Contacts of the helix formed by residues 458 - 472 (chain B) in PDB entry 1ZJA
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 458 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344B GLU* 5.3 3.6 - - - -
348B LYS* 3.7 3.1 - - - +
451B ARG* 3.7 13.9 - - - +
452B GLU* 2.6 43.6 + - - -
455B ASP* 2.8 20.0 + - - -
456B PRO 3.3 1.0 - - - +
457B LYS* 1.3 82.4 - - - +
459B VAL* 1.3 65.0 + - - +
460B TYR 3.5 0.5 + - - -
461B SER* 2.9 16.1 + - - -
462B PHE* 3.1 22.2 + - - +
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Residues in contact with VAL 459 (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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343B ARG* 5.0 0.7 - - - +
344B GLU* 3.9 45.5 + - + +
347B ALA* 4.2 17.3 - - + -
348B LYS* 4.1 11.9 - - + +
367B ASP 4.1 0.9 - - - +
368B GLU 3.5 15.9 - - - +
369B LEU 4.2 8.5 - - - +
370B GLY* 4.0 9.0 - - - +
452B GLU* 3.0 10.9 + - - +
458B SER* 1.3 71.6 - - - +
460B TYR* 1.3 66.5 + - - +
462B PHE* 3.1 4.3 + - - +
463B TYR* 3.0 41.1 + - + -
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Residues in contact with TYR 460 (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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40B TYR* 3.7 39.8 + + - -
43B GLY* 4.0 8.0 + - - -
44B LEU* 3.9 21.6 + - + +
368B GLU* 3.0 22.6 + - + +
369B LEU* 4.6 2.9 - - + -
452B GLU* 3.0 30.0 + - + -
453B ILE* 3.8 41.3 - - + +
459B VAL* 1.3 76.3 - - - +
461B SER* 1.3 72.8 + - - +
463B TYR* 3.2 6.5 + - - +
464B ARG* 3.0 53.9 + - - +
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Residues in contact with SER 461 (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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452B GLU 3.7 3.1 + - - -
453B ILE 4.6 2.9 + - - -
455B ASP 2.6 22.3 + - - -
456B PRO* 3.3 29.1 - - - +
458B SER* 2.9 13.1 + - - -
459B VAL 3.3 0.2 - - - -
460B TYR* 1.3 85.8 - - - +
462B PHE* 1.3 57.1 + - - +
464B ARG* 3.5 8.9 + - - +
465B ASN* 3.0 39.4 + - - +
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Residues in contact with PHE 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LYS* 3.4 42.8 - - + -
351B ALA* 4.4 2.2 - - + -
352B THR* 3.2 27.1 - - - -
456B PRO 5.2 0.2 + - - -
458B SER 3.1 12.8 + - - +
459B VAL 3.1 10.3 + - - +
461B SER* 1.3 75.4 - - - +
463B TYR* 1.3 60.7 + - - +
465B ASN* 3.3 6.6 + - + +
466B LEU* 2.8 55.0 + - + +
529B ILE* 3.5 31.9 - - + -
530B GLU* 3.5 20.4 - - - -
531B SER* 3.5 21.5 - - - -
551B SER* 3.9 2.0 - - - -
552B GLY* 6.4 0.2 - - - -
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Residues in contact with TYR 463 (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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44B LEU* 4.2 11.4 - - + -
331B ALA* 6.0 0.9 - - - +
347B ALA 4.4 5.4 + - - -
350B LEU* 4.8 3.1 - - - +
351B ALA* 3.4 36.2 + - + +
354B THR* 4.8 7.9 + - + -
355B LEU* 4.1 11.9 - - + -
363B ILE* 3.9 39.0 - - + +
367B ASP* 3.4 36.3 + - + +
368B GLU* 3.6 17.0 - - + -
459B VAL* 3.0 30.7 + - + -
460B TYR 3.5 7.6 - - - +
462B PHE* 1.3 78.4 - - + +
464B ARG* 1.3 57.6 + - - +
466B LEU* 3.1 8.4 + - - +
467B ILE* 2.8 36.1 + - + +
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Residues in contact with ARG 464 (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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43B GLY 3.0 28.6 + - - +
44B LEU* 3.8 21.5 - - + +
460B TYR* 3.0 38.4 + - + +
461B SER* 3.6 13.6 + - - +
463B TYR* 1.3 77.1 - - - +
465B ASN* 1.3 77.7 + - - +
467B ILE* 3.3 3.5 + - - +
468B SER* 3.1 25.9 + - - +
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Residues in contact with ASN 465 (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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456B PRO 5.0 3.5 - - - +
