Contacts of the helix formed by residues 344 - 362 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342G GLY 3.5 2.2 + - - -
343G PHE* 1.3 74.8 - - - +
345G ALA* 1.3 55.5 + - - +
346G ASP* 3.1 11.9 - - - +
347G GLU* 2.9 31.7 + - - -
348G MLY 2.5 34.2 + - - +
444G ARG* 4.5 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 345 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339G ASP* 6.0 0.2 - - - -
343G PHE 3.7 1.8 + - - -
344G SER* 1.3 74.4 + - - +
346G ASP* 1.3 52.3 + - - +
348G MLY 2.9 22.4 + - + +
349G THR* 2.4 44.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 346 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344G SER* 3.8 13.7 - - - +
345G ALA* 1.3 76.3 - - - +
347G GLU* 1.3 54.2 + - + +
349G THR* 2.6 12.8 + - - +
350G ALA* 2.5 35.8 + - - +
617G MLY 5.4 11.1 - - - +
618G THR* 5.1 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 347 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343G PHE* 3.5 15.2 - - + -
344G SER* 2.9 38.5 + - - +
346G ASP* 1.3 78.1 - - + +
348G MLY 1.3 60.7 + - - +
350G ALA* 2.8 24.9 + - - +
351G ILE* 2.8 21.9 + - - +
440G TRP* 3.5 33.8 - - + -
444G ARG* 3.4 25.3 + - - -
618G THR* 4.0 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MLY 348 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296G MLY 3.2 34.3 - - - -
335G ASP* 2.5 38.1 + - - -
338G ILE* 3.6 26.7 - - + -
339G ASP* 2.8 36.8 + - - +
343G PHE* 4.6 2.2 - - + +
344G SER 2.5 19.4 + - - +
345G ALA* 3.4 18.6 - - + +
347G GLU* 1.3 72.7 - - - +
349G THR* 1.3 59.8 + - - +
351G ILE* 3.9 10.7 - - - +
352G TYR* 3.3 36.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 349 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302G MET* 4.6 16.8 - - - +
345G ALA* 2.4 28.7 + - - +
346G ASP* 2.6 16.7 + - - +
348G MLY 1.3 76.8 + - - +
350G ALA* 1.3 62.7 + - - -
351G ILE 3.2 1.3 - - - -
352G TYR* 3.1 4.9 + - - +
353G MLY 2.8 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 350 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346G ASP 2.5 18.5 + - - +
347G GLU* 3.2 8.3 - - - +
349G THR* 1.3 67.0 - - - +
351G ILE* 1.3 55.3 + - - +
353G MLY 3.9 5.1 - - - +
354G LEU* 2.5 48.3 + - + +
616G VAL* 4.5 13.9 - - + -
618G THR* 3.7 38.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 351 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232G PHE* 3.7 26.7 - - + -
287G ILE* 5.4 0.4 - - + -
338G ILE* 4.7 21.3 - - + -
343G PHE* 4.7 11.0 - - + -
347G GLU 2.8 22.4 + - - +
348G MLY 3.9 8.5 - - - +
350G ALA* 1.3 77.4 - - - +
352G TYR* 1.3 72.6 + - + +
354G LEU* 3.8 0.9 - - - +
355G THR* 2.6 29.9 + - - +
437G MET* 4.2 12.8 - - + -
440G TRP* 4.1 17.0 - - + -
441G MET* 3.6 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 352 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287G ILE* 4.8 12.8 - - + -
291G ILE* 3.7 28.9 - - + -
299G LEU* 3.8 27.1 - - + -
302G MET* 4.1 22.4 - - + -
303G LEU* 4.2 12.6 - - + +
331G LEU* 4.0 11.1 + - + +
334G THR* 4.9 3.5 - - + +
335G ASP* 2.7 42.2 + - - +
338G ILE* 4.7 10.0 - - + +
348G MLY 3.3 37.2 + - + -
349G THR 3.1 6.0 + - - +
351G ILE* 1.3 87.2 - - + +
353G MLY 1.3 54.8 + - - +
355G THR* 2.6 29.9 + - - -
356G GLY 3.3 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MLY 353 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302G MET* 4.5 10.3 - - + -
303G LEU* 4.0 18.1 - - + +
349G THR* 2.8 41.0 + - + +
350G ALA* 3.9 5.2 - - - +
352G TYR* 1.3 73.4 - - - +
354G LEU* 1.3 62.8 + - + +
356G GLY* 3.3 1.7 + - - -
357G ALA* 3.1 21.3 + - - +
388G TYR* 3.1 54.7 - - - -
389G LEU* 3.4 53.1 - - + +
391G GLY* 4.4 0.9 - - - -
616G VAL* 3.7 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 354 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350G ALA* 2.5 41.5 + - + +
351G ILE 3.8 3.4 - - - +
353G MLY 1.3 76.3 + - + +
355G THR* 1.3 62.5 + - - +
356G GLY 3.3 0.5 + - - -
357G ALA* 3.5 7.3 + - - +
