Contacts of the helix formed by residues 344 - 362 (chain J) in PDB entry 1O1F
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 J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342J GLY 3.5 2.8 + - - -
343J PHE* 1.3 74.6 - - - +
345J ALA* 1.3 53.7 + - - +
346J ASP* 3.8 11.5 - - - +
347J GLU* 2.9 31.6 + - - +
348J MLY 2.5 34.7 + - - +
444J ARG* 4.5 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 345 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339J ASP* 6.0 0.2 - - - -
343J PHE 3.7 1.4 + - - -
344J SER* 1.3 74.6 + - - +
346J ASP* 1.3 51.7 + - - +
348J MLY 2.9 22.7 + - + +
349J THR* 2.4 44.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 346 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344J SER* 3.8 13.5 - - - +
345J ALA* 1.3 76.5 - - - +
347J GLU* 1.3 54.5 + - + +
349J THR* 2.6 12.5 + - - +
350J ALA* 2.5 36.1 + - - +
617J MLY 5.4 11.1 - - - +
618J THR* 5.1 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 347 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343J PHE* 3.5 15.7 - - + -
344J SER* 2.9 37.7 + - - +
346J ASP* 1.3 78.4 - - + +
348J MLY 1.3 58.6 + - - +
350J ALA* 2.8 25.2 + - - +
351J ILE* 2.8 21.8 + - - +
440J TRP* 3.5 33.0 - - + -
444J ARG* 3.4 25.3 + - - -
618J THR* 4.0 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MLY 348 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296J MLY 3.2 33.9 - - - -
335J ASP* 2.5 40.3 + - - -
338J ILE* 3.6 27.9 - - + +
339J ASP* 2.8 35.9 + - - +
343J PHE* 4.6 2.2 - - + +
344J SER 2.5 21.0 + - - +
345J ALA* 3.4 17.9 - - - +
347J GLU* 1.3 72.1 + - - +
349J THR* 1.3 57.4 + - - +
351J ILE* 3.9 9.6 - - - +
352J TYR* 3.3 36.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 349 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302J MET* 4.6 18.2 - - - +
345J ALA* 2.4 29.2 + - - +
346J ASP* 2.6 16.0 + - - +
348J MLY 1.3 76.0 + - - +
350J ALA* 1.3 62.8 + - - -
351J ILE 3.2 1.3 - - - -
352J TYR* 3.1 4.5 + - - +
353J MLY 2.8 47.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 350 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346J ASP 2.5 19.1 + - - +
347J GLU* 3.2 7.4 - - - +
349J THR* 1.3 67.6 - - - +
351J ILE* 1.3 55.4 + - - +
353J MLY 4.6 4.9 - - - -
354J LEU* 2.5 48.6 + - + +
616J VAL* 4.5 13.5 - - + -
618J THR* 3.7 38.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 351 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228J LEU* 5.6 0.2 - - + -
232J PHE* 3.7 26.2 - - + -
338J ILE* 4.7 20.4 - - + -
343J PHE* 4.7 10.5 - - + -
347J GLU 2.8 23.4 + - - +
348J MLY 3.9 9.4 - - - +
350J ALA* 1.3 76.6 - - - +
352J TYR* 1.3 72.3 + - + +
354J LEU* 3.8 1.3 - - - +
355J THR* 2.6 29.9 + - - +
437J MET* 4.2 13.0 - - + -
440J TRP* 4.0 15.9 - - + -
441J MET* 3.6 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 352 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287J ILE* 4.8 12.1 - - + -
291J ILE* 3.7 29.2 - - + -
299J LEU* 3.8 26.2 - - + -
302J MET* 4.1 22.7 - - + -
303J LEU* 4.2 12.3 - - + +
331J LEU* 4.0 11.6 + - + +
334J THR* 4.9 3.5 - - + +
335J ASP* 2.7 43.0 + - - +
338J ILE* 4.7 10.5 - - + +
348J MLY 3.3 37.7 + - + -
349J THR 3.1 6.0 + - - +
351J ILE* 1.3 86.3 - - + +
353J MLY 1.3 56.0 + - - +
355J THR* 2.6 30.9 + - - -
356J GLY 3.3 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MLY 353 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302J MET* 4.5 11.0 - - + -
303J LEU* 4.0 18.1 - - + +
349J THR* 2.8 40.7 + - + +
350J ALA* 3.9 4.9 - - - +
352J TYR* 1.3 71.5 - - - +
354J LEU* 1.3 61.7 + - + +
356J GLY* 3.3 1.6 + - - -
357J ALA* 3.1 21.5 + - - +
388J TYR* 3.1 54.7 - - - -
389J LEU* 3.4 53.1 - - + +
391J GLY* 4.9 0.9 - - - -
616J VAL* 3.7 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 354 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350J ALA* 2.5 41.1 + - + +
351J ILE 3.8 3.1 - - - +
353J MLY 1.3 76.2 + - + +
355J THR* 1.3 62.0 + - - +