461B SER* 3.0 28.2 + - - +
462B PHE* 3.7 7.2 - - - +
464B ARG* 1.3 91.5 - - - +
466B LEU* 1.3 65.1 + - - +
468B SER* 3.3 8.3 + - - +
469B ILE* 3.0 30.8 + - + +
529B ILE* 4.0 18.0 - - + +
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Residues in contact with LEU 466 (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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351B ALA* 3.5 43.1 - - + +
352B THR* 3.5 11.7 - - - +
355B LEU* 3.5 22.1 - - + +
462B PHE* 2.8 46.0 + - + +
463B TYR 3.5 0.7 - - - +
465B ASN* 1.3 72.9 - - - +
467B ILE* 1.3 58.5 + - - +
469B ILE* 3.3 5.6 + - - +
470B ARG* 2.9 31.0 + - - +
529B ILE* 4.0 16.4 - - + +
553B ILE* 3.6 30.7 - - + -
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Residues in contact with ILE 467 (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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11B VAL* 4.2 18.1 - - + +
44B LEU* 3.4 32.1 - - + +
45B GLY* 3.6 27.1 - - - +
46B ILE* 4.3 7.4 - - + -
47B ASP* 5.8 0.4 - - - +
355B LEU* 3.8 19.5 - - + -
363B ILE* 3.9 24.7 - - + -
463B TYR 2.8 21.0 + - - +
464B ARG 3.7 5.2 - - - +
465B ASN 3.2 0.2 - - - -
466B LEU* 1.3 76.6 - - - +
468B SER* 1.3 57.5 + - - +
470B ARG* 3.3 6.1 + - - +
471B HIS* 2.8 31.8 + - + +
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Residues in contact with SER 468 (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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464B ARG* 3.1 16.4 + - - +
465B ASN* 3.6 11.1 + - - -
467B ILE* 1.3 77.2 - - - +
469B ILE* 1.3 63.3 + - - +
471B HIS* 3.2 9.1 + - - +
472B GLU* 3.1 31.0 + - - +
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Residues in contact with ILE 469 (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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465B ASN* 3.0 22.8 + - + +
466B LEU* 3.6 5.4 - - - +
468B SER* 1.3 76.4 - - - +
470B ARG* 1.3 63.2 + - - +
472B GLU* 3.0 24.3 - - - +
473B THR* 2.8 25.3 + - - +
476B LEU* 4.1 17.9 - - + -
528B LEU* 3.8 31.0 - - + +
529B ILE* 3.6 42.4 - - + -
553B ILE* 4.6 10.8 - - + -
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Residues in contact with ARG 470 (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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8B LYS 4.8 0.4 + - - -
9B SER 3.5 24.7 + - - -
10B ALA 3.8 11.1 + - - -
11B VAL* 3.9 19.2 - - - +
355B LEU* 3.1 38.0 + - + +
357B GLN 3.9 6.1 + - - -
359B GLY 3.0 27.3 + - - -
361B PRO* 3.3 14.6 - - - +
466B LEU 2.9 19.7 + - - +
467B ILE 3.6 4.3 - - - +
469B ILE* 1.3 73.4 - - - +
471B HIS* 1.3 64.7 + - - +
473B THR 3.0 20.6 + - - +
476B LEU* 3.6 27.6 + - + +
477B SER* 3.5 31.0 + - - +
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Residues in contact with HIS 471 (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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9B SER 5.4 6.5 + - - -
11B VAL* 6.2 0.6 - - + +
47B ASP* 5.3 12.2 + - - -
467B ILE* 2.8 21.0 + - + +
468B SER* 3.2 9.6 + - - +
470B ARG* 1.3 79.2 - - - +
472B GLU* 1.3 60.4 + - + +
473B THR 3.7 0.9 + - - -
474B PRO* 5.3 1.2 - - - +
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Residues in contact with GLU 472 (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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468B SER* 3.1 18.2 + - - +
469B ILE* 3.0 33.7 - - - +
471B HIS* 1.3 78.8 - - + +
473B THR* 1.3 60.7 + - - +
474B PRO* 3.8 9.5 - - - +
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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
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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