358G VAL* 3.4 21.8 + - - +
389G LEU 4.4 6.7 - - - +
390G MET* 4.1 33.3 - - + +
433G VAL* 4.8 12.9 - - + +
437G MET* 3.8 22.8 - - - +
616G VAL* 5.0 4.5 - - + -
618G THR* 4.4 13.2 - - + -
619G LEU* 4.6 22.7 - - + +
622G LEU* 4.9 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 355 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232G PHE* 3.8 7.3 - - + -
287G ILE* 4.3 24.0 - - + -
288G PHE* 3.4 41.1 - - + -
291G ILE* 4.7 10.8 - - + -
303G LEU* 5.6 0.4 - - - -
351G ILE* 2.6 22.2 + - - +
352G TYR* 2.6 14.8 + - - -
354G LEU* 1.3 73.0 - - - +
356G GLY* 1.3 56.5 + - - -
358G VAL* 4.0 5.6 - - - +
359G MET* 3.5 6.3 + - + +
434G TYR* 5.0 3.6 - - + -
437G MET* 2.9 22.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 356 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303G LEU* 4.5 16.8 - - - +
305G ILE* 5.5 0.4 - - - -
352G TYR 3.3 8.8 + - - -
353G MLY 3.3 3.1 + - - -
354G LEU 3.1 0.4 - - - -
355G THR* 1.3 75.0 - - - +
357G ALA* 1.3 68.0 + - - +
358G VAL 3.1 1.8 - - - -
359G MET* 3.0 29.5 + - - +
360G HIS* 3.0 22.6 + - - -
389G LEU* 4.7 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 357 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353G MLY 3.1 13.1 + - - +
354G LEU* 3.6 11.0 - - - +
356G GLY* 1.3 76.2 - - - +
358G VAL* 1.3 50.9 + - - +
360G HIS* 2.9 15.9 + - - +
361G TYR* 2.8 40.4 + - + -
386G ALA* 4.7 3.6 - - - +
389G LEU* 4.4 10.4 - - + +
390G MET* 3.7 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 358 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G VAL* 3.9 28.3 - - + +
288G PHE* 4.6 11.4 - - + -
314G TYR* 3.4 17.6 - - + -
354G LEU 3.4 16.8 - - - +
355G THR* 4.0 9.2 - - - +
357G ALA* 1.3 82.8 - - + +
359G MET* 1.3 62.7 + - - +
360G HIS 3.3 0.2 + - - -
361G TYR* 3.3 17.1 + - + +
390G MET* 5.3 3.6 - - + -
430G ALA* 4.0 28.7 - - + +
433G VAL* 4.7 15.5 - - + -
434G TYR* 4.8 10.1 - - + +
437G MET* 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 359 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288G PHE* 3.8 29.4 - - + +
291G ILE* 4.6 12.6 - - + -
292G MET* 4.2 25.1 - - + +
303G LEU* 5.2 0.2 - - + -
305G ILE* 3.8 31.6 - - + -
312G TYR* 3.6 45.0 - - + +
314G TYR* 4.5 8.9 - - - +
315G VAL* 4.7 6.5 - - + -
355G THR 3.5 13.9 - - - +
356G GLY* 3.0 20.3 + - - +
358G VAL* 1.3 80.0 - - - +
360G HIS* 1.3 62.8 + - - +
362G GLY* 3.4 10.6 + - - -
363G ASN* 3.8 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 360 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303G LEU 3.2 26.7 - - - -
304G LEU* 3.1 21.3 + - + -
305G ILE* 3.9 15.2 - - + +
312G TYR* 4.2 13.8 + + - -
356G GLY 3.0 14.2 + - - -
357G ALA* 2.9 8.6 + - - +
359G MET* 1.3 78.9 - - - +
361G TYR* 1.3 60.2 + - - +
362G GLY 3.1 0.2 - - - -
363G ASN* 2.7 27.5 + - - +
364G LEU* 3.1 8.4 + - - -
382G VAL* 3.4 29.2 - - + +
385G MLY 4.1 19.4 + - + +
386G ALA* 4.2 10.7 + - + -
389G LEU* 3.9 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 361 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314G TYR* 4.1 5.8 + - + -
357G ALA 2.8 26.9 + - - -
358G VAL* 3.5 12.6 - - + +
359G MET 3.3 0.2 - - - -
360G HIS* 1.3 73.3 - - - +
362G GLY* 1.3 59.3 + - - +
364G LEU* 2.7 41.0 + - + +
386G ALA* 3.6 25.1 - - + -
390G MET* 2.8 37.9 - - + -
392G LEU* 4.6 3.8 - - - +
397G LEU* 4.6 14.5 - - + +
401G LEU* 6.0 3.8 - - + -
426G VAL* 3.7 36.8 - - + +
429G LEU* 4.3 14.1 - - + -
430G ALA* 4.3 10.8 - - + -
433G VAL* 5.6 0.7 - - + -
611G TYR* 3.0 26.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 362 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313G HIS* 4.1 20.5 - - - +
314G TYR* 3.1 43.9 - - - -
359G MET 3.4 5.0 + - - -
360G HIS 3.1 1.2 - - - -
361G TYR* 1.3 79.7 - - - +
363G ASN* 1.3 65.0 + - - +
364G LEU 4.6 1.9 - - - +
365G LYS* 4.2 10.2 + - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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