Contacts of the helix formed by residues 356 - 376 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354K GLN 3.5 4.9 + - - +
355K LEU* 1.3 77.5 - - - +
357K ARG* 1.3 64.1 + - - +
358K GLU* 3.0 10.5 + - - +
359K GLN* 3.0 44.9 + - - +
360K MET* 3.1 9.7 + - - +
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Residues in contact with ARG 357 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356K THR* 1.3 72.2 - - - +
358K GLU* 1.3 57.8 + - - +
360K MET* 3.5 23.8 - - + +
361K LEU* 3.6 14.4 + - - +
412K MET 2.8 22.6 + - - -
413K VAL* 3.7 19.3 - - + +
415K ASN* 3.6 32.6 + - - +
467K GLN 4.8 4.2 + - - -
468K PHE* 3.0 75.0 + - + +
522K PRO* 5.5 2.4 - - - +
523K PRO* 3.5 20.7 - - - +
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Residues in contact with GLU 358 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356K THR* 3.0 9.0 + - - +
357K ARG* 1.3 78.6 - - - +
359K GLN* 1.3 55.1 + - + +
360K MET 3.3 0.2 - - - -
361K LEU* 3.3 7.8 + - + +
362K THR* 2.7 35.7 + - - +
410K LYS* 3.3 26.9 + - - +
413K VAL* 3.5 28.9 - - + +
587K GLU 5.1 1.9 - - - +
588K PHE 5.3 0.7 - - - -
589K ALA* 4.9 15.4 + - + -
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Residues in contact with GLN 359 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354K GLN 4.6 0.9 - - - +
355K LEU* 3.4 29.3 - - + +
356K THR* 3.0 41.0 + - - +
358K GLU* 1.3 77.4 - - + +
360K MET* 1.3 63.6 + - - +
362K THR* 3.0 22.0 + - - +
363K ASN* 2.8 21.7 + - - +
309L GLU* 5.6 4.8 + - - +
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Residues in contact with MET 360 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351K ASP* 4.0 17.5 - - + +
352K SER* 4.2 19.7 - - - +
355K LEU* 3.8 25.3 - - + +
356K THR 3.1 12.3 + - - +
357K ARG* 3.5 51.8 - - + +
358K GLU 3.3 0.2 - - - -
359K GLN* 1.3 77.8 - - - +
361K LEU* 1.3 59.3 + - - +
363K ASN* 3.5 12.3 + - - +
364K ARG* 3.3 18.5 + - - +
443K CYS 5.4 0.4 - - - +
466K ASP 5.9 1.3 - - - +
467K GLN 5.6 5.2 - - - +
468K PHE* 4.5 15.3 - - + -
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Residues in contact with LEU 361 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357K ARG 3.6 3.3 + - - +
358K GLU* 3.3 8.4 + - + +
359K GLN 3.1 0.4 - - - -
360K MET* 1.3 76.6 - - - +
362K THR* 1.3 57.3 + - - +
364K ARG* 2.9 4.4 + - - +
365K PHE* 2.8 55.8 + - + -
409K LEU* 4.2 18.6 - - + +
413K VAL* 3.5 32.1 - - + -
443K CYS* 3.7 33.2 - - + +
468K PHE* 3.5 39.0 - - + -
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Residues in contact with THR 362 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358K GLU* 2.7 22.8 + - - +
359K GLN* 3.0 16.7 + - - +
361K LEU* 1.3 76.3 - - - +
363K ASN* 1.3 59.4 + - - +
365K PHE* 3.5 7.7 + - - +
366K ASN* 2.7 43.5 + - - +
589K ALA* 3.6 25.1 - - + +
591K SER* 3.6 24.5 - - - +
592K ILE* 4.1 8.6 - - + +
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Residues in contact with ASN 363 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281K LYS* 5.7 3.8 - - - +
355K LEU* 3.6 28.1 - - - +
359K GLN* 2.8 22.7 + - - +
360K MET* 3.7 8.6 - - - +
362K THR* 1.3 75.4 - - - +
364K ARG* 1.3 62.6 + - - +
366K ASN* 3.3 11.3 + - - +
367K ASP* 2.7 37.4 + - - +
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Residues in contact with ARG 364 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360K MET 3.3 10.0 + - - +
361K LEU* 2.9 11.3 + - - +
363K ASN* 1.3 79.3 - - - +
365K PHE* 1.3 63.5 + - + +
367K ASP* 3.0 16.3 + - - +
368K LEU* 2.9 39.3 + - + +
371K ARG* 4.0 18.1 - - - +
441K GLU* 2.8 50.5 + - - +
442K LEU 3.5 15.3 - - - +
443K CYS 3.2 26.2 + - - +
444K GLY* 4.2 9.8 - - - -
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Residues in contact with PHE 365 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361K LEU* 2.8 54.7 + - + +
362K THR* 3.8 2.2 - - - +
364K ARG* 1.3 74.3 - - + +
366K ASN* 1.3 59.9 + - - +
368K LEU* 3.6 10.2 + - + +
369K LEU* 3.3 27.3 + - + +
409K LEU* 3.9 28.0 - - + -
442K LEU* 3.9 21.1 - - + -
576K LEU* 3.5 21.9 - - + +
579K LEU* 3.5 27.6 - - + -
588K PHE* 4.1 25.6 - + - -
592K ILE* 3.7 19.7 - - + -
596K ILE* 5.7 0.7 - - + -
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Residues in contact with ASN 366 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362K THR* 2.7 32.3 + - - +
363K ASN* 3.3 11.3 + - - +
364K ARG 3.1 0.6 - - - -
365K PHE* 1.3 76.0 - - - +
367K ASP* 1.3 56.1 + - - +
368K LEU 3.2 0.4 - - - -
369K LEU* 3.1 2.4 + - - -
