Contacts of the helix formed by residues 356 - 376 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354E GLN 3.5 4.9 + - - +
355E LEU* 1.3 76.9 - - - +
357E ARG* 1.3 64.4 + - - +
358E GLU* 3.0 10.4 + - - +
359E GLN* 3.0 44.8 + - - +
360E MET* 3.1 10.3 + - - +
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Residues in contact with ARG 357 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356E THR* 1.3 73.3 - - - +
358E GLU* 1.3 57.9 + - - +
360E MET* 3.5 24.5 - - + +
361E LEU* 3.6 15.1 + - - +
412E MET 2.8 23.4 + - - -
413E VAL* 3.7 18.7 - - + +
415E ASN* 3.7 32.0 + - - +
467E GLN 4.8 4.6 + - - -
468E PHE* 3.0 76.7 + - + +
522E PRO* 5.5 1.8 - - - +
523E PRO* 3.5 19.0 - - - +
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Residues in contact with GLU 358 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356E THR* 3.0 9.4 + - - +
357E ARG* 1.3 78.2 - - - +
359E GLN* 1.3 56.5 + - + +
360E MET 3.3 0.4 - - - -
361E LEU* 3.3 7.0 + - + +
362E THR* 2.7 35.9 + - - +
410E LYS* 3.4 26.1 + - - +
413E VAL* 3.5 28.7 - - + +
587E GLU 5.1 1.4 - - - +
588E PHE 5.4 0.7 - - - -
589E ALA* 4.9 15.4 + - + -
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Residues in contact with GLN 359 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354E GLN 4.7 0.5 - - - +
355E LEU* 3.4 29.5 - - + +
356E THR* 3.0 41.0 + - - +
358E GLU* 1.3 77.4 - - + +
360E MET* 1.3 63.9 + - - +
362E THR* 3.0 20.3 + - - +
363E ASN* 2.8 22.4 + - - +
307F LYS* 5.4 8.1 - - - +
309F GLU* 5.5 4.1 + - - +
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Residues in contact with MET 360 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351E ASP* 4.0 17.5 - - + +
352E SER* 4.2 19.1 - - - +
355E LEU* 3.8 25.8 - - + +
356E THR 3.1 11.5 + - - +
357E ARG* 3.5 52.7 - - + +
359E GLN* 1.3 77.7 - - - +
361E LEU* 1.3 60.3 + - - +
363E ASN* 3.5 12.7 + - - +
364E ARG* 3.3 18.9 + - - +
443E CYS 5.9 0.2 - - - -
466E ASP 5.9 1.3 - - - +
467E GLN 5.6 5.2 - - - +
468E PHE* 4.5 14.8 - - + -
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Residues in contact with LEU 361 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357E ARG 3.6 3.8 + - - +
358E GLU* 3.3 9.3 + - + +
359E GLN 3.1 0.2 - - - -
360E MET* 1.3 77.4 - - - +
362E THR* 1.3 58.5 + - - +
364E ARG* 2.9 5.2 + - + +
365E PHE* 2.8 54.7 + - + -
409E LEU* 4.2 18.6 - - + +
413E VAL* 3.5 32.3 - - + -
443E CYS* 3.7 32.3 - - + +
468E PHE* 3.5 38.4 - - + -
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Residues in contact with THR 362 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358E GLU* 2.7 23.0 + - - +
359E GLN* 3.0 16.6 + - - +
361E LEU* 1.3 76.4 - - - +
363E ASN* 1.3 59.6 + - - +
365E PHE* 3.5 7.2 + - - +
366E ASN* 2.7 43.3 + - - +
589E ALA* 3.6 24.3 - - + +
591E SER* 3.6 24.5 - - - +
592E ILE* 4.1 9.3 - - + +
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Residues in contact with ASN 363 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281E LYS* 5.7 3.1 - - - +
355E LEU* 3.6 28.2 - - - +
359E GLN* 2.8 22.9 + - - +
360E MET* 3.7 8.4 - - - +
362E THR* 1.3 76.4 - - - +
364E ARG* 1.3 62.3 + - - +
366E ASN* 3.2 10.4 + - - +
367E ASP* 2.7 37.7 + - - +
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Residues in contact with ARG 364 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360E MET 3.3 11.1 + - - +
361E LEU* 2.9 10.0 + - - +
363E ASN* 1.3 80.0 - - - +
365E PHE* 1.3 62.5 + - + +
367E ASP* 3.0 16.7 + - - +
368E LEU* 2.9 39.2 + - + +
371E ARG* 4.0 17.8 - - - +
441E GLU* 2.8 50.1 + - - +
442E LEU 3.5 15.7 - - - +
443E CYS 3.2 25.8 + - - +
444E GLY* 4.2 9.4 - - - -
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Residues in contact with PHE 365 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361E LEU* 2.8 55.1 + - + +
362E THR* 3.8 2.2 - - - +
364E ARG* 1.3 73.2 - - + +
366E ASN* 1.3 61.3 + - - +
368E LEU* 3.5 10.3 + - + +
369E LEU* 3.3 26.7 + - + +
409E LEU* 3.9 27.6 - - + -
442E LEU* 3.9 20.6 - - + -
576E LEU* 3.5 22.0 - - + +
579E LEU* 3.5 28.0 - - + -
588E PHE* 4.2 24.5 - + - -
592E ILE* 3.7 20.4 - - + -
596E ILE* 5.6 0.4 - - + -
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Residues in contact with ASN 366 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362E THR* 2.7 35.1 + - - +
363E ASN* 3.2 11.3 + - - +
364E ARG 3.1 0.6 - - - -
365E PHE* 1.3 76.2 - - - +
367E ASP* 1.3 56.6 + - - +
369E LEU* 3.1 2.1 + - - -
