Contacts of the helix formed by residues 344 - 362 (chain M) in PDB entry 1MVW
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 SER 344 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342M GLY 3.5 2.6 + - - -
343M PHE* 1.3 73.3 - - - +
345M ALA* 1.3 55.1 + - - +
346M ASP* 3.8 11.3 - - - +
347M GLU* 2.9 31.3 + - - -
348M MLY 2.5 34.4 + - - +
444M ARG* 4.5 0.8 - - - +
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Residues in contact with ALA 345 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339M ASP* 6.0 0.2 - - - -
343M PHE 3.7 2.0 + - - -
344M SER* 1.3 72.8 + - - +
346M ASP* 1.3 51.8 + - - +
348M MLY 2.9 22.6 + - + +
349M THR* 2.4 44.2 + - - +
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Residues in contact with ASP 346 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344M SER* 3.8 13.5 - - - +
345M ALA* 1.3 76.4 - - - +
347M GLU* 1.3 54.5 + - + +
349M THR* 2.6 12.8 + - - +
350M ALA* 2.5 36.0 + - - +
617M MLY 5.4 11.3 - - - +
618M THR* 5.1 5.2 + - - -
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Residues in contact with GLU 347 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343M PHE* 3.5 15.9 - - + -
344M SER* 2.9 38.1 + - - +
346M ASP* 1.3 78.4 - - + +
348M MLY 1.3 59.0 + - - +
350M ALA* 2.8 25.1 + - - +
351M ILE* 2.8 21.5 + - - +
440M TRP* 3.5 33.8 - - + -
444M ARG* 3.4 25.4 + - - -
618M THR* 4.0 9.4 + - - +
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Residues in contact with MLY 348 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296M MLY 3.2 34.1 - - - -
335M ASP* 2.5 38.7 + - - -
338M ILE* 3.6 28.5 - - + -
339M ASP* 2.8 36.1 + - - +
343M PHE* 4.6 1.1 - - + +
344M SER 2.5 20.5 + - - +
345M ALA* 3.0 17.7 - - + +
347M GLU* 1.3 73.6 + - - +
349M THR* 1.3 57.7 + - - +
351M ILE* 3.9 10.2 - - - +
352M TYR* 3.3 36.8 + - + -
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Residues in contact with THR 349 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302M MET* 4.6 17.8 - - - +
345M ALA* 2.4 28.8 + - - +
346M ASP* 2.6 16.1 + - - -
348M MLY 1.3 76.8 + - - +
350M ALA* 1.3 62.7 + - - +
351M ILE 3.2 1.3 - - - -
352M TYR* 3.1 5.1 + - - +
353M MLY 2.8 46.7 + - + +
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Residues in contact with ALA 350 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346M ASP 2.5 19.1 + - - +
347M GLU 3.2 8.1 - - - +
349M THR* 1.3 67.9 - - - +
351M ILE* 1.3 56.1 + - + +
353M MLY 4.6 4.9 - - - -
354M LEU* 2.5 48.4 + - + +
616M VAL* 4.5 13.2 - - + -
618M THR* 3.7 38.6 - - + +
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Residues in contact with ILE 351 (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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232M PHE* 3.7 26.7 - - + -
287M ILE* 5.4 0.4 - - + -
338M ILE* 4.7 20.9 - - + -
343M PHE* 4.7 10.5 - - + -
347M GLU 2.8 23.5 + - - +
348M MLY 3.9 10.3 - - - +
350M ALA* 1.3 77.2 - - - +
352M TYR* 1.3 72.0 + - + +
354M LEU* 3.8 0.9 - - - +
355M THR* 2.6 30.1 + - - +
437M MET* 4.2 13.5 - - + -
440M TRP* 4.0 16.4 - - + -
441M MET* 3.6 36.8 - - + -
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Residues in contact with TYR 352 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287M ILE* 4.8 12.8 - - + -
291M ILE* 3.7 28.7 - - + -
299M LEU* 3.8 25.8 - - + -
302M MET* 4.1 23.6 - - + -
303M LEU* 4.2 13.4 - - + +
331M LEU* 4.0 11.8 + - + +
334M THR* 4.9 3.7 - - + +
335M ASP* 2.7 42.3 + - - +
338M ILE* 4.7 10.7 - - + +
348M MLY 3.3 37.2 + - + -
349M THR 3.1 6.2 + - - +
351M ILE* 1.3 87.2 - - + +
353M MLY 1.3 55.3 + - - +
355M THR* 2.6 31.2 + - - -
356M GLY 3.3 6.4 + - - -
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Residues in contact with MLY 353 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302M MET* 4.5 10.5 - - + -
303M LEU* 4.0 17.4 - - + +
349M THR* 2.8 42.3 + - + +
350M ALA* 3.9 4.0 - - - +
352M TYR* 1.3 72.4 - - - +
354M LEU* 1.3 61.4 + - + +
356M GLY* 3.3 1.6 + - - -
357M ALA* 3.1 21.5 + - - +
388M TYR* 3.1 54.3 - - - -
389M LEU* 3.4 52.5 - - + +
391M GLY* 4.9 0.7 - - - -
616M VAL* 3.7 26.2 - - + -
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Residues in contact with LEU 354 (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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350M ALA* 2.5 40.6 + - + +
351M ILE 3.8 3.1 - - - +
353M MLY 1.3 76.6 - - + +
355M THR* 1.3 61.5 + - - +
