Contacts of the helix formed by residues 344 - 362 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342D GLY 3.5 2.6 + - - -
343D PHE* 1.3 74.6 - - - +
345D ALA* 1.3 56.5 + - - +
346D ASP* 3.1 12.0 - - - +
347D GLU* 2.9 31.5 + - - -
348D MLY 2.5 34.7 + - - +
444D ARG* 4.5 0.8 - - - +
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Residues in contact with ALA 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339D ASP* 6.0 0.2 - - - -
343D PHE 3.7 1.8 + - - -
344D SER* 1.3 72.4 + - - +
346D ASP* 1.3 51.4 + - - +
348D MLY 2.9 23.1 + - + +
349D THR* 2.4 44.8 + - - +
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Residues in contact with ASP 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344D SER* 3.8 13.5 - - - +
345D ALA* 1.3 77.2 - - - +
347D GLU* 1.3 53.2 + - + +
349D THR* 2.6 12.7 + - - +
350D ALA* 2.5 35.7 + - - +
617D MLY 5.4 11.1 - - - +
618D THR* 5.1 5.2 + - - -
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Residues in contact with GLU 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343D PHE* 3.5 15.9 - - + -
344D SER* 2.9 39.2 + - - +
346D ASP* 1.3 78.0 - - + +
348D MLY 1.3 58.7 + - - +
350D ALA* 2.8 25.1 + - - +
351D ILE* 2.8 21.1 + - - +
440D TRP* 3.5 34.4 - - + -
444D ARG* 3.4 24.2 + - - -
618D THR* 4.0 9.6 + - - +
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Residues in contact with MLY 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296D MLY 3.2 34.3 - - - -
335D ASP* 2.5 38.5 + - - -
338D ILE* 3.6 27.1 - - + -
339D ASP* 2.8 35.0 + - - +
343D PHE* 4.9 1.1 - - - +
344D SER 2.5 20.2 + - - +
345D ALA* 3.4 17.0 - - + +
347D GLU* 1.3 72.9 + - - +
349D THR* 1.3 58.3 + - - +
351D ILE* 3.9 10.7 - - - +
352D TYR* 3.3 37.7 + - + -
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Residues in contact with THR 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D MET* 4.6 17.5 - - + +
345D ALA* 2.4 29.3 + - - +
346D ASP* 2.6 16.5 + - - +
348D MLY 1.3 76.5 + - - +
350D ALA* 1.3 63.2 + - - +
351D ILE 3.2 1.1 - - - -
352D TYR* 3.1 4.7 + - - +
353D MLY 2.8 46.1 + - + +
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Residues in contact with ALA 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346D ASP 2.5 18.9 + - - +
347D GLU 3.2 7.9 - - - +
349D THR* 1.3 67.4 - - - +
351D ILE* 1.3 55.0 + - + +
353D MLY 4.6 4.9 - - - -
354D LEU* 2.5 48.6 + - + +
616D VAL* 4.5 13.7 - - + -
618D THR* 3.7 38.8 - - + +
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Residues in contact with ILE 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D PHE* 3.7 26.7 - - + -
287D ILE* 5.4 0.4 - - + -
338D ILE* 4.7 21.5 - - + -
343D PHE* 4.7 10.8 - - + -
347D GLU 2.8 22.6 + - - +
348D MLY 3.9 8.7 - - - +
350D ALA* 1.3 77.4 - - - +
352D TYR* 1.3 72.0 + - + +
354D LEU* 3.8 1.3 - - - +
355D THR* 2.6 30.1 + - - +
437D MET* 4.2 13.2 - - + -
440D TRP* 4.0 16.4 - - + -
441D MET* 3.6 36.6 - - + -
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Residues in contact with TYR 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287D ILE* 4.8 13.2 - - + -
291D ILE* 3.7 28.9 - - + -
299D LEU* 3.8 26.0 - - + -
302D MET* 4.1 22.4 - - + -
303D LEU* 4.2 13.4 - - + +
331D LEU* 4.0 12.3 + - + +
334D THR* 4.9 3.6 - - + +
335D ASP* 2.7 42.3 + - - +
338D ILE* 4.7 10.5 - - + +
348D MLY 3.3 38.1 + - + -
349D THR 3.1 6.3 + - - +
351D ILE* 1.3 85.9 - - + +
353D MLY 1.3 54.5 + - - +
355D THR* 2.6 30.7 + - - -
356D GLY 3.3 6.9 + - - -
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Residues in contact with MLY 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302D MET* 4.5 10.1 - - + -
303D LEU* 4.0 17.7 - - + -
349D THR* 2.8 41.0 + - + +
350D ALA* 3.9 4.0 - - - +
352D TYR* 1.3 72.5 - - - +
354D LEU* 1.3 62.4 + - + +
356D GLY* 3.3 1.7 + - - -
357D ALA* 3.1 22.0 + - - +
388D TYR* 3.1 54.5 - - - -
389D LEU* 3.4 51.6 - - + +
391D GLY* 4.4 0.9 - - - -
616D VAL* 3.7 25.1 - - + -
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Residues in contact with LEU 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350D ALA* 2.5 41.3 + - + +
351D ILE* 3.8 3.8 - - - +
353D MLY 1.3 75.8 + - + +
355D THR* 1.3 59.3 + - - +
356D GLY 3.3 0.5 + - - -
