Contacts of the helix formed by residues 408 - 431 (chain B) in PDB entry 2X1L
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 ALA 408 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B PHE* 4.5 1.6 - - - +
403B HIS* 2.6 26.3 + - - +
406B VAL* 3.9 15.9 - - + -
407B PRO* 1.3 75.0 - - - +
409B MET* 1.3 64.4 + - - +
410B HIS* 3.2 28.0 - - + -
411B LEU* 3.1 27.7 + - + +
412B ALA 3.4 7.4 + - - -
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Residues in contact with MET 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ALA* 3.9 20.9 - - + +
31B ALA* 4.5 2.2 - - + -
32B ILE* 3.9 13.2 - - + -
329B LEU* 4.0 34.1 - - + +
334B PHE* 3.8 45.9 - - + +
404B PHE* 3.8 31.9 - - + -
407B PRO* 3.7 22.4 - - - -
408B ALA* 1.3 74.6 - - - +
410B HIS* 1.3 57.2 + - - +
412B ALA* 3.2 9.9 + - - +
413B LEU* 2.9 34.5 + - + +
468B VAL* 5.7 0.2 - - + -
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Residues in contact with HIS 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B LEU 3.3 21.2 + - - +
330B ARG* 4.1 12.2 - - - +
332B VAL 3.9 10.5 - - - +
333B PRO* 3.7 25.1 - - + +
334B PHE* 3.1 30.4 + - + +
408B ALA* 3.7 30.4 - - + -
409B MET* 1.3 77.5 - - - +
411B LEU* 1.3 85.1 + - + +
413B LEU* 3.4 5.7 + - - +
414B GLU* 3.0 41.5 + - - +
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Residues in contact with LEU 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B HIS* 3.6 33.0 + - + +
406B VAL* 6.1 0.7 - - + -
408B ALA* 3.1 20.7 + - + +
410B HIS* 1.3 105.5 - - + +
412B ALA* 1.3 60.4 + - - +
414B GLU* 3.4 20.8 + - - +
415B ALA* 3.0 28.4 + - - +
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Residues in contact with ALA 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B VAL* 3.9 15.3 - - + +
403B HIS* 3.7 25.2 - - + -
404B PHE* 3.7 28.9 - - + -
408B ALA 3.4 2.2 + - - +
409B MET 3.2 10.4 + - - +
411B LEU* 1.3 78.7 - - - +
413B LEU* 1.3 58.3 + - + +
415B ALA* 3.3 3.3 + - - +
416B ILE* 3.1 35.9 + - + +
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Residues in contact with LEU 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B TYR* 3.9 24.5 - - + -
329B LEU* 3.7 44.0 - - + +
330B ARG* 3.8 24.2 - - + +
404B PHE* 6.5 0.2 - - + -
409B MET* 2.9 16.3 + - + +
410B HIS 3.7 3.8 - - - +
412B ALA* 1.3 74.3 - - + +
414B GLU* 1.3 60.8 + - - +
416B ILE* 3.5 4.2 + - + -
417B TRP* 3.0 37.0 + - + +
465B LEU* 3.7 28.9 - - + -
468B VAL* 4.0 20.9 - - + -
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Residues in contact with GLU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ARG* 3.5 39.7 + - - +
410B HIS* 3.0 29.5 + - - +
411B LEU* 3.6 24.3 - - - +
413B LEU* 1.3 76.8 - - - +
415B ALA* 1.3 55.8 + - - +
417B TRP* 3.8 1.2 - - - +
418B SER* 2.9 30.2 + - - -
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Residues in contact with ALA 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B LEU* 3.6 17.1 - - + +
399B ARG* 3.4 35.3 + - + +
400B VAL* 4.7 1.8 - - + -
403B HIS* 4.7 5.6 - - - +
411B LEU 3.0 17.9 + - - +
412B ALA* 3.6 8.1 - - - +
413B LEU 3.3 0.2 - - - -
414B GLU* 1.3 77.4 - - - +
416B ILE* 1.3 61.5 + - - +
418B SER* 3.3 8.0 + - - -
419B VAL* 3.3 18.2 + - - +
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Residues in contact with ILE 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B LEU* 4.0 16.8 - - + -
