Contacts of the helix formed by residues 349 - 364 (chain B) in PDB entry 1Z10
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 MET 349 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B GLU* 3.3 23.3 - - + +
331B ILE* 3.6 43.5 - - + +
334B VAL* 3.9 12.1 - - + -
335B ILE* 3.6 31.9 - - + -
345B ASP* 3.3 20.2 - - - +
346B ARG* 3.0 11.7 + - - +
348B LYS* 1.3 82.1 - - - +
350B PRO* 1.3 67.3 - - - +
351B TYR 3.2 2.7 - - - -
352B MET* 4.1 15.7 - - + -
353B GLU* 3.1 21.1 + - - +
450B PHE* 3.8 16.3 - - + -
454B THR* 4.7 1.6 - - + -
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Residues in contact with PRO 350 (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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330B GLU* 3.4 8.5 - - - +
346B ARG 4.9 1.3 - - - +
347B ALA 4.6 4.3 - - - +
348B LYS* 3.4 9.9 - - - +
349B MET* 1.3 89.6 - - - +
351B TYR* 1.3 58.2 + - - +
353B GLU* 3.4 8.3 + - + +
354B ALA* 2.8 29.6 + - - +
417B LEU* 3.8 4.3 - - - +
421B GLY 3.5 18.2 - - - +
422B GLN* 4.2 2.7 - - - -
423B PHE* 3.6 32.9 - - + +
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Residues in contact with TYR 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B VAL* 3.6 37.9 - - - +
326B LYS* 3.3 50.8 + - + +
327B VAL* 3.8 13.2 - - + -
330B GLU* 2.9 22.8 + - + +
350B PRO* 1.3 76.9 - - - +
352B MET* 1.3 60.8 + - - +
354B ALA* 3.1 4.3 + - - +
355B VAL* 2.9 53.1 + - + +
413B PRO* 3.8 11.0 - - + +
414B GLN* 4.3 9.2 + - - -
417B LEU* 4.0 26.7 - - + +
421B GLY 5.1 0.4 + - - -
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Residues in contact with MET 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B VAL* 3.3 39.5 - - + -
330B GLU* 2.8 18.2 + - - +
331B ILE* 3.8 16.2 - - + -
349B MET* 3.9 13.9 - - + +
351B TYR* 1.3 76.5 - - - +
353B GLU* 1.3 59.4 + - - +
355B VAL* 3.2 10.4 + - - +
356B ILE* 2.9 45.6 + - + +
450B PHE* 3.8 9.9 - - + -
453B PHE* 4.5 8.1 - - - +
454B THR* 3.3 41.7 - - + +
457B MET* 4.7 1.8 - - + -
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Residues in contact with GLU 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ARG* 2.7 53.7 + - + +
349B MET 3.1 18.9 + - - +
350B PRO* 3.6 7.6 - - + +
352B MET* 1.3 78.9 - - - +
354B ALA* 1.3 60.0 + - - +
356B ILE* 3.5 7.3 + - - +
357B HIS* 2.8 50.3 + - + -
423B PHE* 3.8 22.7 - - + -
446B ARG* 4.4 7.0 + - - -
450B PHE* 3.8 12.3 - - - +
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Residues in contact with ALA 354 (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 PRO 2.8 16.0 + - - +
351B TYR 3.1 3.3 + - - +
353B GLU* 1.3 75.9 - - - +
355B VAL* 1.3 53.8 + - - +
357B HIS* 3.3 2.8 + - - +
358B GLU* 2.8 34.8 + - - +
413B PRO* 3.5 11.8 - - + +
416B PHE* 3.7 18.7 - - + +
417B LEU* 3.4 39.3 - - + -
423B PHE* 3.9 1.8 - - - -
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Residues in contact with VAL 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B LEU* 4.2 13.5 - - + -
323B VAL* 3.7 24.0 - - + -
327B VAL* 4.0 7.9 - - + -
351B TYR* 2.9 46.6 + - + +
352B MET* 3.2 12.1 + - - +
354B ALA* 1.3 74.5 - - - +
356B ILE* 1.3 61.1 + - + +
358B GLU* 3.2 1.8 + - - +
359B ILE* 2.9 51.3 + - + +
411B PHE* 4.4 4.5 - - + -
413B PRO* 3.7 14.6 - - + -
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Residues in contact with ILE 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B MET* 2.9 35.3 + - + +
353B GLU* 4.1 8.3 - - - +
355B VAL* 1.3 76.9 - - + +
357B HIS* 1.3 67.6 + - + +
359B ILE* 3.2 8.9 + - + +
360B GLN* 3.0 27.2 + - + +
446B ARG* 5.7 4.7 - - - -
449B LEU* 4.0 33.2 - - + +
450B PHE* 3.6 45.3 - - + +
453B PHE* 3.9 21.3 - - + -
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Residues in contact with HIS 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B GLU* 2.8 42.7 + - + +
354B ALA 3.6 4.9 - - - +
355B VAL 3.2 0.2 - - - -
356B ILE* 1.3 80.1 - - + +
358B GLU* 1.3 57.2 + - - +
360B GLN* 3.1 2.1 + - - -
