Contacts of the helix formed by residues 409 - 426 (chain B) in PDB entry 4I5L
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 SER 409 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A ARG* 5.4 2.1 + - - -
403B ASP* 5.4 2.1 + - - -
405B ASP* 5.6 4.0 - - - -
407B ALA* 3.4 4.0 + - - -
408B LEU* 1.3 75.8 - - - +
410B MET* 1.3 65.2 + - - +
411B PHE* 3.4 10.8 + - - +
412B GLU* 2.9 45.1 + - - +
413B LEU* 3.0 15.6 + - - +
451B GLY 5.5 4.9 - - - -
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Residues in contact with MET 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B LEU 4.2 0.2 + - - -
409B SER* 1.3 74.2 - - - +
411B PHE* 1.3 56.2 + - - +
413B LEU* 3.4 8.5 + - - +
414B GLU* 2.9 53.3 + - - +
434B PHE* 3.8 20.8 - - + -
435B GLN* 4.6 9.9 - - - +
438B LEU* 4.1 19.5 - - + -
295C ARG* 4.5 18.6 - - - -
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Residues in contact with PHE 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ASP* 4.2 12.6 - - - -
219A SER* 5.0 4.3 - - - -
257A TRP* 5.1 13.9 - + + -
258A ARG* 3.5 61.2 - - + +
402B LEU* 4.4 18.2 - - + -
409B SER* 3.2 8.3 + - - +
410B MET* 1.3 78.5 - - - +
412B GLU* 1.3 68.7 + - + +
414B GLU* 3.8 8.7 - - + +
415B TYR* 2.9 43.7 + + + +
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Residues in contact with GLU 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B MET* 3.9 11.9 - - - +
401B ASP* 3.4 2.3 - - - +
402B LEU* 3.2 29.4 + - + -
403B ASP* 2.6 49.5 + - - +
405B ASP* 4.7 0.2 - - - -
407B ALA 2.8 23.8 - - - +
408B LEU* 3.3 7.2 - - + +
409B SER* 2.9 29.5 + - - +
411B PHE* 1.3 82.2 - - + +
413B LEU* 1.3 63.7 + - + +
415B TYR* 3.3 9.7 + - - +
416B PHE* 3.2 23.7 + - - -
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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
----------------------------------------------------------
400B MET* 3.7 26.2 - - + -
408B LEU* 3.9 17.9 - - + +
409B SER 3.0 20.0 + - - +
410B MET* 3.8 7.9 - - - +
412B GLU* 1.3 74.3 - - - +
414B GLU* 1.3 59.3 + - - +
416B PHE* 3.4 3.3 + - - -
417B TYR* 2.9 29.1 + - - +
434B PHE* 3.9 8.3 - - + -
438B LEU* 3.8 28.5 - - + -
453B ILE* 4.1 18.6 - - + -
467B PHE* 3.8 15.9 - - + -
471B PHE* 3.5 26.3 - - + -
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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
----------------------------------------------------------
410B MET* 2.9 41.6 + - - +
411B PHE* 3.8 8.4 - - + +
413B LEU* 1.3 77.1 - - - +
415B TYR* 1.3 62.8 + - - +
417B TYR* 4.2 0.7 - - + -
418B GLU* 2.9 30.0 + - + +
434B PHE* 3.6 35.8 - - + +
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Residues in contact with TYR 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B LYS* 2.7 86.0 + - + +
353B ASP* 5.8 2.1 - - - +
354B ARG* 5.7 2.1 - - + +
402B LEU* 3.6 38.5 - - + +
411B PHE* 2.9 33.9 + + + +
412B GLU 3.4 4.7 - - - +
413B LEU 3.3 0.2 - - - -
414B GLU* 1.3 78.2 - - - +
416B PHE* 1.3 75.2 + + - +
418B GLU* 3.7 5.3 - - - +
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Residues in contact with PHE 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B SER* 4.8 3.3 + - - -
350B LYS* 4.1 20.6 - - + -
351B MET* 3.8 39.5 - - + -
354B ARG* 4.3 2.0 - - + -
399B CYS 3.8 20.4 - - - -
400B MET* 3.6 43.7 - - + -
402B LEU* 3.8 19.1 - - + -
412B GLU 3.2 21.9 + - - -
413B LEU* 3.4 5.5 + - - +
414B GLU 3.3 0.4 - - - -
415B TYR* 1.3 82.4 - + - +
417B TYR* 1.3 65.3 + - - +
419B GLU* 3.3 14.7 + - - +
420B GLN* 3.4 8.0 + - - +
471B PHE* 3.5 31.7 - - + +
472B PHE* 4.7 2.5 - - + -
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Residues in contact with TYR 417 (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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413B LEU 2.9 18.2 + - - +
414B GLU* 3.1 3.3 + - + +
416B PHE* 1.3 75.2 - - - +
418B GLU* 1.3 66.7 + - - +
420B GLN* 3.2 12.0 + - + +
421B CYS* 3.0 39.8 + - - -
424B LEU* 5.8 3.7 - - + +
431B ALA* 4.3 3.1 - - + +
432B LEU* 2.6 48.0 + - - +
434B PHE* 3.6 42.0 - + + -
