Contacts of the helix formed by residues 443 - 456 (chain B) in PDB entry 5ZOJ
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 ASN 443 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A PRO* 3.7 34.1 - - + +
306A SER* 6.0 3.7 - - - -
273B PHE* 2.6 39.1 + - - +
274B TRP 3.2 5.8 + - - +
275B CYS* 3.8 6.4 - - - -
276B SER* 3.2 26.1 + - - -
291B HIS* 5.4 0.4 + - - -
441B HIS* 3.8 9.0 - - - +
442B LEU* 1.3 70.3 - - - +
444B GLY* 1.3 66.2 + - - +
446B LEU* 3.7 8.8 - - - +
447B GLN* 3.0 25.1 + - - +
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Residues in contact with GLY 444 (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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274B TRP* 4.2 7.0 + - - +
443B ASN* 1.3 76.3 - - - +
445B PRO* 1.3 69.8 - - - +
447B GLN* 3.0 15.2 + - - +
448B TRP* 3.1 34.7 + - - -
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Residues in contact with PRO 445 (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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274B TRP 5.6 0.2 - - - +
385B PHE* 3.5 33.7 - - + -
387B ASN* 4.1 9.4 - - - +
390B PHE* 3.5 23.5 - - + -
412B CYS* 3.6 15.7 - - + -
442B LEU* 3.4 22.4 - - + +
444B GLY* 1.3 88.2 - - - +
446B LEU* 1.3 55.7 + - - +
448B TRP* 3.2 18.6 + - + -
449B LEU* 2.8 30.7 + - - +
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Residues in contact with LEU 446 (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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303A THR* 2.9 45.9 + - + +
305A PRO* 4.2 8.7 - - + -
315A LEU* 4.3 16.8 - - + -
409B THR* 4.8 8.1 - - + +
412B CYS* 3.7 24.7 - - + -
441B HIS* 3.4 31.4 - - + +
442B LEU 3.2 22.1 + - - +
443B ASN* 3.7 19.1 - - - +
444B GLY 3.2 0.2 - - - -
445B PRO* 1.3 76.6 - - - +
447B GLN* 1.3 58.2 + - - +
449B LEU* 3.5 6.4 + - + +
450B ASP 2.9 22.5 + - - -
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Residues in contact with GLN 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ASP* 3.9 16.0 - - - +
305A PRO* 4.2 6.9 - - + +
306A SER* 4.7 13.7 - - - +
443B ASN 3.0 12.1 + - - +
444B GLY* 3.0 12.3 + - - +
446B LEU* 1.3 75.0 - - - +
448B TRP* 1.3 74.4 + - + +
450B ASP* 3.2 7.3 + - - +
451B LYS* 3.1 49.3 + - + +
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Residues in contact with TRP 448 (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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340B TYR* 5.7 1.6 - - - -
387B ASN* 3.5 55.9 - - + -
388B GLN* 5.6 4.0 - - - -
390B PHE* 3.8 15.0 - + - -
391B ALA* 5.0 9.4 - - + -
394B LEU* 4.0 12.1 - - + -
444B GLY* 3.1 23.7 + - - -
445B PRO* 3.6 22.0 - - + +
447B GLN* 1.3 88.0 - - + +
449B LEU* 1.3 62.5 + - - +
451B LYS* 3.2 18.7 + - + +
452B VAL* 3.3 16.5 + - - +
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Residues in contact with LEU 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A THR* 4.0 9.6 - - + +
390B PHE* 4.3 6.7 - - + -
394B LEU* 3.7 26.8 - - + +
405B VAL* 3.2 29.8 - - + +
408B LEU* 4.0 9.9 - - + +
409B THR* 3.6 46.0 - - + +
412B CYS* 4.4 6.3 - - - -
445B PRO 2.8 21.2 + - - +
446B LEU* 3.7 5.2 - - + +
448B TRP* 1.3 72.9 - - - +
450B ASP* 1.3 57.2 + - - +
452B VAL* 3.2 1.7 + - - -
453B LEU* 2.8 34.9 + - + +
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Residues in contact with ASP 450 (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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302A PHE* 3.4 7.6 - - - +
303A THR* 3.5 10.9 + - - +
304A ASP* 3.3 25.9 + - + +
310A ARG* 2.7 46.5 + - - -
446B LEU 2.9 14.9 + - - +
447B GLN 3.4 9.0 - - - +
448B TRP 3.2 0.4 - - - -
449B LEU* 1.3 76.4 - - - +
451B LYS* 1.3 77.1 + - - +
453B LEU* 3.1 5.3 + - - -
454B THR* 2.9 33.5 + - - +
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Residues in contact with LYS 451 (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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304A ASP* 4.2 13.5 + - - -
310A ARG* 5.7 1.1 - - - +
447B GLN* 3.1 44.4 + - + +
448B TRP* 3.2 11.0 + - + +
450B ASP* 1.3 84.8 + - - +
452B VAL* 1.3 62.9 + - + +
454B THR* 3.4 14.0 + - - +
455B GLN* 3.9 16.8 + - - +
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Residues in contact with VAL 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B LEU* 3.9 24.7 - - + -
398B VAL* 3.6 30.7 - - + -
405B VAL* 3.8 17.7 - - + -
448B TRP 3.3 11.8 + - - +
449B LEU 3.2 7.0 + - - +
450B ASP 3.1 0.4 - - - -
451B LYS* 1.3 78.8 - - + +
453B LEU* 1.3 64.9 + - - +
455B GLN* 3.2 7.3 + - - +
456B MET* 3.1 31.5 + - + +
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Residues in contact with LEU 453 (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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302A PHE* 3.8 30.4 - - + -
303A THR* 4.0 27.4 - - + +
402B PHE* 3.8 32.2 - - + -
405B VAL* 4.0 19.3 - - + -
406B TYR* 4.0 33.7 - - + +
449B LEU* 2.8 33.4 + - + +
450B ASP* 3.1 4.5 + - - +
452B VAL* 1.3 73.1 - - - +
454B THR* 1.3 62.8 + - - +
456B MET* 3.3 19.1 + - + +
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Residues in contact with THR 454 (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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302A PHE* 4.0 25.3 - - + -
310A ARG* 3.8 28.5 - - - +
334A ARG* 4.6 14.0 + - - -
450B ASP* 2.9 27.4 + - - +
451B LYS* 3.4 12.1 + - - +
453B LEU* 1.3 76.1 - - - +
455B GLN* 1.3 67.3 + - - +
456B MET 3.5 3.1 + - - -
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Residues in contact with GLN 455 (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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451B LYS 3.9 13.9 - - - +
452B VAL* 3.2 10.3 + - - +
454B THR* 1.3 81.8 + - - +
456B MET* 1.3 63.7 + - - +
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Residues in contact with MET 456 (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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398B VAL* 3.9 31.4 - - - +
401B GLY* 3.8 10.1 - - - +
402B PHE* 3.7 54.0 - - + +
405B VAL* 4.2 15.0 - - + -
452B VAL* 3.1 26.4 + - + +
453B LEU* 3.3 16.8 + - - +
454B THR 4.5 2.5 - - - -
455B GLN* 1.3 82.8 - - - +
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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
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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