Contacts of the helix formed by residues 344 - 362 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A GLY 3.5 2.4 + - - -
343A PHE* 1.3 75.1 - - - +
345A ALA* 1.3 55.2 + - - +
346A ASP* 3.8 11.5 - - - +
347A GLU* 2.9 31.4 + - - -
348A MLY 2.5 34.5 + - - +
444A ARG* 4.5 0.6 - - - +
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Residues in contact with ALA 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ASP* 6.0 0.2 - - - -
343A PHE 3.7 2.0 + - - -
344A SER* 1.3 73.7 + - - +
346A ASP* 1.3 51.1 + - - +
348A MLY 2.9 22.7 + - + +
349A THR* 2.4 45.2 + - - +
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Residues in contact with ASP 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A SER* 3.8 13.9 - - - +
345A ALA* 1.3 76.1 - - - +
347A GLU* 1.3 54.2 + - + +
349A THR* 2.6 12.8 + - - -
350A ALA* 2.5 36.2 + - - +
617A MLY 5.4 11.3 - - - +
618A THR* 5.1 5.2 + - - -
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Residues in contact with GLU 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A PHE* 3.5 15.9 - - + -
344A SER* 2.9 39.1 + - - +
346A ASP* 1.3 79.2 + - + +
348A MLY 1.3 59.2 + - - +
350A ALA* 2.8 25.5 + - - +
351A ILE* 2.8 21.1 + - - +
440A TRP* 3.5 33.8 - - + -
444A ARG* 3.4 26.0 + - - -
618A THR* 4.0 8.9 + - - +
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Residues in contact with MLY 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A MLY 3.2 33.7 - - - -
335A ASP* 2.5 38.7 + - - -
338A ILE* 3.6 28.0 - - + -
339A ASP* 2.8 36.4 + - - +
343A PHE* 4.8 1.1 - - - +
344A SER 2.5 20.5 + - - +
345A ALA* 3.0 17.9 - - + +
347A GLU* 1.3 74.0 + - - +
349A THR* 1.3 57.9 + - - +
351A ILE* 3.9 10.4 - - - +
352A TYR* 3.3 37.1 + - + -
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Residues in contact with THR 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A MET* 4.6 16.7 - - - +
345A ALA* 2.4 28.3 + - - +
346A ASP* 2.6 16.3 + - - -
348A MLY 1.3 76.8 + - - +
350A ALA* 1.3 62.9 + - - +
351A ILE 3.2 1.1 - - - -
352A TYR* 3.1 5.5 + - - +
353A MLY 2.8 47.3 + - + +
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Residues in contact with ALA 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ASP 2.5 19.1 + - - +
347A GLU 3.2 7.6 - - - +
349A THR* 1.3 67.9 - - - +
351A ILE* 1.3 55.8 + - + +
353A MLY 4.6 4.9 - - - -
354A LEU* 2.5 48.4 + - + +
616A VAL* 4.5 13.2 - - + -
618A THR* 3.7 38.8 - - + +
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Residues in contact with ILE 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A PHE* 3.7 26.5 - - + -
287A ILE* 5.4 0.4 - - + -
338A ILE* 4.7 20.4 - - + -
343A PHE* 4.7 10.5 - - + -
347A GLU 2.8 23.7 + - - +
348A MLY 3.9 9.9 - - - +
350A ALA* 1.3 77.1 - - - +
352A TYR* 1.3 73.0 + - + +
354A LEU* 3.8 1.1 - - - +
355A THR* 2.6 30.1 + - - +
437A MET* 4.2 13.0 - - + -
440A TRP* 4.0 16.1 - - + -
441A MET* 3.6 37.0 - - + -
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Residues in contact with TYR 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A ILE* 4.8 12.8 - - + -
291A ILE* 3.7 28.5 - - + -
299A LEU* 3.8 25.8 - - + -
302A MET* 4.1 23.6 - - + -
303A LEU* 4.2 13.0 - - + +
331A LEU* 4.0 11.8 + - + +
334A THR* 4.9 3.9 - - + +
335A ASP* 2.7 42.5 + - - +
338A ILE* 4.7 10.2 - - + +
348A MLY 3.3 37.6 + - + -
349A THR* 3.1 6.3 + - - +
351A ILE* 1.3 86.6 - - + +
353A MLY 1.3 55.6 + - - +
355A THR* 2.6 31.0 + - - -
356A GLY 3.3 6.6 + - - -
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Residues in contact with MLY 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A MET* 4.6 10.3 - - + -
303A LEU* 4.0 17.9 - - + +
349A THR* 2.8 42.3 + - + +
350A ALA* 3.9 3.8 - - - +
352A TYR* 1.3 72.6 - - - +
354A LEU* 1.3 61.7 + - + +
356A GLY* 3.3 1.8 + - - -
357A ALA* 3.1 21.7 + - - +
388A TYR* 3.1 54.1 - - - -
389A LEU* 3.4 51.0 - - + +
391A GLY* 4.9 0.7 - - - -
616A VAL* 3.7 25.8 - - + -
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Residues in contact with LEU 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A ALA* 2.5 40.0 + - + +
351A ILE 3.8 3.1 - - - +
353A MLY 1.3 76.6 + - + +
355A THR* 1.3 61.4 + - - +
356A GLY 3.3 0.5 + - - -
357A ALA* 3.5 7.0 + - - +
358A VAL* 3.4 22.0 + - - +
389A LEU 4.4 7.0 - - - +