437B CYS* 3.6 26.5 - - + +
470B THR* 4.0 23.3 - - + -
471B PHE* 4.0 11.4 - + + -
477B TYR* 5.4 4.9 + + - -
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Residues in contact with GLU 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B LYS* 2.6 34.3 + - - +
414B GLU* 2.9 16.1 + - + +
415B TYR* 3.7 5.2 - - - +
417B TYR* 1.3 76.9 - - - +
419B GLU* 1.3 59.6 + - - +
421B CYS* 3.4 10.4 + - - +
422B ARG* 2.6 70.9 + - - +
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Residues in contact with GLU 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B HIS* 5.2 0.3 - - - -
348B SER* 3.6 11.0 - - - -
349B THR* 2.9 36.9 + - - -
350B LYS* 3.0 39.2 + - + +
416B PHE 3.3 9.6 + - - +
417B TYR 3.2 0.6 - - - -
418B GLU* 1.3 84.7 + - - +
420B GLN* 1.3 66.0 + - - +
422B ARG* 3.1 27.4 + - - +
423B ARG* 2.9 37.7 + - + +
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Residues in contact with GLN 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B SER* 3.9 4.9 - - - -
416B PHE 3.4 4.6 + - - +
417B TYR* 3.2 18.1 + - + +
419B GLU* 1.3 75.9 - - - +
421B CYS* 1.3 56.8 + - - +
423B ARG* 3.2 28.8 + - - +
424B LEU* 2.9 37.1 + - + +
469B ASP 3.4 15.4 + - - -
470B THR* 3.3 23.9 + - - +
471B PHE* 3.1 27.3 - - - +
472B PHE* 3.6 7.7 - - - -
473B ASN 3.5 6.5 + - - +
474B ILE* 3.2 26.1 - - + +
477B TYR* 4.9 3.4 - - - +
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Residues in contact with CYS 421 (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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417B TYR* 3.0 46.0 + - - -
418B GLU* 3.4 12.8 - - - +
420B GLN* 1.3 73.8 - - - +
422B ARG* 1.3 60.6 + - + +
424B LEU* 3.4 1.7 + - - +
425B ASP* 3.0 30.8 + - - +
431B ALA* 3.8 26.5 - - + +
432B LEU 4.4 2.0 - - - -
433B PRO* 6.0 0.7 - - - -
434B PHE 5.7 0.4 - - - -
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Residues in contact with ARG 422 (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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350B LYS* 4.6 4.8 - - - +
418B GLU* 2.6 53.3 + - - +
419B GLU* 3.7 26.5 - - - +
421B CYS* 1.3 76.2 - - + +
423B ARG* 1.3 62.3 + - + +
425B ASP* 3.4 10.3 - - - +
426B SER* 3.3 23.9 + - - -
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Residues in contact with ARG 423 (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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345B HIS* 2.3 41.2 + - - -
346B ALA* 3.3 17.1 + - - +
347B LEU 3.1 10.3 + - - -
348B SER* 3.3 18.2 - - - +
419B GLU* 2.9 36.4 + - + +
420B GLN* 3.2 27.9 + - - +
421B CYS 3.2 0.2 - - - -
422B ARG* 1.3 78.3 - - + +
424B LEU* 1.3 64.8 + - - +
426B SER* 3.4 15.7 + - - -
427B MET* 3.4 20.6 + - - +
472B PHE 3.8 0.2 + - - -
474B ILE* 3.3 31.3 - - + +
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Residues in contact with LEU 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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417B TYR* 5.8 2.9 - - + +
420B GLN* 2.9 21.9 + - + +
421B CYS 3.4 3.8 + - - +
423B ARG* 1.3 72.8 - - - +
425B ASP* 1.3 66.6 + - - +
427B MET* 3.1 9.8 + - - +
429B ILE* 2.9 58.0 + - + +
431B ALA* 4.0 26.7 - - + -
474B ILE* 3.8 28.5 - - + -
477B TYR* 3.9 24.2 - - + +
478B LEU* 4.2 22.4 - - + -
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Residues in contact with ASP 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B CYS 3.0 18.2 + - - +
422B ARG* 3.4 12.2 - - - +
424B LEU* 1.3 75.2 - - - +
426B SER* 1.3 54.1 + - - +
428B ALA* 2.8 26.7 + - - +
429B ILE 3.7 6.0 + - - -
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Residues in contact with SER 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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422B ARG 3.3 12.0 + - - -
423B ARG* 3.4 13.1 + - - -
424B LEU 3.3 0.6 - - - -
425B ASP* 1.3 76.8 - - - +
427B MET* 1.3 60.1 + - - +
428B ALA 3.3 1.1 + - - -
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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