400B VAL* 4.0 21.3 - - + -
404B PHE* 6.3 0.2 - - + -
412B ALA* 3.1 20.1 + - + +
413B LEU* 3.9 5.4 - - + +
415B ALA* 1.3 75.4 - - - +
417B TRP* 1.3 70.4 + - + +
419B VAL* 3.2 5.7 + - - +
420B LEU* 2.9 28.8 + - + +
461B ALA* 4.1 27.3 - - + +
464B LEU* 4.0 26.9 - - + +
465B LEU* 3.8 27.1 - - + -
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Residues in contact with TRP 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B TYR* 3.5 40.8 - + - -
330B ARG* 4.5 13.2 - - - +
352B ASP* 2.7 41.0 + - + +
353B LEU* 3.7 18.4 - - + -
356B GLU* 3.5 30.2 - - + +
357B LEU* 3.8 26.0 - - + -
413B LEU* 3.0 28.8 + - + +
414B GLU 4.0 2.7 - - - +
416B ILE* 1.3 75.9 - - + +
418B SER* 1.3 59.7 + - - +
419B VAL 3.3 0.2 - - - -
420B LEU* 3.7 15.2 - - + +
421B GLY* 2.8 26.0 + - - -
465B LEU* 3.6 31.4 - - + -
469B MET* 4.4 1.1 - - + -
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Residues in contact with SER 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B ARG* 5.6 2.9 - - - -
414B GLU 2.9 18.5 + - - -
415B ALA* 3.4 10.3 - - - -
416B ILE 3.3 0.2 - - - -
417B TRP* 1.3 75.7 - - - +
419B VAL* 1.3 59.0 + - - +
421B GLY* 3.5 1.8 + - - -
422B ALA* 3.2 24.9 + - - +
425B ARG* 4.7 4.2 + - - -
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Residues in contact with VAL 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B LEU* 4.2 5.6 - - + +
392B ALA* 3.6 34.3 - - + +
393B ALA* 4.0 22.9 - - + +
396B LEU* 3.8 19.7 - - + -
399B ARG* 5.4 3.4 - - - +
415B ALA 3.3 11.4 + - - +
416B ILE 3.2 8.4 + - - +
418B SER* 1.3 77.5 - - - +
420B LEU* 1.3 59.0 + - + +
422B ALA* 3.2 7.8 + - - +
423B ALA* 2.9 26.3 + - - +
457B VAL* 4.0 19.1 - - + -
461B ALA* 6.5 0.9 - - + -
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Residues in contact with LEU 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B GLU* 4.4 9.6 - - + +
357B LEU* 3.9 29.4 - - + -
360B LEU* 3.9 22.3 - - + +
416B ILE* 2.9 26.2 + - + +
417B TRP* 3.4 44.4 + - + +
419B VAL* 1.3 76.7 - - + +
421B GLY* 1.3 57.6 + - - +
423B ALA* 3.4 5.9 + - - +
424B ASN* 3.0 35.1 + - - -
457B VAL* 4.9 9.0 - - + +
458B VAL* 5.3 3.8 - - + -
461B ALA* 3.9 20.2 - - + -
465B LEU* 4.9 0.4 - - + -
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Residues in contact with GLY 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B GLU* 3.9 20.4 - - - -
417B TRP 2.8 16.9 + - - -
418B SER* 3.9 2.7 - - - -
419B VAL 3.2 0.2 - - - -
420B LEU* 1.3 74.7 - - - +
422B ALA* 1.3 58.2 + - - +
424B ASN* 3.3 3.3 + - - +
425B ARG* 3.0 46.0 + - - +
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Residues in contact with ALA 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B LEU* 3.7 15.1 - - + +
392B ALA* 5.8 4.5 - - + -
418B SER 3.2 14.3 + - - +
419B VAL* 3.5 10.1 - - - +
421B GLY* 1.3 75.7 - - - +
423B ALA* 1.3 57.9 + - - +
425B ARG* 3.4 23.6 + - - +
426B TYR* 2.8 29.5 + - - +
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Residues in contact with ALA 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B LEU* 4.0 19.1 - - + +
389B LEU* 3.6 16.5 - - + +
419B VAL 2.9 13.2 + - - +
420B LEU 3.6 9.2 - - - +
422B ALA* 1.3 78.7 - - - +
424B ASN* 1.3 56.3 + - - +
426B TYR* 3.6 6.5 - - - +
427B PHE* 2.9 28.8 + - - +
454B THR* 5.2 5.0 - - + +
457B VAL* 3.8 25.4 - - + -
