Contacts of the helix formed by residues 356 - 376 (chain H) in PDB entry 4E2I
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 THR 356 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354H GLN 3.5 5.1 + - - +
355H LEU* 1.3 77.1 - - - +
357H ARG* 1.3 63.9 + - - +
358H GLU* 3.0 10.8 + - - +
359H GLN* 3.0 45.5 + - - +
360H MET* 3.1 9.5 + - - +
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Residues in contact with ARG 357 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355H LEU 3.8 0.2 + - - -
356H THR* 1.3 73.1 - - - +
358H GLU* 1.3 58.8 + - - +
360H MET* 3.5 23.8 + - + +
361H LEU* 3.6 15.1 + - - +
412H MET 2.8 23.2 + - - -
413H VAL* 3.7 19.5 - - + +
415H ASN* 3.7 32.9 + - - +
467H GLN 4.8 4.0 + - - -
468H PHE* 3.0 75.7 + - + +
522H PRO* 5.5 2.2 - - - +
523H PRO* 3.5 19.4 - - - +
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Residues in contact with GLU 358 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356H THR* 3.0 9.2 + - - +
357H ARG* 1.3 78.4 - - - +
359H GLN* 1.3 55.1 + - + +
360H MET 3.3 0.4 - - - -
361H LEU* 3.3 6.5 + - + +
362H THR* 2.7 36.4 + - - +
410H LYS* 3.3 26.2 + - - +
413H VAL* 3.5 28.9 - - + +
587H GLU 5.1 1.4 - - - +
588H PHE 5.4 0.5 - - - -
589H ALA* 4.9 15.7 + - + -
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Residues in contact with GLN 359 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354H GLN 4.6 1.2 - - - +
355H LEU* 3.4 30.0 - - + +
356H THR* 3.0 39.9 + - - +
358H GLU* 1.3 77.6 - - + +
360H MET* 1.3 63.7 + - - +
362H THR* 3.0 20.4 + - - +
363H ASN* 2.8 22.0 + - - +
309I GLU* 5.6 3.9 + - - +
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Residues in contact with MET 360 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351H ASP* 4.0 16.8 - - + +
352H SER* 4.2 19.5 - - - +
355H LEU* 3.8 26.2 - - + +
356H THR 3.1 11.7 + - - +
357H ARG* 3.5 52.0 - - + +
359H GLN* 1.3 78.3 - - - +
361H LEU* 1.3 60.5 + - - +
363H ASN* 3.5 12.3 + - - +
364H ARG* 3.3 18.0 + - - +
443H CYS 5.4 0.4 - - - +
466H ASP 5.9 2.0 - - - +
467H GLN 5.6 4.9 - - - +
468H PHE* 4.5 14.6 - - + -
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Residues in contact with LEU 361 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357H ARG 3.6 2.4 + - - +
358H GLU* 3.3 9.7 + - + +
359H GLN 3.1 0.4 - - - -
360H MET* 1.3 76.4 - - - +
362H THR* 1.3 58.5 + - - +
364H ARG* 2.9 4.1 + - - +
365H PHE* 2.8 55.1 + - + -
409H LEU* 4.2 19.1 - - + +
413H VAL* 3.5 31.9 - - + -
443H CYS* 3.7 32.1 - - + +
468H PHE* 3.5 38.8 - - + -
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Residues in contact with THR 362 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358H GLU* 2.7 22.8 + - - +
359H GLN* 3.1 16.2 - - - +
361H LEU* 1.3 77.2 - - - +
363H ASN* 1.3 59.7 + - - +
365H PHE* 3.5 7.2 + - - +
366H ASN* 2.7 42.0 + - - +
589H ALA* 3.6 24.8 - - + +
591H SER* 3.6 24.0 - - - +
592H ILE* 4.1 9.1 - - + +
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Residues in contact with ASN 363 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281H LYS* 5.7 3.4 - - - +
355H LEU* 3.6 28.2 - - - +
359H GLN* 2.8 22.5 + - - +
360H MET* 3.7 8.3 - - - +
361H LEU 3.1 0.2 - - - -
362H THR* 1.3 76.4 - - - +
364H ARG* 1.3 62.8 + - - +
366H ASN* 3.3 9.7 + - - +
367H ASP* 2.7 36.9 + - - +
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Residues in contact with ARG 364 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360H MET 3.3 10.3 + - - +
361H LEU* 2.9 11.1 + - - +
363H ASN* 1.3 79.1 - - - +
365H PHE* 1.3 64.3 + - + +
367H ASP* 3.0 17.6 + - - +
368H LEU* 2.9 39.0 + - + +
371H ARG* 4.0 18.5 - - - +
441H GLU* 2.8 49.7 + - - +
442H LEU 3.5 15.0 - - - +
443H CYS 3.2 26.5 + - - +
444H GLY* 4.2 10.2 - - - -
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Residues in contact with PHE 365 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361H LEU* 2.8 54.6 + - + +
362H THR* 3.8 3.1 - - - +
364H ARG* 1.3 73.0 - - + +
366H ASN* 1.3 60.8 + - - +
368H LEU* 3.5 10.9 + - + +
369H LEU* 3.3 27.9 + - + +
409H LEU* 3.9 27.4 - - + -
442H LEU* 3.9 22.0 - - + -
576H LEU* 3.5 22.0 - - + +
579H LEU* 3.5 28.0 - - + -
588H PHE* 4.2 25.4 - + - -
592H ILE* 3.7 19.3 - - + -
596H ILE* 5.6 0.4 - - + -
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Residues in contact with ASN 366 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362H THR* 2.7 32.1 + - - +
363H ASN* 3.3 12.6 + - - +
364H ARG 3.1 0.8 - - - -
365H PHE* 1.3 77.3 - - - +