356M GLY 3.3 0.7 + - - -
357M ALA* 3.5 6.6 + - - +
358M VAL* 3.4 22.2 + - - +
389M LEU 4.4 7.2 - - - +
390M MET* 4.1 33.9 - - + +
433M VAL* 4.8 13.5 - - + +
437M MET* 3.8 22.2 - - - +
616M VAL* 5.0 5.2 - - + -
618M THR* 4.4 13.0 - - + -
619M LEU* 4.6 22.2 - - + +
622M LEU* 4.9 4.7 - - + -
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Residues in contact with THR 355 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232M PHE* 3.8 7.1 - - + -
287M ILE* 4.3 23.8 - - + -
288M PHE* 3.4 42.2 - - + -
291M ILE* 4.7 10.5 - - + -
303M LEU* 5.6 0.2 - - - -
351M ILE* 2.6 21.5 + - - +
352M TYR* 2.6 15.3 + - - -
354M LEU* 1.3 72.5 - - - +
356M GLY* 1.3 56.1 + - - -
358M VAL* 4.0 5.9 - - - +
359M MET* 3.5 7.2 + - + +
434M TYR* 5.0 3.8 - - + -
437M MET* 2.9 21.9 - - + +
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Residues in contact with GLY 356 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303M LEU* 4.5 16.8 - - - +
305M ILE* 5.5 0.2 - - - -
352M TYR 3.3 7.7 + - - -
353M MLY 3.3 3.3 + - - -
354M LEU 3.1 0.6 - - - -
355M THR* 1.3 76.0 - - - +
357M ALA* 1.3 67.6 + - - +
358M VAL 3.1 1.6 - - - -
359M MET* 3.0 30.2 + - - +
360M HIS* 3.0 22.3 + - - -
389M LEU* 4.7 1.6 - - - -
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Residues in contact with ALA 357 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353M MLY 3.1 12.9 + - - +
354M LEU 3.6 10.1 - - - +
356M GLY* 1.3 76.6 - - - +
358M VAL* 1.3 51.6 + - - +
360M HIS* 2.9 15.2 + - - +
361M TYR* 2.8 41.1 + - + -
386M ALA* 4.7 3.4 - - - +
389M LEU* 4.4 10.9 - - + +
390M MET* 3.7 39.7 - - + -
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Residues in contact with VAL 358 (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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275M VAL* 3.9 28.0 - - + +
288M PHE* 4.6 10.8 - - + -
314M TYR* 3.4 17.3 - - + -
354M LEU 3.4 17.3 - - - +
355M THR* 4.0 9.0 - - - +
357M ALA* 1.3 81.9 - - + +
359M MET* 1.3 62.7 + - - +
360M HIS 3.3 0.2 + - - -
361M TYR* 3.3 16.9 + - + +
390M MET* 5.3 3.1 - - + -
430M ALA* 4.0 28.9 - - + +
433M VAL* 4.7 15.0 - - + -
434M TYR* 4.8 10.5 - - + +
437M MET* 6.5 0.4 - - + -
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Residues in contact with MET 359 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288M PHE* 3.8 30.3 - - + +
291M ILE* 4.6 12.3 - - + -
292M MET* 4.2 25.1 - - + +
305M ILE* 3.8 32.1 - - + -
312M TYR* 3.6 45.0 - - + +
314M TYR* 4.5 9.1 - - - +
315M VAL* 4.7 5.8 - - + -
355M THR 3.5 13.0 - - - +
356M GLY* 3.0 19.5 + - - +
358M VAL* 1.3 80.0 - - - +
360M HIS* 1.3 63.4 + - - +
362M GLY* 3.4 10.2 + - - -
363M ASN* 3.8 5.2 + - - +
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Residues in contact with HIS 360 (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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303M LEU 3.2 26.7 - - - -
304M LEU* 3.1 22.8 + - + -
305M ILE* 3.9 14.5 - - + +
312M TYR* 4.2 12.3 + + - -
356M GLY 3.0 14.2 + - - -
357M ALA* 2.9 8.9 + - - +
359M MET* 1.3 80.2 - - - +
361M TYR* 1.3 60.5 + - - +
362M GLY 3.1 0.2 - - - -
363M ASN* 2.7 27.0 + - - +
364M LEU* 3.1 7.8 + - - +
382M VAL* 3.4 28.5 - - + +
385M MLY 4.1 20.1 + - + +
386M ALA* 4.2 11.2 + - + -
389M LEU* 3.9 13.8 - - + +
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Residues in contact with TYR 361 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314M TYR* 4.1 5.8 - - + -
357M ALA 2.8 26.9 + - - -
358M VAL* 3.5 13.0 - - + +
359M MET 3.3 0.4 - - - -
360M HIS* 1.3 73.1 - - - +
362M GLY* 1.3 59.8 + - - +
364M LEU* 2.7 40.2 + - + +
386M ALA* 3.6 26.5 - - + -
390M MET* 2.8 36.6 - - + -
392M LEU* 4.6 4.2 - - - +
397M LEU* 4.6 14.0 - - + +
401M LEU* 6.0 3.6 - - + -
426M VAL* 3.7 38.3 - - + +
429M LEU* 4.3 14.4 - - + -
430M ALA* 4.3 11.0 - - + -
433M VAL* 5.6 0.7 - - + -
607M VAL* 6.2 0.2 - - + -
611M TYR* 3.0 26.7 + - - -
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Residues in contact with GLY 362 (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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313M HIS* 4.1 19.8 - - - +
314M TYR* 3.1 44.3 - - - -
358M VAL 3.6 0.2 + - - -
359M MET 3.4 5.5 + - - -
360M HIS 3.1 1.0 - - - -
361M TYR* 1.3 78.8 - - - +
363M ASN* 1.3 62.8 - - - +
364M LEU 3.4 1.7 - - - +
365M LYS* 4.2 10.7 + - - -
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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