361B ARG* 2.8 26.5 + - - +
416B PHE* 3.7 22.7 - + + -
423B PHE* 3.4 30.7 - + - -
425B LYS* 6.2 0.2 - - - -
429B PHE* 3.4 49.5 - + - -
446B ARG* 3.6 35.9 + - - -
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Residues in contact with GLU 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B ALA 2.8 18.2 + - - +
355B VAL* 3.2 4.9 + - - +
357B HIS* 1.3 74.1 - - - +
359B ILE* 1.3 61.8 + - - +
361B ARG* 2.7 41.7 + - - +
362B PHE* 2.9 29.2 + - - +
410B ASP 3.3 0.7 - - - +
411B PHE* 3.3 24.0 - - + -
412B ASN 2.7 37.7 + - - +
413B PRO* 4.0 10.1 - - + -
415B HIS* 2.9 8.9 + - - +
416B PHE* 3.4 13.2 - - + -
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Residues in contact with ILE 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B THR* 3.8 25.4 - - + +
312B TYR* 4.9 1.6 - - + -
313B GLY* 3.7 33.9 - - - +
316B LEU* 4.6 8.4 - - + +
317B LEU* 4.6 6.1 - - + -
355B VAL* 2.9 36.4 + - + +
356B ILE* 3.5 7.4 - - + +
358B GLU* 1.3 76.5 - - - +
360B GLN* 1.3 58.6 + - - +
363B GLY* 2.8 30.1 + - - -
365B VAL* 5.9 0.2 - - - +
411B PHE* 3.8 20.4 - - + -
453B PHE* 3.7 30.5 - - + -
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Residues in contact with GLN 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B THR* 4.1 18.7 + - + +
356B ILE* 3.0 21.5 + - + +
357B HIS* 3.6 7.2 + - - +
359B ILE* 1.3 78.8 - - - +
361B ARG* 1.3 62.3 + - - +
363B GLY* 5.1 0.2 - - - -
364B ASP* 3.2 19.6 + - - +
365B VAL* 4.8 3.9 + - - +
399B LEU* 3.9 5.5 - - - +
429B PHE* 3.4 28.8 - - + -
431B PRO* 3.9 18.0 - - + +
432B PHE* 3.5 31.7 - - - -
446B ARG* 3.9 9.5 - - - -
449B LEU* 3.7 15.3 - - + +
500B HEM 3.6 20.4 - - - +
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Residues in contact with ARG 361 (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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357B HIS 2.8 15.9 + - - +
358B GLU* 2.7 32.9 + - - +
360B GLN* 1.3 81.3 - - - +
362B PHE* 1.3 74.6 + - - +
364B ASP* 3.5 7.1 + - - +
399B LEU* 3.0 69.5 + - + +
400B ARG* 4.1 8.3 + - - +
405B PHE* 3.6 30.2 - - + -
408B PRO* 2.8 30.7 + - - +
410B ASP 2.7 29.7 + - - -
415B HIS* 3.2 13.9 + - - -
416B PHE* 4.1 6.5 - - + -
429B PHE* 4.9 1.3 - - + -
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Residues in contact with PHE 362 (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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312B TYR* 4.2 10.4 + + - -
316B LEU* 3.7 29.6 - - + -
358B GLU 2.9 18.9 + - - +
359B ILE 4.1 1.6 - - - +
361B ARG* 1.3 90.1 - - - +
363B GLY* 1.3 63.1 + - - +
364B ASP* 3.3 5.2 + - - +
400B ARG* 4.3 10.6 + - - +
408B PRO 5.0 1.6 - - - -
409B GLN* 3.5 24.9 - - - -
410B ASP 3.8 6.5 - - - -
411B PHE* 3.7 38.4 - + + -
473B VAL* 3.8 35.4 - - + -
474B SER* 6.1 0.7 - - - -
482B THR* 5.6 0.9 - - - +
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Residues in contact with GLY 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B TYR* 3.7 30.6 - - - -
316B LEU* 5.0 0.2 - - - +
359B ILE 2.8 23.2 + - - -
362B PHE* 1.3 73.1 - - - +
364B ASP* 1.3 70.4 + - - +
365B VAL* 2.9 10.8 + - - +
482B THR* 3.3 19.9 - - - +
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Residues in contact with ASP 364 (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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55B TYR* 5.0 1.2 - - - -
360B GLN 3.2 16.4 + - - -
361B ARG 3.7 12.1 - - - +
362B PHE 3.3 4.9 - - - +
363B GLY* 1.3 76.5 - - - +
365B VAL* 1.3 60.3 + - - +
366B ILE 3.4 4.1 + - - +
367B PRO* 3.2 29.8 - - - +
395B LEU* 4.8 0.2 - - - +
396B GLY* 3.2 25.1 + - - -
399B LEU* 3.4 13.8 - - + +
400B ARG* 3.3 29.9 + - - +
431B PRO* 6.1 0.7 - - - -
482B THR* 2.7 27.5 + - + +
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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
------------------------------------------------------------
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