Contacts of the helix formed by residues 286 - 301 (chain M) in PDB entry 1L0V
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 PRO 286 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268M MET* 4.3 1.6 - - - -
280M LYS* 4.0 17.7 - - + +
285M GLY* 1.3 83.5 - - - +
287M ARG* 1.3 70.4 + - - +
288M ASP* 3.1 4.4 + - + +
289M LYS* 3.1 51.2 + - + +
290M VAL* 3.3 7.8 + - - +
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Residues in contact with ARG 287 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230M GLN* 2.9 36.9 + - - +
231M TYR 3.0 28.7 + - - +
232M HIS* 3.8 19.8 + - - +
233M PRO* 4.1 9.3 - - + +
285M GLY 3.2 4.6 + - - -
286M PRO* 1.3 70.5 - - - +
288M ASP* 1.3 77.6 + - - +
290M VAL* 3.6 4.9 + - - +
291M SER* 3.2 23.5 + - - +
355M HIS* 4.7 1.4 - - - -
389M ASN* 6.2 2.5 - - - -
390M ARG* 4.4 9.4 + - - +
802M OAA 1.8 43.4 + - - -
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Residues in contact with ASP 288 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286M PRO* 3.2 3.6 - - + +
287M ARG* 1.3 92.4 - - - +
289M LYS* 1.3 71.6 + - + +
291M SER* 3.0 12.5 + - - -
292M GLN* 3.1 26.2 + - - +
389M ASN* 4.2 8.9 - - - +
530M GLY* 3.4 33.7 - - - +
531M ALA* 4.4 9.0 + - - +
533M GLN* 4.9 4.6 + - - +
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Residues in contact with LYS 289 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266M TYR* 4.2 15.6 + - + +
267M GLY* 4.5 10.5 + - - +
268M MET* 3.5 25.1 - - + -
286M PRO* 3.1 41.7 + - + +
288M ASP* 1.3 81.9 - - + +
290M VAL* 1.3 55.9 + - - +
292M GLN* 2.6 35.4 + - - +
293M ALA* 2.9 10.6 + - - -
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Residues in contact with VAL 290 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233M PRO* 4.2 17.0 - - + -
248M ARG* 5.2 4.3 - - - +
254M LEU* 4.1 21.3 - - + -
262M TYR* 4.7 3.5 + - - +
263M LEU* 4.0 17.2 - - + +
268M MET* 3.2 24.4 - - + +
283M GLU 4.9 5.8 - - - +
285M GLY* 3.4 23.3 - - - +
286M PRO 3.3 13.9 - - - +
287M ARG* 3.7 6.5 - - - +
289M LYS* 1.3 73.1 - - - +
291M SER* 1.3 64.3 + - - +
293M ALA* 3.0 19.1 + - - +
294M PHE* 3.5 5.2 + - - +
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Residues in contact with SER 291 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231M TYR* 4.2 11.3 + - - -
232M HIS 4.4 0.2 - - - -
233M PRO* 3.7 32.9 - - - +
287M ARG* 3.2 12.8 + - - +
288M ASP* 3.0 11.2 + - - -
289M LYS 2.8 2.0 + - - -
290M VAL* 1.3 76.9 - - - +
292M GLN* 1.3 62.1 + - - +
294M PHE* 3.3 19.6 + - - +
295M TRP* 3.9 2.6 + - - +
352M PRO* 3.8 15.3 - - - +
465M ILE* 4.5 18.8 - - - +
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Residues in contact with GLN 292 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288M ASP* 3.6 26.5 - - - +
289M LYS* 2.6 17.9 + - - +
291M SER* 1.3 68.1 - - - +
293M ALA* 1.3 57.5 + - - +
294M PHE 2.9 2.5 - - - -
295M TRP* 2.7 32.7 + - - +
296M HIS* 2.9 21.0 + - - +
465M ILE* 5.1 12.1 - - + +
466M TYR* 2.8 39.7 + - + +
533M GLN* 3.8 25.3 + - + +
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Residues in contact with ALA 293 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262M TYR* 4.0 7.2 - - + -
263M LEU* 3.8 23.1 - - + -
266M TYR* 4.2 18.1 - - + -
268M MET* 4.8 1.6 - - + -
289M LYS 2.9 8.6 + - - +
290M VAL* 3.0 18.8 - - - +
292M GLN* 1.3 75.5 - - - +
294M PHE* 1.3 54.1 + - - -
296M HIS* 3.3 17.2 + - - +
297M GLU* 2.8 31.6 + - - +
