Contacts of the helix formed by residues 356 - 376 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B GLN 3.5 5.1 + - - +
355B LEU* 1.3 77.2 - - - +
357B ARG* 1.3 62.6 + - - +
358B GLU* 3.0 11.2 + - - +
359B GLN* 3.0 44.7 + - - +
360B MET* 3.1 10.4 + - - +
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Residues in contact with ARG 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B THR* 1.3 73.6 - - - +
358B GLU* 1.3 59.5 + - - +
360B MET* 3.5 23.3 - - + +
361B LEU* 3.6 14.7 + - - +
412B MET 2.8 23.2 + - - -
413B VAL* 3.7 18.8 - - + +
415B ASN* 3.6 32.0 + - - +
467B GLN 4.8 3.8 + - - -
468B PHE* 3.0 74.7 + - + +
522B PRO* 5.5 2.6 - - - +
523B PRO* 3.5 19.6 - - - +
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Residues in contact with GLU 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B THR* 3.0 9.7 + - - +
357B ARG* 1.3 79.1 - - - +
359B GLN* 1.3 55.3 + - + +
360B MET 3.3 0.4 - - - -
361B LEU* 3.3 7.1 + - + +
362B THR* 2.7 35.8 + - - +
410B LYS* 3.4 25.7 + - - +
413B VAL* 3.5 28.2 - - + +
587B GLU 5.1 1.7 - - - +
588B PHE 5.3 0.5 - - - +
589B ALA* 4.9 16.3 + - + -
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Residues in contact with GLN 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B GLN 4.6 0.9 - - - +
355B LEU* 3.4 29.1 - - + +
356B THR* 3.0 41.4 + - - +
358B GLU* 1.3 77.6 - - + +
360B MET* 1.3 64.1 + - - +
362B THR* 3.0 20.1 + - - +
363B ASN* 2.8 22.3 + - - +
309C GLU* 5.9 1.4 + - - -
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Residues in contact with MET 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B ASP* 3.9 16.6 - - + +
352B SER* 4.2 20.9 - - - +
355B LEU* 3.8 26.4 - - + +
356B THR 3.1 12.0 + - - +
357B ARG* 3.5 51.8 - - + +
358B GLU 3.3 0.2 - - - -
359B GLN* 1.3 78.8 - - - +
361B LEU* 1.3 61.4 + - - +
363B ASN* 3.5 11.8 + - - +
364B ARG* 3.3 18.4 + - - +
443B CYS 5.4 0.4 - - - +
466B ASP 5.9 1.3 - - - +
467B GLN 5.6 4.7 - - - +
468B PHE* 4.6 14.6 - - + -
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Residues in contact with LEU 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ARG 3.6 3.5 + - - +
358B GLU* 3.3 9.3 + - + +
359B GLN 3.1 0.4 - - - -
360B MET* 1.3 76.7 - - - +
362B THR* 1.3 58.6 + - - +
364B ARG* 2.9 4.1 + - + +
365B PHE* 2.8 55.2 + - + -
409B LEU* 4.2 18.6 - - + +
413B VAL* 3.5 32.1 - - + -
443B CYS* 3.7 33.0 - - + +
468B PHE* 3.5 37.9 - - + -
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Residues in contact with THR 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B GLU* 2.7 23.0 + - - +
359B GLN* 3.1 16.1 - - - +
361B LEU* 1.3 75.6 - - - +
363B ASN* 1.3 59.8 - - - +
365B PHE* 3.5 7.3 + - - +
366B ASN* 2.7 43.8 + - - +
589B ALA* 3.6 24.9 - - + +
591B SER* 3.6 24.5 - - - +
592B ILE* 4.1 8.4 - - + +
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Residues in contact with ASN 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B LYS* 5.7 3.6 - - - +
355B LEU* 3.6 28.8 - - - +
359B GLN* 2.8 22.1 + - - +
360B MET* 3.7 7.7 - - - +
361B LEU 3.1 0.2 - - - -
362B THR* 1.3 75.1 - - - +
364B ARG* 1.3 62.3 + - - +
366B ASN* 3.3 10.8 + - - +
367B ASP* 2.7 37.0 + - - +
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Residues in contact with ARG 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B MET 3.3 11.3 + - - +
361B LEU* 2.9 11.1 + - - +
363B ASN* 1.3 78.9 - - - +
365B PHE* 1.3 61.8 + - - +
367B ASP* 3.0 15.6 + - - +
368B LEU* 2.9 39.7 + - + +
371B ARG* 4.0 18.1 - - - +
441B GLU* 2.8 50.1 + - - +
442B LEU 3.5 15.5 - - - +
443B CYS 3.2 26.2 + - - +
444B GLY* 4.2 9.8 - - - -
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Residues in contact with PHE 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B LEU* 2.8 55.5 + - + +
362B THR* 3.8 2.5 - - - +
364B ARG* 1.3 73.1 - - + +
366B ASN* 1.3 61.6 + - - +
368B LEU* 3.6 10.7 + - + +
369B LEU* 3.3 27.3 + - + +
409B LEU* 3.9 28.0 - - + -
442B LEU* 3.9 21.5 - - + -
576B LEU* 3.6 21.6 - - + +
579B LEU* 3.5 27.1 - - + -
588B PHE* 4.1 25.6 - + - -
592B ILE* 3.7 19.7 - - + -
596B ILE* 5.6 0.4 - - + -
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Residues in contact with ASN 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B THR* 2.7 32.3 + - - +
363B ASN* 3.3 12.2 + - - +
364B ARG 3.1 0.6 - - - -
365B PHE* 1.3 76.3 - - - +
367B ASP* 1.3 56.1 + - - +