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Residues in contact with ASN 424 (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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355B ASN 5.1 1.4 - - - +
356B GLU* 2.9 50.0 + - - +
360B LEU* 3.4 29.6 + - - +
363B ARG* 4.0 13.7 + - - +
420B LEU 3.0 19.2 + - - -
421B GLY 3.6 7.4 - - - +
423B ALA* 1.3 74.9 - - - +
425B ARG* 1.3 59.6 + - + +
427B PHE* 3.4 3.5 + - - +
428B SER* 3.0 32.2 + - - -
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Residues in contact with ARG 425 (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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418B SER 4.7 3.4 + - - -
421B GLY* 3.0 32.2 + - - +
422B ALA* 3.4 25.8 + - - +
424B ASN* 1.3 73.1 - - + +
426B TYR* 1.3 60.2 + - - +
428B SER* 3.9 5.7 - - - -
429B ALA* 3.1 30.5 + - - +
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Residues in contact with TYR 426 (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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385B GLU* 4.0 22.7 - - + -
386B ASP* 2.5 35.1 + - - -
389B LEU* 3.6 28.5 - - + -
422B ALA 2.8 18.0 + - - +
423B ALA* 3.6 5.4 - - + +
425B ARG* 1.3 74.8 - - - +
427B PHE* 1.3 67.1 + - - +
429B ALA* 3.4 4.4 + - - +
430B GLN* 3.1 52.9 + - + +
450B VAL* 3.5 39.7 - - + +
453B THR* 3.6 12.8 - - + -
454B THR* 3.8 16.2 - - - -
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Residues in contact with PHE 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B LEU* 4.5 7.9 - - + -
363B ARG* 3.7 52.3 - - + +
364B SER* 4.3 19.3 - - - -
367B MET* 4.1 17.3 - - + -
423B ALA 2.9 18.1 + - - +
424B ASN* 3.4 8.3 + - - +
426B TYR* 1.3 80.9 - - - +
428B SER* 1.3 60.7 + - - +
430B GLN* 4.9 2.2 - - - -
431B GLU 3.5 1.9 + - - -
432B PRO* 3.3 53.5 - - + +
433B TRP* 3.7 10.2 - + - -
450B VAL* 4.9 2.2 - - + -
451B LEU* 4.4 9.6 - - + -
454B THR* 3.7 27.4 - - + +
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Residues in contact with SER 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B ARG* 4.5 11.4 + - - -
424B ASN 3.0 17.6 + - - -
425B ARG* 3.9 6.5 - - - -
426B TYR 3.2 0.2 - - - -
427B PHE* 1.3 75.5 - - - +
429B ALA* 1.3 64.3 + - - +
431B GLU* 3.4 20.8 + - - +
433B TRP* 3.7 16.2 - - - -
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Residues in contact with ALA 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B ARG 3.1 18.8 + - - +
426B TYR* 4.0 4.7 - - - +
428B SER* 1.3 76.4 - - - +
430B GLN* 1.3 66.6 + - + +
431B GLU* 3.6 9.1 + - - +
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Residues in contact with GLN 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B GLU* 4.2 19.6 + - - +
426B TYR* 3.1 44.0 + - + +
427B PHE 4.3 2.0 - - - +
428B SER 3.3 0.2 - - - -
429B ALA* 1.3 79.9 - - - +
431B GLU* 1.3 71.8 + - - +
432B PRO 3.5 0.2 - - - -
435B LEU* 3.4 17.7 - - - +
446B ARG* 3.2 36.2 + - - +
450B VAL* 3.4 34.6 - - + +
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Residues in contact with GLU 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B PHE 3.5 0.2 + - - -
428B SER 3.4 20.9 + - - +
429B ALA 3.3 6.8 - - - +
430B GLN* 1.3 81.3 - - - +
432B PRO* 1.4 67.1 - - - +
433B TRP* 3.2 22.7 + - + -
434B VAL* 3.1 40.6 + - + +
435B LEU* 3.2 11.8 + - + +
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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