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Residues in contact with PHE 294 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262M TYR* 4.8 10.3 - - - +
290M VAL 3.5 4.1 + - - +
291M SER* 3.3 13.8 + - - +
292M GLN 2.8 2.0 + - - -
293M ALA* 1.3 75.3 - - - +
295M TRP* 1.3 63.2 + + + +
296M HIS 3.0 1.8 - - - -
297M GLU* 3.1 6.8 + - - +
298M TRP* 2.4 55.0 + + + +
303M THR* 4.8 7.4 - - + -
310M ASP* 4.8 7.2 - - + -
311M VAL* 4.1 10.8 - - - -
312M VAL* 3.6 49.4 - - + -
351M ARG* 4.0 20.4 - - + -
352M PRO* 3.6 35.4 - - + -
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Residues in contact with TRP 295 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291M SER 3.9 1.7 + - - +
292M GLN* 2.7 16.2 + - - +
294M PHE* 1.3 83.8 - + + +
296M HIS* 1.3 55.9 - - - +
298M TRP* 3.1 27.1 - + - +
299M ARG* 2.7 86.6 + - + +
460M GLU* 6.0 0.9 - - - -
461M GLU 6.1 1.1 - - - -
464M GLY* 6.4 0.4 - - - -
465M ILE* 3.7 31.6 - - + -
466M TYR* 3.5 56.4 - + + -
535M LEU* 5.7 4.4 - - + +
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Residues in contact with HIS 296 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266M TYR* 3.4 38.8 - + + +
292M GLN* 2.9 25.3 + - + +
293M ALA* 3.3 15.0 - - - +
295M TRP* 1.3 77.0 - + - +
297M GLU* 1.3 66.3 + - - +
299M ARG* 3.1 17.7 + - - +
300M LYS* 3.2 19.5 + - + +
466M TYR* 3.2 43.1 + + - -
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Residues in contact with GLU 297 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256M ASN* 3.0 16.3 - - + +
260M TYR* 5.4 0.8 - - - -
262M TYR* 3.5 41.4 - - + +
265M ASP* 6.0 0.2 - - - +
266M TYR* 3.3 15.7 + - + +
293M ALA 2.8 19.6 + - - +
294M PHE* 3.6 7.2 - - - +
296M HIS* 1.3 69.2 - - - +
298M TRP* 1.3 69.3 + - - +
299M ARG 3.3 0.2 + - - -
300M LYS* 3.4 9.3 + - - +
301M GLY 3.2 3.8 + - - -
302M ASN* 2.7 68.4 + - + +
303M THR* 4.1 2.5 - - + -
312M VAL* 4.8 9.2 - - + -
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Residues in contact with TRP 298 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294M PHE* 2.4 40.9 + + + +
295M TRP* 3.1 39.0 - + - +
297M GLU* 1.3 67.9 - - - +
299M ARG* 1.3 98.7 + - - +
301M GLY* 3.0 16.5 + - - -
303M THR* 3.1 32.8 + - + +
310M ASP* 3.5 30.1 + - + -
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Residues in contact with ARG 299 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295M TRP* 2.7 68.1 + - + +
296M HIS* 3.1 12.1 + - - +
298M TRP* 1.3 96.0 - - - +
300M LYS* 1.3 61.8 + - + +
301M GLY* 3.4 0.5 + - - -
535M LEU* 5.8 4.0 - - - +
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Residues in contact with LYS 300 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265M ASP* 4.1 18.0 + - - +
266M TYR* 3.7 19.8 + - - +
296M HIS* 3.2 11.8 + - + +
297M GLU* 3.5 25.5 + - - +
298M TRP 3.3 0.4 - - - -
299M ARG* 1.3 77.4 - - + +
301M GLY* 1.3 57.8 + - - +
302M ASN* 3.6 16.9 - - - +
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Residues in contact with GLY 301 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257M LYS* 3.5 21.8 + - - -
298M TRP 3.0 14.4 + - - -
299M ARG 3.2 0.4 - - - -
300M LYS* 1.3 79.4 - - - +
302M ASN* 1.3 60.0 + - - +
303M THR* 2.9 21.8 + - - +
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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
------------------------------------------------------------
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