Contacts of the helix formed by residues 305 - 324 (chain M) in PDB entry 6LTJ
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 305 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304M GLY* 1.3 70.2 - - - -
306M GLU* 1.3 56.9 + - - -
307M PHE 2.7 17.6 + - - -
308M VAL* 3.0 23.9 + - - +
488N ARG 3.8 1.8 - - - -
489N ASN* 3.1 28.8 - - - +
523O MET 5.2 0.4 + - - -
41R PHE* 3.8 2.4 - - - -
43R ASP* 3.6 13.9 - - - -
50R GLN* 3.7 10.9 + - - -
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Residues in contact with GLU 306 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270M VAL* 3.3 36.9 - - + +
271M GLY 4.7 2.8 + - - -
305M GLY* 1.3 71.4 - - - -
307M PHE* 1.3 52.5 + - - +
309M THR* 2.5 23.3 + - - +
310M THR* 2.6 31.4 + - + -
488N ARG* 3.1 30.7 + - + +
489N ASN* 4.1 1.2 - - - +
41R PHE* 5.6 0.9 - - - -
43R ASP* 3.8 5.7 - - - +
44R SER* 3.9 8.4 + - - -
45R GLN* 3.7 27.5 + - - +
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Residues in contact with PHE 307 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268M ILE* 3.9 26.2 - - + -
270M VAL* 3.6 35.0 - - + -
273M ILE* 3.7 39.3 - - + -
275M LEU* 4.2 23.3 - - + -
298M CYS* 4.0 14.1 - - - -
303M LEU* 4.0 29.4 - - + -
304M GLY 3.3 20.8 + - - +
305M GLY 2.7 4.8 + - - -
306M GLU* 1.3 74.4 + - - +
308M VAL* 1.3 65.7 + - - +
310M THR* 2.9 5.4 + - - -
311M ILE* 2.8 30.2 + - + +
41R PHE* 4.0 10.3 - + - -
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Residues in contact with VAL 308 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294M ALA* 3.4 19.4 - - + +
295M LEU* 4.0 42.2 - - + +
298M CYS* 3.5 19.6 - - + -
304M GLY* 5.4 3.4 - - - -
305M GLY 3.0 19.3 + - - +
307M PHE* 1.3 79.2 - - - +
309M THR* 1.3 65.9 + - + +
312M ALA* 3.5 4.9 + - - +
489N ASN 3.2 29.6 - - - +
490N LEU* 4.5 0.4 - - - +
491N ALA* 3.9 16.1 - - + +
56R TRP* 6.4 0.2 - - + -
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Residues in contact with THR 309 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203M ALA 4.6 9.5 + - - -
204M PHE* 5.9 3.4 - - - -
306M GLU* 2.5 25.7 + - - +
308M VAL* 1.3 79.1 - - + +
310M THR* 1.3 55.8 + - - +
312M ALA* 3.0 8.6 + - - +
313M TYR* 2.7 34.8 + - - +
487N ARG 3.7 4.7 - - - +
488N ARG* 3.1 32.6 + - - +
490N LEU 3.2 35.0 - - - +
491N ALA* 4.1 3.8 - - - +
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Residues in contact with THR 310 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203M ALA* 4.7 17.9 - - + +
268M ILE* 3.6 21.6 - - + +
270M VAL* 4.1 6.1 - - + +
306M GLU* 2.6 40.6 + - + +
307M PHE* 2.9 16.1 + - - -
309M THR* 1.3 75.0 + - - +
311M ILE* 1.3 53.3 + - - +
313M TYR* 3.0 13.2 + - - +
314M SER* 2.5 39.5 + - - -
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Residues in contact with ILE 311 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266M LEU* 3.7 17.5 - - + -
268M ILE* 3.5 24.2 - - + +
275M LEU* 3.8 25.8 - - + -
293M PHE* 4.7 0.4 - - + -
294M ALA* 3.7 23.8 - - + +
297M LEU* 4.1 15.9 - - + -
298M CYS* 3.6 27.6 - - - -
301M LEU* 5.7 0.4 - - + -
307M PHE* 2.8 21.2 + - + +
310M THR* 1.3 77.8 + - - +
312M ALA* 1.3 65.4 + - - +
314M SER* 3.0 1.9 + - - -
315M ILE* 2.8 34.6 + - + +
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Residues in contact with ALA 312 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205M THR* 5.4 2.5 - - - +
290M PRO* 4.1 12.3 - - - +
291M GLU* 4.3 24.2 - - + +
294M ALA* 3.8 13.2 - - + +
308M VAL 3.5 13.0 + - - +
309M THR* 3.0 10.8 + - - +
311M ILE* 1.3 81.4 - - - +
313M TYR* 1.3 65.7 + - - +
315M ILE* 3.0 10.9 + - - +
316M ARG* 3.0 18.8 + - - +
491N ALA* 4.4 3.4 - - + -
492N GLY 5.9 0.2 - - - +
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Residues in contact with TYR 313 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188M PRO* 3.5 28.9 - - + -
189M ILE 3.6 18.6 - - - -
190M ARG* 2.6 51.8 + - + +
203M ALA* 3.8 24.9 - - + +
204M PHE* 3.7 18.2 - - - +
205M THR* 4.3 11.3 + - - +
309M THR 2.7 14.7 + - - +
310M THR* 3.4 13.2 - - - +
312M ALA* 1.3 73.3 - - - +
314M SER* 1.3 85.4 + - - +
316M ARG* 3.0 5.6 + - - +
317M GLY* 2.8 24.7 + - - -
372M THR* 4.7 1.4 - - - +
376M ARG* 4.6 0.9 + - - -
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Residues in contact with SER 314 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266M LEU* 3.4 23.7 - - - +
267M ASN 5.2 0.3 + - - -
268M ILE* 4.3 10.9 - - - +
310M THR 2.5 22.3 + - - -
311M ILE* 3.3 6.1 - - - -
313M TYR* 1.3 82.0 - - - +
315M ILE* 1.3 65.2 + - - +
317M GLY* 3.0 4.0 + - - +
318M GLN* 2.9 35.4 + - - +