368B LEU 3.2 0.2 - - - -
369B LEU* 3.1 2.2 + - - -
370B ASP* 2.7 37.9 + - - +
591B SER 5.3 3.1 + - - +
592B ILE* 3.4 27.5 - - - +
595B ARG* 3.2 31.7 + - - +
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Residues in contact with ASP 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B LYS* 3.5 27.3 + - - -
363B ASN* 2.7 28.0 + - - +
364B ARG* 3.0 20.0 + - - +
366B ASN* 1.3 77.2 - - - +
368B LEU* 1.3 61.6 + - + +
370B ASP* 3.1 27.0 + - - +
371B ARG* 3.5 19.7 + - - +
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Residues in contact with LEU 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B ARG* 2.9 38.2 + - + +
365B PHE* 3.7 10.3 - - + +
367B ASP* 1.3 78.1 - - + +
369B LEU* 1.3 59.3 + - - +
371B ARG* 3.7 13.1 + - - +
372B MET* 3.1 24.3 + - - +
441B GLU* 3.7 22.0 - - + +
442B LEU* 3.5 41.7 - - + +
572B GLY 4.6 2.9 - - - +
573B ILE* 3.3 29.5 - - + +
576B LEU* 3.5 20.2 - - + -
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Residues in contact with LEU 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B PHE 3.3 18.3 + - - +
366B ASN* 3.1 2.6 + - - +
368B LEU* 1.3 77.4 - - - +
370B ASP* 1.3 54.1 + - - +
371B ARG 3.2 0.7 - - - -
372B MET* 3.1 26.9 + - - +
373B ASP* 2.7 36.9 + - - +
576B LEU* 3.5 12.6 - - + -
580B ILE* 3.9 17.3 - - + -
592B ILE* 4.5 9.9 - - + -
595B ARG* 3.2 50.9 - - + +
596B ILE* 4.8 9.6 - - + -
599B TRP* 3.8 19.7 - - + +
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Residues in contact with ASP 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B ASN* 2.7 25.4 + - - +
367B ASP* 3.1 25.9 + - - +
369B LEU* 1.3 76.7 - - - +
371B ARG* 1.3 61.6 + - + +
373B ASP* 3.3 12.0 + - - +
374B ILE* 3.2 26.1 - - + +
595B ARG* 3.2 18.7 + - - +
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Residues in contact with ARG 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B ARG* 4.0 24.7 - - - +
367B ASP* 3.5 19.9 + - - +
368B LEU* 3.8 14.5 - - - +
369B LEU 3.2 0.4 - - - -
370B ASP* 1.3 75.8 - - + +
372B MET* 1.3 60.0 + - - +
374B ILE* 3.1 12.5 + - - +
375B MET* 2.9 41.7 + - - +
441B GLU* 3.4 30.3 + - - +
573B ILE* 4.1 17.8 - - + +
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Residues in contact with MET 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B LEU 3.1 11.4 - - - +
369B LEU* 3.1 33.4 + - + +
371B ARG* 1.3 73.7 - - - +
373B ASP* 1.3 56.5 + - - +
374B ILE 3.0 4.9 - - - -
375B MET* 3.4 8.7 - - - -
376B PHE* 2.8 59.5 + - + +
573B ILE* 3.5 20.0 - - + -
576B LEU* 3.5 18.4 - - + -
577B LEU* 3.4 41.1 - - + -
580B ILE* 5.5 0.9 - - + -
599B TRP* 3.6 20.6 - - + -
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Residues in contact with ASP 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B LEU 2.7 22.0 + - - +
370B ASP* 3.3 9.3 + - - +
372B MET* 1.3 74.6 - - - +
374B ILE* 1.3 60.5 + - + +
376B PHE 5.3 0.4 - - - -
377B GLY* 3.9 14.6 - - - -
595B ARG* 2.8 25.1 + - - -
599B TRP* 3.2 24.8 + - - -
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Residues in contact with ILE 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B PRO* 3.7 31.6 - - + -
314B TYR* 4.3 11.7 - - - +
315B LYS* 5.4 7.6 - - + +
370B ASP* 3.2 22.7 - - + +
371B ARG* 3.1 8.7 + - - +
372B MET 3.0 0.8 - - - -
373B ASP* 1.3 81.4 - - + +
375B MET* 1.3 63.7 + - - +
376B PHE 3.3 1.1 - - - -
377B GLY* 3.2 7.6 + - - -
379B THR* 3.5 27.1 + - - +
380B GLY* 3.1 23.4 + - - -
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Residues in contact with MET 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B ARG* 2.9 31.0 + - - +
372B MET* 3.4 18.2 - - - -
374B ILE* 1.3 78.6 - - - +
376B PHE* 1.3 86.3 + - + +
377B GLY 3.2 1.8 + - - +
380B GLY* 3.3 18.2 - - - +
381B SER 4.5 0.4 - - - +
382B ALA* 3.3 45.2 + - + +
387B TRP* 3.5 39.0 - - + -
573B ILE* 4.4 7.0 - - + -
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Residues in contact with PHE 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B MET* 2.8 60.4 + - + +
373B ASP* 4.6 1.3 - - - -
375B MET* 1.3 104.3 - - + +
377B GLY* 1.3 58.6 + - - +
382B ALA* 3.8 13.0 - - + -
383B ASP 4.0 1.3 - - - -
384B ILE* 3.4 51.8 - - + -
387B TRP* 3.8 25.1 - + + -
573B ILE* 4.7 0.7 - - + -
577B LEU* 4.6 0.9 - - + -
599B TRP* 3.9 17.7 - + + -
602B ARG* 3.5 30.5 + - - +
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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