356J GLY 3.3 0.7 + - - -
357J ALA* 3.5 6.8 + - - +
358J VAL* 3.4 21.8 + - - +
389J LEU 4.4 7.0 - - - +
390J MET* 4.1 33.7 - - + +
433J VAL* 4.8 13.5 - - + +
437J MET* 3.8 22.2 - - - +
440J TRP* 6.3 0.2 - - + -
616J VAL* 5.0 4.5 - - + -
618J THR* 4.4 13.0 - - + -
619J LEU* 4.6 23.6 - - + +
622J LEU* 4.9 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 355 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232J PHE* 3.8 7.4 - - + -
287J ILE* 4.3 23.8 - - + -
288J PHE* 3.4 42.2 - - + -
291J ILE* 4.7 10.8 - - + -
303J LEU* 5.6 0.4 - - - -
351J ILE* 2.6 21.1 + - - +
352J TYR* 2.6 14.7 + - - -
354J LEU* 1.3 72.7 - - - +
356J GLY* 1.3 56.4 + - - -
358J VAL* 4.0 6.2 - - - +
359J MET* 3.5 6.5 + - + +
434J TYR* 5.0 3.8 - - + -
437J MET* 2.9 22.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 356 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303J LEU* 4.5 17.2 - - - +
305J ILE* 5.5 0.4 - - - -
352J TYR 3.3 8.0 + - - -
353J MLY 3.3 3.1 + - - -
354J LEU 3.1 0.6 - - - -
355J THR* 1.3 77.1 - - - +
357J ALA* 1.3 65.2 + - - +
358J VAL 3.1 1.8 - - - -
359J MET* 3.0 30.2 + - - +
360J HIS* 3.0 22.5 + - - -
389J LEU* 4.7 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 357 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353J MLY 3.1 12.3 + - - +
354J LEU 3.6 10.3 - - - +
356J GLY* 1.3 76.2 - - - +
358J VAL* 1.3 51.7 + - - +
360J HIS* 2.9 15.3 + - - +
361J TYR* 2.8 41.2 + - + -
386J ALA* 4.7 3.4 - - - +
389J LEU* 4.4 11.7 - - + +
390J MET* 3.7 39.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 358 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275J VAL* 3.9 28.7 - - + +
288J PHE* 4.6 12.1 - - + -
314J TYR* 3.4 16.3 - - + -
354J LEU 3.4 17.3 - - - +
355J THR* 4.0 8.5 - - - +
357J ALA* 1.3 82.7 - - + +
359J MET* 1.3 63.6 + - - +
361J TYR* 3.3 17.0 + - + +
390J MET* 5.3 2.7 - - + -
430J ALA* 4.0 28.5 - - + +
433J VAL* 4.7 15.7 - - + -
434J TYR* 4.8 9.6 - - + +
437J MET* 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 359 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288J PHE* 3.8 30.1 - - + +
291J ILE* 4.6 12.6 - - + -
292J MET* 4.2 25.6 - - + +
305J ILE* 3.8 31.2 - - + -
312J TYR* 3.6 43.5 - - + +
314J TYR* 4.5 9.1 - - - +
315J VAL* 4.7 6.3 - - + -
355J THR 3.5 13.7 - - - +
356J GLY* 3.0 19.6 + - - +
358J VAL* 1.3 80.2 - - - +
360J HIS* 1.3 63.1 + - - +
362J GLY* 3.4 10.9 + - - -
363J ASN* 3.8 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 360 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303J LEU 3.2 27.1 - - - -
304J LEU* 3.1 20.9 + - + -
305J ILE* 3.9 14.5 - - + +
312J TYR* 4.2 12.8 + + - -
356J GLY 3.0 15.4 + - - -
357J ALA* 2.9 9.7 + - - +
359J MET* 1.3 79.4 - - - +
361J TYR* 1.3 60.1 + - - +
362J GLY 3.1 0.2 - - - -
363J ASN* 2.7 26.7 + - - +
364J LEU* 3.1 7.8 + - - -
382J VAL* 3.4 28.9 - - + +
385J MLY 4.1 19.9 - - + +
386J ALA* 4.2 11.4 + - + -
389J LEU* 3.9 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 361 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314J TYR* 4.1 6.7 + - + -
357J ALA 2.8 28.2 + - - -
358J VAL* 3.5 12.6 - - + +
359J MET 3.3 0.2 - - - -
360J HIS* 1.3 73.3 - - - +
362J GLY* 1.3 58.9 + - - +
364J LEU* 2.7 41.1 + - + +
386J ALA* 3.6 26.5 - - + -
390J MET* 2.8 36.1 - - + -
392J LEU* 4.6 4.2 - - - +
397J LEU* 4.6 14.3 - - + +
401J LEU* 6.0 4.0 - - + -
426J VAL* 3.7 37.3 - - + +
429J LEU* 4.3 14.6 - - + -
430J ALA* 4.3 11.0 - - + -
433J VAL* 5.6 0.7 - - + -
607J VAL* 6.2 0.2 - - + -
611J TYR* 3.0 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 362 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313J HIS* 4.1 20.4 - - - +
314J TYR* 3.1 44.8 - - - -
359J MET 3.4 5.5 + - - -
360J HIS 3.1 1.0 - - - -
361J TYR* 1.3 79.6 - - - +
363J ASN* 1.3 63.9 + - - +
364J LEU 3.4 1.9 - - - +
365J LYS* 4.2 10.0 + - - -
----------------------------------------------------------
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