390A MET* 4.1 33.9 - - + +
433A VAL* 4.8 13.5 - - + +
437A MET* 3.8 22.2 - - - +
616A VAL* 5.0 4.9 - - + -
618A THR* 4.4 13.0 - - + -
619A LEU* 4.6 22.4 - - + +
622A LEU* 4.9 4.7 - - + -
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Residues in contact with THR 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A PHE* 3.8 7.5 - - + -
287A ILE* 4.3 23.8 - - + -
288A PHE* 3.4 42.4 - - + -
291A ILE* 4.7 9.9 - - + -
303A LEU* 5.6 0.2 - - - -
351A ILE* 2.6 20.9 + - - +
352A TYR* 2.6 15.1 + - - -
354A LEU* 1.3 73.1 - - - +
356A GLY* 1.3 55.7 + - - -
358A VAL* 4.0 5.7 - - - +
359A MET* 3.5 7.5 + - + +
434A TYR* 5.0 4.0 - - + -
437A MET* 2.9 21.9 - - + +
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Residues in contact with GLY 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A LEU* 4.5 16.8 - - - +
305A ILE* 5.5 0.4 - - - -
352A TYR 3.3 8.1 + - - -
353A MLY 3.3 3.3 + - - -
354A LEU 3.1 0.4 - - - -
355A THR* 1.3 76.7 - - - +
357A ALA* 1.3 67.2 - - - +
358A VAL 3.1 1.6 - - - -
359A MET* 3.0 29.6 + - - +
360A HIS* 3.0 22.1 + - - -
389A LEU* 4.7 1.6 - - - -
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Residues in contact with ALA 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A MLY 3.1 12.9 + - - +
354A LEU 3.6 10.5 - - - +
356A GLY* 1.3 76.7 - - - +
358A VAL* 1.3 50.9 + - - +
360A HIS* 2.9 15.0 + - - +
361A TYR* 2.8 40.8 + - + -
386A ALA* 4.7 3.6 - - - +
389A LEU* 4.4 10.6 - - + +
390A MET* 3.7 38.8 - - + -
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Residues in contact with VAL 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A VAL* 3.9 28.5 - - + +
288A PHE* 4.6 10.8 - - + -
314A TYR* 3.4 17.2 - - + -
354A LEU 3.4 17.7 - - - +
355A THR* 4.0 9.0 - - - +
357A ALA* 1.3 81.3 - - + +
359A MET* 1.3 62.8 + - - +
360A HIS 3.3 0.2 + - - -
361A TYR* 3.3 16.5 + - + +
390A MET* 5.3 2.9 - - + -
430A ALA* 4.0 28.5 - - + +
433A VAL* 4.7 15.3 - - + -
434A TYR* 4.8 10.5 - - + +
437A MET* 6.5 0.4 - - + -
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Residues in contact with MET 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A PHE* 3.8 30.3 - - + +
291A ILE* 4.6 11.9 - - + -
292A MET* 4.2 25.4 - - + +
305A ILE* 3.8 31.4 - - + -
312A TYR* 3.6 44.5 - - + +
314A TYR* 4.5 8.9 - - - +
315A VAL* 4.7 6.3 - - + -
355A THR 3.5 14.1 - - - +
356A GLY* 3.0 19.7 + - - +
358A VAL* 1.3 80.3 - - - +
360A HIS* 1.3 64.2 + - - +
362A GLY* 3.4 10.2 + - - -
363A ASN* 3.8 5.4 + - - +
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Residues in contact with HIS 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A LEU 3.2 27.1 - - - -
304A LEU* 3.1 22.4 + - + -
305A ILE* 3.9 14.7 - - + +
312A TYR* 4.2 12.7 + + - -
356A GLY 3.0 14.8 + - - -
357A ALA* 2.9 8.9 + - - +
359A MET* 1.3 80.0 - - - +
361A TYR* 1.3 61.0 + - - +
362A GLY 3.1 0.2 - - - -
363A ASN* 2.7 26.7 + - - +
364A LEU* 3.1 7.8 + - - +
382A VAL* 3.4 28.7 - - + +
385A MLY 4.1 20.5 + - + +
386A ALA* 4.2 11.0 + - + -
389A LEU* 3.9 14.1 - - + +
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Residues in contact with TYR 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A TYR* 4.1 5.8 - - + -
357A ALA 2.8 27.5 + - - -
358A VAL* 3.5 12.6 - - + +
359A MET 3.3 0.4 - - - -
360A HIS* 1.3 72.3 - - - +
362A GLY* 1.3 59.8 + - - +
364A LEU* 2.7 40.9 + - + +
386A ALA* 3.6 26.7 - - + -
390A MET* 2.8 36.7 - - + -
392A LEU* 4.6 4.2 - - - +
397A LEU* 4.6 14.4 - - + +
401A LEU* 6.0 4.0 - - + -
426A VAL* 3.7 38.8 - - + +
429A LEU* 4.3 14.4 - - + -
430A ALA* 4.3 10.8 - - + -
433A VAL* 5.6 0.7 - - + -
607A VAL* 6.2 0.2 - - + -
611A TYR* 3.0 26.3 + - - -
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Residues in contact with GLY 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A HIS* 4.1 19.8 - - - +
314A TYR* 3.1 43.6 - - - -
358A VAL 3.6 0.2 + - - -
359A MET 3.4 5.7 + - - -
360A HIS 3.1 1.0 - - - -
361A TYR* 1.3 78.8 - - - +
363A ASN* 1.3 63.4 - - - +
364A LEU 3.4 1.9 - - - +
365A LYS* 4.2 10.2 + - - -
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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
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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