Contacts of the helix formed by residues 356 - 376 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354L GLN 3.5 4.9 + - - +
355L LEU* 1.3 77.4 - - - +
357L ARG* 1.3 64.4 + - - +
358L GLU* 3.0 10.2 + - - +
359L GLN* 3.0 45.4 + - - +
360L MET* 3.1 9.7 + - - +
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Residues in contact with ARG 357 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356L THR* 1.3 73.0 - - - +
358L GLU* 1.3 59.0 + - - +
360L MET* 3.5 24.0 + - + +
361L LEU* 3.6 14.0 + - - +
412L MET 2.8 23.8 + - - -
413L VAL* 3.7 19.0 - - + +
415L ASN* 3.7 32.6 + - - +
467L GLN 4.8 3.6 + - - -
468L PHE* 3.0 75.7 + - + +
522L PRO* 5.5 2.4 - - - +
523L PRO* 3.5 20.0 - - - +
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Residues in contact with GLU 358 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356L THR* 3.0 9.0 + - - +
357L ARG* 1.3 78.6 - - - +
359L GLN* 1.3 55.7 + - + +
360L MET 3.3 0.2 - - - -
361L LEU* 3.4 6.8 + - + +
362L THR* 2.7 35.9 + - - +
410L LYS* 3.3 26.6 + - - +
413L VAL* 3.5 29.9 - - + +
587L GLU 5.1 1.4 - - - +
588L PHE 5.4 0.5 - - - -
589L ALA* 4.9 15.5 + - + -
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Residues in contact with GLN 359 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309G GLU* 5.1 9.0 + - - +
354L GLN 4.6 1.0 - - - +
355L LEU* 3.4 30.3 - - + +
356L THR* 3.0 40.1 + - - +
358L GLU* 1.3 77.3 - - + +
360L MET* 1.3 63.7 + - - +
362L THR* 3.0 21.3 + - - +
363L ASN* 2.8 21.9 + - - +
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Residues in contact with MET 360 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351L ASP* 4.0 17.7 - - + +
352L SER* 4.2 20.0 - - - +
355L LEU* 3.8 25.8 - - + +
356L THR 3.1 12.5 + - - +
357L ARG* 3.5 51.8 - - + +
358L GLU 3.3 0.2 - - - -
359L GLN* 1.3 76.8 - - - +
361L LEU* 1.3 61.4 + - - +
363L ASN* 3.5 12.7 + - - +
364L ARG* 3.3 18.2 + - - +
443L CYS 5.4 0.6 - - - +
466L ASP 5.9 1.6 - - - +
467L GLN 5.6 5.2 - - - +
468L PHE* 4.5 14.1 - - + -
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Residues in contact with LEU 361 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357L ARG 3.6 2.9 + - - +
358L GLU* 3.4 9.1 + - + +
359L GLN 3.1 0.4 - - - -
360L MET* 1.3 77.9 - - - +
362L THR* 1.3 56.4 + - - +
364L ARG* 2.9 3.9 + - - +
365L PHE* 2.8 54.7 + - + -
409L LEU* 4.2 18.8 - - + +
413L VAL* 3.5 32.1 - - + -
443L CYS* 3.7 32.1 - - + +
468L PHE* 3.5 39.3 - - + -
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Residues in contact with THR 362 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358L GLU* 2.7 23.1 + - - +
359L GLN* 3.1 16.8 - - - +
361L LEU* 1.3 77.6 - - - +
363L ASN* 1.3 59.8 + - - +
365L PHE* 3.5 7.4 + - - +
366L ASN* 2.7 43.1 + - - +
589L ALA* 3.6 25.3 - - + +
591L SER* 3.6 24.0 - - - +
592L ILE* 4.1 8.4 - - + +
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Residues in contact with ASN 363 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281L LYS* 5.7 3.6 - - - +
355L LEU* 3.6 28.3 - - - +
359L GLN* 2.8 23.6 + - - +
360L MET* 3.7 7.9 - - - +
361L LEU 3.1 0.2 - - - -
362L THR* 1.3 76.0 - - - +
364L ARG* 1.3 61.7 + - - +
366L ASN* 3.3 10.3 + - - +
367L ASP* 2.7 37.2 + - - +
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Residues in contact with ARG 364 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360L MET 3.3 10.3 + - - +
361L LEU* 2.9 11.1 + - - +
363L ASN* 1.3 79.3 - - - +
365L PHE* 1.3 63.0 + - - +
367L ASP* 3.0 14.9 + - - +
368L LEU* 2.9 41.1 + - + +
371L ARG* 4.0 18.7 - - - +
441L GLU* 2.8 49.7 + - - +
442L LEU 3.5 15.3 - - - +
443L CYS 3.2 27.7 + - - +
444L GLY* 4.2 9.8 - - - -
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Residues in contact with PHE 365 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361L LEU* 2.8 54.7 + - + +
362L THR* 3.8 2.5 - - - +
364L ARG* 1.3 73.9 - - + +
366L ASN* 1.3 61.2 + - - +
368L LEU* 3.5 10.5 + - + +
369L LEU* 3.3 27.0 + - - +
409L LEU* 3.9 27.8 - - + -
442L LEU* 3.9 22.7 - - + -
576L LEU* 3.5 22.5 - - + +
579L LEU* 3.5 27.4 - - + -
588L PHE* 4.2 24.9 - + - -
592L ILE* 3.7 19.3 - - + -
596L ILE* 5.6 0.7 - - + -
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Residues in contact with ASN 366 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362L THR* 2.7 32.9 + - - +
363L ASN* 3.3 11.9 + - - +
364L ARG 3.1 0.8 - - - -
365L PHE* 1.3 77.1 - - - +
367L ASP* 1.3 57.1 + - - +
368L LEU 3.2 0.2 - - - -
369L LEU* 3.1 2.2 + - - -
370L ASP* 2.7 37.1 + - - +