367H ASP* 1.3 55.5 + - - +
369H LEU* 3.1 2.6 + - - -
370H ASP* 2.7 36.9 + - - +
591H SER 5.3 2.5 + - - +
592H ILE* 3.4 28.4 - - - +
595H ARG* 3.2 32.7 + - - +
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Residues in contact with ASP 367 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281H LYS* 3.5 26.6 + - - -
363H ASN* 2.7 28.2 + - - +
364H ARG* 3.0 20.0 + - - +
366H ASN* 1.3 76.4 - - - +
368H LEU* 1.3 61.7 + - - +
370H ASP* 3.1 26.1 + - - +
371H ARG* 3.5 20.7 + - - +
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Residues in contact with LEU 368 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364H ARG* 2.9 36.2 + - + +
365H PHE* 3.7 11.0 - - + +
366H ASN 3.2 0.2 - - - -
367H ASP* 1.3 77.9 - - - +
369H LEU* 1.3 59.5 + - - +
371H ARG* 3.7 13.1 + - - +
372H MET* 3.1 23.7 + - - +
441H GLU* 3.7 22.0 - - + +
442H LEU* 3.5 42.2 - - + +
572H GLY 4.6 2.9 - - - +
573H ILE* 3.3 29.5 - - + +
576H LEU* 3.5 20.9 - - + -
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Residues in contact with LEU 369 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365H PHE 3.3 17.9 + - - +
366H ASN* 3.1 2.8 + - - +
368H LEU* 1.3 77.7 - - - +
370H ASP* 1.3 53.5 + - - +
371H ARG 3.2 0.4 - - - -
372H MET* 3.1 27.2 + - - +
373H ASP* 2.7 36.2 + - - +
576H LEU* 3.5 12.6 - - + -
580H ILE* 3.9 16.8 - - + -
592H ILE* 4.5 10.1 - - + -
595H ARG* 3.2 51.6 - - + +
596H ILE* 4.8 10.1 - - + -
599H TRP* 3.8 19.7 - - + +
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Residues in contact with ASP 370 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366H ASN* 2.7 25.8 + - - +
367H ASP* 3.1 25.6 + - - +
369H LEU* 1.3 77.4 - - - +
371H ARG* 1.3 62.4 + - + +
373H ASP* 3.3 11.4 + - - +
374H ILE* 3.2 24.9 + - + +
595H ARG* 3.2 18.1 + - - +
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Residues in contact with ARG 371 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364H ARG* 4.0 24.4 - - - +
367H ASP* 3.5 20.4 + - - +
368H LEU* 3.8 15.0 - - - +
369H LEU 3.2 0.2 - - - -
370H ASP* 1.3 75.5 - - + +
372H MET* 1.3 59.0 + - - +
374H ILE* 3.1 12.5 + - - +
375H MET* 2.9 41.3 + - - +
441H GLU* 3.4 30.5 + - - +
573H ILE* 4.1 16.5 - - + +
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Residues in contact with MET 372 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368H LEU 3.1 11.7 - - - +
369H LEU* 3.1 33.1 + - + +
371H ARG* 1.3 73.1 - - - +
373H ASP* 1.3 55.7 + - - +
374H ILE 3.0 5.2 - - - -
375H MET* 3.4 9.6 - - - -
376H PHE* 2.8 60.1 + - + +
573H ILE* 3.5 20.2 - - + -
576H LEU* 3.5 18.8 - - + -
577H LEU* 3.4 39.9 - - + -
580H ILE* 5.5 0.7 - - + -
599H TRP* 3.6 20.2 - - + -
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Residues in contact with ASP 373 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369H LEU 2.7 22.1 + - - +
370H ASP* 3.3 9.5 + - - +
372H MET* 1.3 73.8 - - - +
374H ILE* 1.3 59.8 + - + +
376H PHE 4.8 0.9 - - - -
377H GLY* 4.0 14.5 - - - -
595H ARG* 2.8 24.6 + - - -
599H TRP* 3.2 25.0 + - - -
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Residues in contact with ILE 374 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311H PRO* 3.7 32.3 - - + -
314H TYR* 4.3 11.7 - - - +
315H LYS* 5.4 7.2 - - + +
370H ASP* 3.2 22.0 - - + +
371H ARG* 3.5 8.3 - - - +
372H MET 3.0 0.6 - - - -
373H ASP* 1.3 82.2 - - + +
375H MET* 1.3 63.7 + - - +
376H PHE 3.3 0.9 - - - -
377H GLY* 3.2 7.7 + - - -
379H THR* 3.5 27.3 + - - +
380H GLY* 3.1 23.0 + - - -
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Residues in contact with MET 375 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371H ARG* 2.9 31.4 + - - +
372H MET* 3.4 18.2 - - - +
374H ILE* 1.3 78.4 - - - +
376H PHE* 1.3 86.6 + - + +
377H GLY 3.2 2.1 + - - +
380H GLY* 3.3 17.8 - - - +
381H SER 4.5 0.7 - - - +
382H ALA* 3.3 43.1 + - + +
387H TRP* 3.5 39.3 - - + -
573H ILE* 4.4 7.2 - - + -
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Residues in contact with PHE 376 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372H MET* 2.8 60.4 + - + +
373H ASP 4.6 1.3 - - - -
375H MET* 1.3 101.4 - - + +
377H GLY* 1.3 58.9 + - - +
382H ALA* 3.8 13.9 - - + -
383H ASP 4.0 1.3 - - - -
384H ILE* 3.4 51.4 - - + -
387H TRP* 3.8 26.2 - + + -
573H ILE* 4.7 0.7 - - + -
577H LEU* 4.5 1.1 - - + -
599H TRP* 3.9 17.3 - + + -
602H ARG* 3.5 31.1 + - - +
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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