370K ASP* 2.7 37.9 + - - +
591K SER 5.4 2.7 + - - +
592K ILE* 3.4 27.5 - - - +
595K ARG* 3.2 32.4 + - - +
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Residues in contact with ASP 367 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281K LYS* 3.5 27.9 + - - -
363K ASN* 2.7 27.8 + - - +
364K ARG* 3.0 19.6 + - - +
366K ASN* 1.3 76.0 - - - +
368K LEU* 1.3 63.5 + - + +
370K ASP* 3.1 27.3 + - - +
371K ARG* 3.5 19.5 + - - +
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Residues in contact with LEU 368 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364K ARG* 2.9 36.2 + - + +
365K PHE* 3.7 11.7 - - - +
366K ASN 3.2 0.2 - - - -
367K ASP* 1.3 77.3 - - + +
369K LEU* 1.3 60.3 + - - +
371K ARG* 3.7 13.1 + - - +
372K MET* 3.1 23.7 + - - +
441K GLU* 3.7 21.8 - - + +
442K LEU* 3.5 41.5 - - + +
572K GLY 4.6 2.7 - - - +
573K ILE* 3.3 30.1 - - + +
576K LEU* 3.5 19.7 - - + -
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Residues in contact with LEU 369 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365K PHE 3.3 18.6 + - - +
366K ASN* 3.1 3.2 + - - +
368K LEU* 1.3 78.0 - - - +
370K ASP* 1.3 54.8 + - - +
371K ARG 3.2 0.2 - - - -
372K MET* 3.1 27.2 + - - +
373K ASP* 2.8 37.3 + - - +
576K LEU* 3.5 12.3 - - + -
580K ILE* 3.9 16.2 - - + -
592K ILE* 4.5 9.6 - - + -
595K ARG* 3.2 50.9 - - + +
596K ILE* 4.8 10.3 - - + -
599K TRP* 3.8 19.5 - - + +
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Residues in contact with ASP 370 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366K ASN* 2.7 25.5 + - - +
367K ASP* 3.1 26.3 + - - +
369K LEU* 1.3 78.0 - - - +
371K ARG* 1.3 62.6 + - + +
373K ASP* 3.3 12.0 + - - +
374K ILE* 3.2 25.9 - - + +
595K ARG* 3.2 18.5 + - - +
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Residues in contact with ARG 371 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364K ARG* 4.0 25.1 - - - +
367K ASP* 3.5 18.4 + - - +
368K LEU* 3.8 16.0 - - - +
369K LEU 3.2 0.4 - - - -
370K ASP* 1.3 76.3 - - + +
372K MET* 1.3 59.0 + - - +
374K ILE* 3.1 11.6 + - - +
375K MET* 2.9 41.5 + - - +
441K GLU* 3.4 29.7 + - - +
573K ILE* 4.1 17.1 - - + +
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Residues in contact with MET 372 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368K LEU 3.1 12.8 - - - +
369K LEU* 3.1 32.7 + - + +
371K ARG* 1.3 72.7 - - - +
373K ASP* 1.3 56.8 + - - +
374K ILE 2.9 4.7 - - - -
375K MET* 3.4 9.2 - - - -
376K PHE* 2.8 60.3 + - + +
573K ILE* 3.5 20.4 - - + -
576K LEU* 3.5 18.4 - - + -
577K LEU* 3.4 39.3 - - + -
580K ILE* 5.5 0.9 - - + -
599K TRP* 3.6 18.4 - - + -
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Residues in contact with ASP 373 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369K LEU* 2.8 22.1 + - - +
370K ASP* 3.3 9.1 + - - +
372K MET* 1.3 75.2 - - - +
374K ILE* 1.3 61.2 + - + +
376K PHE* 4.8 1.1 - - - -
377K GLY* 4.0 14.0 - - - -
595K ARG* 2.8 24.7 + - - -
599K TRP* 3.2 24.6 + - - -
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Residues in contact with ILE 374 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308K LYS 6.2 0.2 - - - +
311K PRO* 3.7 31.0 - - + -
314K TYR* 4.3 11.9 - - - +
315K LYS* 5.4 8.1 - - + +
370K ASP* 3.2 21.5 - - + +
371K ARG* 3.1 9.2 + - - +
372K MET 2.9 0.6 - - - -
373K ASP* 1.3 81.5 - - + +
375K MET* 1.3 62.3 + - - +
376K PHE 3.3 1.1 - - - -
377K GLY* 3.2 7.8 + - - -
379K THR* 3.5 28.2 + - - +
380K GLY* 3.1 23.6 + - - -
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Residues in contact with MET 375 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371K ARG* 2.9 31.3 + - - +
372K MET* 3.4 18.2 - - - -
374K ILE* 1.3 76.9 - - - +
376K PHE* 1.3 85.4 + - + +
377K GLY 3.2 2.2 + - - +
380K GLY* 3.3 18.2 - - - +
381K SER 5.1 0.4 - - - +
382K ALA* 3.3 42.5 + - + +
387K TRP* 3.5 40.2 - - + -
573K ILE* 4.4 7.2 - - + -
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Residues in contact with PHE 376 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372K MET* 2.8 59.5 + - + +
373K ASP* 4.6 1.6 - - - -
375K MET* 1.3 102.5 - - + +
377K GLY* 1.3 59.3 + - - +
382K ALA* 3.8 13.0 - - + -
383K ASP 4.0 0.9 - - - -
384K ILE* 3.4 53.2 - - + -
387K TRP* 3.8 25.4 - + + -
573K ILE* 4.7 1.1 - - + -
577K LEU* 4.6 0.7 - - + -
599K TRP* 3.9 18.1 - + + -
602K ARG* 3.5 29.7 + - - +
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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