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Residues in contact with ILE 315 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264M ILE* 3.8 21.3 - - + -
266M LEU* 3.8 17.5 - - + -
279M PHE* 4.2 4.7 - - + -
281M TRP* 4.5 9.0 - - + -
290M PRO* 3.8 28.0 - - + +
293M PHE* 3.3 39.0 - - + -
311M ILE* 2.8 29.0 + - + +
312M ALA 3.0 5.8 + - - +
314M SER* 1.3 74.4 - - - +
316M ARG* 1.3 64.1 + - - +
318M GLN* 3.0 9.5 + - - +
319M LEU* 2.8 31.4 + - + +
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Residues in contact with ARG 316 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186M LEU* 3.5 35.0 + - - +
188M PRO* 4.2 17.7 - - + +
205M THR* 4.1 22.2 - - - -
290M PRO* 4.0 28.7 - - + +
291M GLU* 2.5 50.4 + - - -
312M ALA 3.0 15.7 + - - +
313M TYR* 3.0 5.3 + - - +
315M ILE* 1.3 74.0 - - - +
317M GLY* 1.3 64.6 + - - +
319M LEU* 3.0 13.0 + - - +
320M SER* 2.7 25.6 + - - -
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Residues in contact with GLY 317 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188M PRO* 4.0 11.8 - - - +
313M TYR* 2.8 18.5 + - - -
314M SER* 3.4 4.9 - - - -
316M ARG* 1.3 75.1 - - - +
318M GLN* 1.3 62.1 + - - +
320M SER* 2.8 25.7 + - - -
321M TRP* 3.0 8.2 + - - +
375M MET* 6.2 1.1 - - - -
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Residues in contact with GLN 318 (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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263M ILE 4.9 1.6 - - - +
264M ILE* 3.8 22.8 - - + +
265M LYS* 2.3 52.7 + - - +
266M LEU* 3.9 0.2 - - - +
314M SER* 2.9 29.1 + - - +
315M ILE* 3.6 5.2 - - - +
317M GLY* 1.3 74.2 - - - +
319M LEU* 1.3 65.0 + - - +
321M TRP* 2.9 8.8 + - - +
322M HIS* 2.9 37.1 + - + -
375M MET* 5.3 17.2 - - + +
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Residues in contact with LEU 319 (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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262M VAL* 5.0 2.7 - - + -
264M ILE* 4.0 12.3 - - + -
281M TRP* 3.8 25.8 - - + +
283M MET* 3.6 30.3 - - + -
290M PRO* 3.9 18.6 - - + -
315M ILE* 2.8 37.0 + - + +
316M ARG* 3.4 11.7 - - - +
318M GLN* 1.3 72.3 - - - +
320M SER* 1.3 57.0 + - - +
322M HIS* 3.0 6.6 + - - +
323M GLN* 2.9 38.0 + - + +
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Residues in contact with SER 320 (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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188M PRO* 4.5 6.4 - - - +
248M TYR* 4.0 30.2 - - - -
249M PRO* 4.9 1.1 - - - -
316M ARG 2.7 16.8 + - - -
317M GLY* 2.8 19.9 + - - -
319M LEU* 1.3 72.7 - - - +
321M TRP* 1.3 59.6 + - - +
323M GLN* 4.1 9.2 - - - -
324M LYS* 2.7 37.4 + - - +
379M ALA* 5.1 0.2 - - - +
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Residues in contact with TRP 321 (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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317M GLY 3.0 10.0 + - - +
318M GLN* 2.9 10.8 + - - +
320M SER* 1.3 76.7 + - - +
322M HIS* 1.3 88.1 + + - +
324M LYS* 4.0 4.3 - - - +
325M THR* 2.8 52.6 + - + +
375M MET* 3.3 60.2 + - + +
378M LEU* 3.9 29.5 - - + +
379M ALA* 3.7 14.8 - - + -
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Residues in contact with HIS 322 (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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262M VAL* 3.3 40.6 - - + +
263M ILE* 4.1 18.8 + - + -
264M ILE* 5.0 1.7 - - + +
283M MET* 3.6 20.0 - - - -
318M GLN* 2.9 40.5 + - + +
319M LEU* 3.0 7.8 + - - +
321M TRP* 1.3 102.1 - + - +
323M GLN* 1.3 65.2 + - - +
325M THR* 2.9 16.6 + - - -
326M TYR 3.1 20.0 + - - -
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Residues in contact with GLN 323 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249M PRO* 5.1 3.6 - - + -
283M MET* 3.1 40.7 - - - +
319M LEU* 2.9 25.7 + - + +
320M SER* 4.2 4.0 - - - -
322M HIS* 1.3 77.3 - - - +
324M LYS* 1.3 76.6 + - - +
325M THR 3.2 0.2 + - - -
326M TYR* 3.5 8.5 + - - -
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Residues in contact with LYS 324 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247M SER 5.2 4.0 - - - -
249M PRO* 2.5 46.8 - - - +
320M SER* 2.7 30.1 + - - +
321M TRP 4.0 4.7 - - - +
323M GLN* 1.3 82.2 - - - +
325M THR* 1.3 65.0 + - + +
326M TYR 3.5 1.0 + - - -
379M ALA* 3.6 42.2 - - + +
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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
------------------------------------------------------------
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