591L SER 5.4 2.2 + - - +
592L ILE* 3.4 28.1 - - - +
595L ARG* 3.2 32.4 + - - +
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Residues in contact with ASP 367 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281L LYS* 3.6 26.3 + - - -
363L ASN* 2.7 27.0 + - - +
364L ARG* 3.0 19.4 + - - +
366L ASN* 1.3 76.7 - - - +
368L LEU* 1.3 62.6 + - + +
370L ASP* 3.1 26.3 + - - +
371L ARG* 3.5 20.5 + - - +
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Residues in contact with LEU 368 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364L ARG* 2.9 37.7 + - + +
365L PHE* 3.7 11.0 - - - +
366L ASN 3.2 0.2 - - - -
367L ASP* 1.3 77.1 - - - +
369L LEU* 1.3 59.7 + - - +
371L ARG* 3.7 12.4 + - - +
372L MET* 3.1 23.4 + - - +
441L GLU* 3.7 22.0 - - + +
442L LEU* 3.5 42.0 - - + +
572L GLY 4.6 2.7 - - - +
573L ILE* 3.3 29.8 - - + +
576L LEU* 3.5 20.6 - - + -
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Residues in contact with LEU 369 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365L PHE 3.3 18.1 + - - +
366L ASN* 3.1 2.8 + - - +
368L LEU* 1.3 77.2 - - - +
370L ASP* 1.3 57.9 + - - +
371L ARG 3.2 0.4 - - - -
372L MET* 3.1 27.0 + - - +
373L ASP* 2.8 33.5 + - - +
576L LEU* 3.5 12.1 - - + -
580L ILE* 3.9 17.0 - - + -
592L ILE* 4.5 9.6 - - + -
595L ARG* 3.2 50.5 - - + +
596L ILE* 4.8 9.9 - - + -
599L TRP* 3.8 20.6 - - + +
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Residues in contact with ASP 370 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366L ASN* 2.7 24.9 + - - +
367L ASP* 3.1 25.6 + - - +
369L LEU* 1.3 77.4 - - - +
371L ARG* 1.3 63.4 + - + +
373L ASP* 3.3 10.8 + - - +
374L ILE* 3.2 26.6 + - + +
595L ARG* 3.2 17.5 + - - +
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Residues in contact with ARG 371 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364L ARG* 4.0 24.9 - - - +
367L ASP* 3.5 20.1 + - - +
368L LEU* 3.8 15.8 - - - +
369L LEU 3.2 0.2 - - - -
370L ASP* 1.3 76.2 - - + +
372L MET* 1.3 57.8 + - - +
374L ILE* 3.1 12.7 + - - +
375L MET* 2.9 41.6 + - - +
441L GLU* 3.4 29.3 + - - +
573L ILE* 4.1 17.5 - - + +
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Residues in contact with MET 372 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368L LEU 3.1 11.9 - - - +
369L LEU* 3.1 33.1 + - + +
371L ARG* 1.3 72.6 - - - +
373L ASP* 1.3 57.3 + - - +
374L ILE 3.0 4.9 - - - -
375L MET* 3.4 9.6 - - - -
376L PHE* 2.8 59.4 + - + +
573L ILE* 3.5 20.2 - - + -
576L LEU* 3.5 17.9 - - + -
577L LEU* 3.4 39.5 - - + -
580L ILE* 5.5 0.9 - - + -
599L TRP* 3.6 18.8 - - + -
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Residues in contact with ASP 373 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369L LEU 2.8 21.5 + - - +
370L ASP* 3.3 10.1 + - - +
372L MET* 1.3 75.4 - - - +
374L ILE* 1.3 61.1 + - + +
376L PHE* 4.6 0.8 - - - -
377L GLY* 4.0 14.2 - - - -
595L ARG* 2.8 24.6 + - - -
599L TRP* 3.2 24.2 + - - -
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Residues in contact with ILE 374 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311L PRO* 3.7 31.4 - - + -
314L TYR* 4.3 11.7 - - - +
315L LYS* 5.4 7.4 - - + +
370L ASP* 3.2 21.8 - - + +
371L ARG* 3.1 8.9 + - - +
372L MET 3.0 0.6 - - - -
373L ASP* 1.3 81.8 - - + +
375L MET* 1.3 63.8 + - - +
376L PHE 3.3 0.7 - - - -
377L GLY* 3.2 7.5 + - - -
379L THR* 3.5 27.4 + - - +
380L GLY* 3.1 24.0 + - - -
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Residues in contact with MET 375 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371L ARG* 2.9 30.0 + - - +
372L MET* 3.4 18.8 - - - +
374L ILE* 1.3 78.2 - - - +
376L PHE* 1.3 86.6 + - + +
377L GLY 3.2 2.0 + - - +
380L GLY* 3.3 18.3 - - - -
381L SER 5.1 0.4 - - - +
382L ALA* 3.3 43.9 + - + +
387L TRP* 3.5 39.3 - - + -
573L ILE* 4.4 7.6 - - + -
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Residues in contact with PHE 376 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372L MET* 2.8 61.3 + - + +
373L ASP* 4.6 1.3 - - - -
375L MET* 1.3 101.9 - - + +
377L GLY* 1.3 59.5 + - - +
382L ALA* 3.8 13.9 - - + -
383L ASP 4.0 1.3 - - - -
384L ILE* 3.4 53.2 - - + -
387L TRP* 3.8 26.2 - + + -
573L ILE* 4.7 0.7 - - + -
577L LEU* 4.6 0.4 - - + -
599L TRP* 3.9 17.3 - + + -
602L ARG* 3.5 30.2 + - - +
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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
------------------------------------------------------------
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