370E ASP* 2.7 37.6 + - - +
591E SER 5.4 2.7 + - - +
592E ILE* 3.4 25.1 - - - +
595E ARG* 3.2 32.5 + - - +
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Residues in contact with ASP 367 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281E LYS* 3.6 26.9 + - - -
363E ASN* 2.7 29.1 + - - +
364E ARG* 3.0 18.6 + - - +
366E ASN* 1.3 76.5 - - - +
368E LEU* 1.3 63.6 + - + +
370E ASP* 3.1 27.0 + - - +
371E ARG* 3.5 19.7 + - - +
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Residues in contact with LEU 368 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364E ARG* 2.9 36.6 + - + +
365E PHE* 3.6 11.4 - - + +
366E ASN 3.2 0.2 - - - -
367E ASP* 1.3 77.7 - - + +
369E LEU* 1.3 59.4 + - - +
371E ARG* 3.7 13.0 + - - +
372E MET* 3.1 23.6 + - - +
441E GLU* 3.7 21.3 - - + +
442E LEU* 3.5 41.3 - - + +
572E GLY 4.6 3.1 - - - +
573E ILE* 3.3 29.8 - - + +
576E LEU* 3.5 20.4 - - + -
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Residues in contact with LEU 369 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365E PHE 3.3 18.3 + - - +
366E ASN* 3.1 3.4 + - - +
368E LEU* 1.3 77.6 - - - +
370E ASP* 1.3 58.4 + - - +
371E ARG 3.2 0.4 - - - -
372E MET* 3.1 27.6 + - - +
373E ASP* 2.8 33.2 + - - +
576E LEU* 3.5 12.8 - - + -
580E ILE* 3.9 16.4 - - + -
592E ILE* 4.5 9.4 - - + -
595E ARG* 3.2 49.8 - - + +
596E ILE* 4.8 10.1 - - + -
599E TRP* 3.8 19.5 - - + +
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Residues in contact with ASP 370 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366E ASN* 2.7 26.1 + - - +
367E ASP* 3.1 25.7 - - - +
369E LEU* 1.3 77.6 - - - +
371E ARG* 1.3 63.2 + - + +
373E ASP* 3.3 11.7 + - - +
374E ILE* 3.2 25.0 + - + +
595E ARG* 3.2 17.5 + - - +
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Residues in contact with ARG 371 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364E ARG* 4.0 24.4 - - - +
367E ASP* 3.5 18.8 + - - +
368E LEU* 3.8 14.6 - - - +
369E LEU 3.2 0.4 - - - -
370E ASP* 1.3 76.3 - - + +
372E MET* 1.3 57.7 + - - +
374E ILE* 3.1 12.7 + - - +
375E MET* 2.9 41.3 + - - +
441E GLU* 3.4 30.7 + - - +
573E ILE* 4.1 17.3 - - + +
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Residues in contact with MET 372 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368E LEU 3.1 12.1 - - - +
369E LEU* 3.1 33.2 + - + +
371E ARG* 1.3 72.4 - - - +
373E ASP* 1.3 56.8 + - - +
374E ILE 2.9 5.2 - - - -
375E MET* 3.4 9.4 - - - -
376E PHE* 2.8 60.0 + - + +
573E ILE* 3.5 20.9 - - + -
576E LEU* 3.5 18.4 - - + -
577E LEU* 3.4 39.0 - - + -
580E ILE* 5.5 0.9 - - + -
599E TRP* 3.6 19.3 - - + -
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Residues in contact with ASP 373 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369E LEU* 2.8 22.6 + - - +
370E ASP* 3.3 9.3 + - - +
372E MET* 1.3 73.4 - - - +
374E ILE* 1.3 60.7 + - + +
376E PHE* 4.6 1.1 - - - -
377E GLY* 4.0 15.0 - - - -
595E ARG* 2.8 24.7 + - - -
599E TRP* 3.2 25.0 + - - -
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Residues in contact with ILE 374 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311E PRO* 3.7 30.7 - - + -
314E TYR* 4.3 12.6 - - - +
315E LYS* 5.3 7.9 - - + +
370E ASP* 3.2 22.2 - - + +
371E ARG* 3.4 8.5 - - - +
372E MET 2.9 0.6 - - - -
373E ASP* 1.3 82.0 - - + +
375E MET* 1.3 63.1 + - - +
376E PHE 3.3 1.3 - - - -
377E GLY* 3.2 7.7 + - - -
379E THR* 3.5 28.0 + - - +
380E GLY* 3.1 23.4 + - - -
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Residues in contact with MET 375 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371E ARG* 2.9 30.7 + - - +
372E MET* 3.4 18.6 - - - -
374E ILE* 1.3 77.8 - - - +
376E PHE* 1.3 85.4 + - + +
377E GLY 3.2 2.0 + - - +
380E GLY* 3.3 18.8 - - - +
381E SER 5.1 0.2 - - - +
382E ALA* 3.3 44.1 + - + +
387E TRP* 3.5 39.5 - - + -
573E ILE* 4.4 7.0 - - + -
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Residues in contact with PHE 376 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372E MET* 2.8 64.6 + - + +
373E ASP* 4.6 1.3 - - - -
375E MET* 1.3 97.9 - - + +
377E GLY* 1.3 58.9 + - - +
382E ALA* 3.8 13.2 - - + -
383E ASP 4.0 1.3 - - - -
384E ILE* 3.4 52.7 - - + -
387E TRP* 3.8 26.0 - + + -
573E ILE* 4.7 0.9 - - + -
577E LEU* 4.6 0.7 - - + -
599E TRP* 3.9 17.0 - + + -
602E ARG* 3.5 30.9 + - - +
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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