74.2 - - - +
295A LEU* 1.3 53.7 + - - +
296A ALA* 3.1 14.5 + - - +
320A GLU* 5.9 0.4 - - - -
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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