357D ALA* 3.5 6.9 + - - +
358D VAL* 3.4 22.3 + - - +
389D LEU 4.4 7.0 - - - +
390D MET* 4.1 34.2 - - + +
433D VAL* 4.8 13.5 - - + +
437D MET* 3.8 21.7 - - - +
616D VAL* 5.0 5.2 - - + -
618D THR* 4.4 12.3 - - + -
619D LEU* 4.6 21.8 - - + +
622D LEU* 4.9 4.7 - - + -
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Residues in contact with THR 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D PHE* 3.8 7.3 - - + -
287D ILE* 4.3 23.1 - - + -
288D PHE* 3.4 42.0 - - + -
291D ILE* 4.7 11.0 - - + -
303D LEU* 5.6 0.2 - - - -
351D ILE* 2.6 21.9 + - - +
352D TYR* 2.6 15.6 + - - -
354D LEU* 1.3 71.9 - - - +
356D GLY* 1.3 57.8 + - - -
358D VAL* 4.0 5.9 - - - +
359D MET* 3.5 5.9 + - - +
434D TYR* 5.0 3.8 - - + -
437D MET* 2.9 21.9 - - + +
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Residues in contact with GLY 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D LEU* 4.5 16.8 - - - +
305D ILE* 5.5 0.4 - - - -
352D TYR 3.3 7.9 + - - -
353D MLY 3.3 2.9 + - - -
354D LEU 3.1 0.4 - - - -
355D THR* 1.3 77.7 - - - +
357D ALA* 1.3 65.5 + - - +
358D VAL 3.1 1.8 - - - -
359D MET* 3.0 29.8 + - - +
360D HIS* 3.0 23.1 + - - -
389D LEU* 4.7 1.6 - - - -
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Residues in contact with ALA 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353D MLY 3.1 12.3 + - - +
354D LEU 3.6 10.8 - - - +
356D GLY* 1.3 76.0 - - - +
358D VAL* 1.3 51.6 + - - +
360D HIS* 2.9 15.2 + - - +
361D TYR* 2.8 40.4 + - + -
386D ALA* 4.7 4.0 - - - +
389D LEU* 4.4 10.0 - - + +
390D MET* 3.7 39.5 - - + -
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Residues in contact with VAL 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D VAL* 3.9 27.6 - - + +
288D PHE* 4.6 11.7 - - + -
314D TYR* 3.4 17.2 - - + -
354D LEU 3.4 17.9 - - - +
355D THR* 4.0 8.7 - - - +
356D GLY 3.1 0.2 - - - -
357D ALA* 1.3 82.6 - - + +
359D MET* 1.3 63.1 + - - +
360D HIS 3.3 0.2 + - - -
361D TYR* 3.3 17.7 + - + +
390D MET* 5.3 3.4 - - + -
430D ALA* 4.0 27.6 - - + +
433D VAL* 4.7 14.8 - - + -
434D TYR* 4.8 10.5 - - + +
437D MET* 6.5 0.7 - - + -
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Residues in contact with MET 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288D PHE* 3.8 29.8 - - + +
291D ILE* 4.6 12.6 - - + -
292D MET* 4.2 25.8 - - + +
303D LEU* 5.2 0.2 - - + -
305D ILE* 3.8 31.4 - - + -
312D TYR* 3.6 43.4 - - + +
314D TYR* 4.5 9.3 - - - +
315D VAL* 4.7 6.1 - - + -
355D THR 3.5 13.9 - - - +
356D GLY* 3.0 20.2 + - - +
358D VAL* 1.3 78.8 - - - +
360D HIS* 1.3 62.7 + - - +
362D GLY* 3.4 10.4 + - - -
363D ASN* 3.8 6.1 + - - +
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Residues in contact with HIS 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303D LEU 3.2 26.9 - - - -
304D LEU* 3.1 22.1 + - + -
305D ILE* 3.9 14.7 - - + +
312D TYR* 4.2 13.2 + + - -
356D GLY 3.0 13.8 + - - -
357D ALA* 2.9 8.4 + - - +
359D MET* 1.3 79.2 - - - +
361D TYR* 1.3 60.4 + - - +
362D GLY 3.1 0.4 - - - -
363D ASN* 2.7 27.0 + - - +
364D LEU* 3.1 8.6 + - - +
382D VAL* 3.4 27.8 - - + +
385D MLY 4.1 19.6 - - + +
386D ALA* 4.2 11.4 + - + -
389D LEU* 3.9 13.7 - - + +
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Residues in contact with TYR 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314D TYR* 4.1 6.1 - - + -
357D ALA 2.8 27.4 + - - -
358D VAL* 3.5 12.3 - - + +
360D HIS* 1.3 73.5 - - - +
362D GLY* 1.3 59.5 + - - +
364D LEU* 2.7 40.8 + - + +
386D ALA* 3.6 26.0 - - + -
390D MET* 2.8 37.1 - - + -
392D LEU* 4.6 4.0 - - - +
397D LEU* 4.6 14.3 - - + +
401D LEU* 6.0 3.8 - - + -
426D VAL* 3.7 37.8 - - + +
429D LEU* 4.3 13.9 - - + -
430D ALA* 4.3 10.8 - - + -
433D VAL* 5.6 0.7 - - + -
611D TYR* 3.0 26.8 + - - -
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Residues in contact with GLY 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313D HIS* 4.1 19.7 - - - +
314D TYR* 3.1 45.0 - - - -
359D MET 3.4 5.9 + - - -
360D HIS 3.1 0.8 - - - -
361D TYR* 1.3 79.3 - - - +
363D ASN* 1.3 63.8 - - - +
364D LEU 3.4 1.1 - - - +
365D 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
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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