Contacts of the helix formed by residues 395 - 406 (chain B) in PDB entry 1JZ3
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 HIS 395 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ASP* 6.2 0.2 - - + -
210B ARG* 3.4 35.6 - - + +
211B ASP* 3.7 28.8 + - - -
358B GLU* 2.7 19.2 + - - +
367B MET* 4.1 28.8 + - + -
368B ASP* 5.9 0.6 - - - -
372B MET* 3.6 13.4 - - + +
394B ASN* 1.3 75.4 - - - +
396B PRO* 1.3 80.9 - - + +
397B LEU* 2.9 45.0 + - + +
398B TRP* 3.0 18.4 + - - +
399B TYR* 3.6 2.1 - - - -
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Residues in contact with PRO 396 (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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32B PRO* 5.2 15.2 - - + +
144B ASP* 4.1 32.3 - - + +
210B ARG* 5.0 1.6 - - - -
394B ASN 3.2 4.2 - - - +
395B HIS* 1.3 100.6 - - + +
397B LEU* 1.3 63.5 + - - +
398B TRP 3.1 0.9 + - - -
399B TYR* 3.3 23.6 + - + +
400B THR* 3.7 8.7 + - - -
446B ARG* 4.2 18.2 - - - +
450B HIS* 4.8 2.8 + - - +
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Residues in contact with LEU 397 (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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369B GLU* 3.6 49.8 - - + +
372B MET* 4.1 6.3 - - - -
395B HIS* 2.9 25.5 + - + +
396B PRO* 1.3 79.4 - - - +
398B TRP* 1.3 65.3 + - - +
400B THR* 3.1 21.6 + - + -
401B LEU* 3.0 38.3 + - + +
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Residues in contact with TRP 398 (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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356B ARG* 3.5 52.9 - - - -
372B MET* 3.7 36.6 - - + +
375B ASP* 4.7 0.4 - - + -
376B ILE* 3.5 35.7 - - + -
379B MET* 4.5 7.9 - - + -
387B VAL* 4.0 25.7 - - + +
389B CYS* 4.2 12.5 - - - -
394B ASN* 3.3 29.9 + - + +
395B HIS 3.0 15.2 + - - +
397B LEU* 1.3 78.7 - - - +
399B TYR* 1.3 64.5 + + - +
401B LEU* 3.2 3.8 + - - +
402B CYS* 3.0 48.6 + - - -
407B LEU* 4.9 0.2 - - + -
409B VAL* 4.9 1.7 - - + +
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Residues in contact with TYR 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B CYS* 4.3 4.8 - - - -
393B PRO* 3.5 0.2 - - - +
394B ASN* 2.8 41.7 + - + +
395B HIS 3.6 5.2 - - - -
396B PRO* 3.5 15.7 - - + +
397B LEU 3.2 0.2 - - - -
398B TRP* 1.3 75.7 - + - +
400B THR* 1.3 61.6 + - - +
402B CYS* 3.2 3.3 + - - +
403B ASP* 2.8 35.9 + - - +
409B VAL* 4.4 13.7 - - + -
411B ASP* 2.7 39.3 + - + -
446B ARG* 3.2 24.1 + - - -
447B ASP* 3.3 11.9 - - - -
450B HIS* 3.4 32.3 - + + +
452B SER* 3.6 5.4 + - - +
453B VAL* 3.8 21.3 - - + -
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Residues in contact with THR 400 (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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45B ASP* 5.2 1.6 - - - +
329B ASP* 4.4 4.0 + - - +
396B PRO 3.7 4.7 + - - -
397B LEU* 3.1 26.1 + - + -
399B TYR* 1.3 78.1 - - - +
401B LEU* 1.3 65.3 + - + +
403B ASP* 3.3 8.6 + - - +
404B ARG* 3.1 63.8 + - - +
450B HIS* 3.6 14.7 - - - -
8404B DMS 5.6 2.1 + - - -
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Residues in contact with LEU 401 (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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369B GLU* 4.5 11.0 - - + +
372B MET* 3.7 34.3 - - + -
373B VAL* 3.9 19.3 - - + +
376B ILE* 3.7 19.1 - - + -
397B LEU* 3.0 37.7 + - + +
398B TRP* 3.7 5.6 - - - +
399B TYR 3.2 0.2 - - - -
400B THR* 1.3 78.0 - - + +
402B CYS* 1.3 60.2 + - - +
404B ARG* 4.5 6.7 - - + +
405B TYR* 2.8 56.4 + - + +
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Residues in contact with CYS 402 (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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301B TRP* 3.9 2.6 - - - -
376B ILE* 4.5 4.5 - - - -
387B VAL* 4.4 0.7 - - - -
398B TRP* 3.0 55.2 + - - +
399B TYR* 3.8 2.0 - - - +
401B LEU* 1.3 76.8 - - - +
403B ASP* 1.3 65.2 + - - +
405B TYR* 5.0 0.9 - - - -
406B GLY* 2.9 23.7 + - - +
407B LEU* 3.1 27.9 + - + +
409B VAL* 3.7 17.7 - - + -
452B SER* 3.6 21.1 - - - +
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Residues in contact with ASP 403 (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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301B TRP* 2.9 26.8 + - - +
306B PRO* 3.6 4.3 - - - +
308B LEU* 3.7 14.1 - - + +
329B ASP* 4.5 11.9 - - - +
399B TYR 2.8 15.8 + - - +
400B THR* 3.4 10.3 + - - +
401B LEU 3.2 0.2 - - - -
402B CYS* 1.3 81.3 - - - +
404B ARG* 1.3 62.2 + - + +
450B HIS* 2.6 28.8 + - - -
451B PRO* 3.3 22.3 - - + +
452B SER* 2.6 41.1 + - - -
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Residues in contact with ARG 404 (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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45B ASP* 2.8 34.8 + - - +
306B PRO* 3.5 15.8 - - - +
308B LEU* 3.7 20.6 - - + +
310B ARG* 4.1 1.2 - - - +
329B ASP* 2.9 31.6 + - - +
400B THR* 3.1 36.2 + - - +
401B LEU* 4.1 8.4 - - + +
403B ASP* 1.3 80.9 - - + +
405B TYR* 1.3 68.0 + - + +
406B GLY 3.3 0.2 - - - -
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Residues in contact with TYR 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B PRO* 3.7 11.5 - - - +
373B VAL* 3.6 28.2 - - + +
376B ILE* 3.7 27.8 - - + -
377B LEU* 3.7 19.9 - - + +
380B LYS* 3.3 24.5 + - + -
401B LEU* 2.8 53.2 + - + +
402B CYS* 5.0 0.4 - - - -
404B ARG* 1.3 79.2 - - + +
406B GLY* 1.3 60.6 + - - +
407B LEU* 5.6 0.2 - - + -
707B ALA* 3.5 38.0 + - + -
708B TRP* 4.4 12.2 - + + -
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Residues in contact with GLY 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B TRP* 4.2 3.8 - - - -
303B ALA* 3.7 19.2 - - - +
306B PRO* 3.9 17.7 - - - -
380B LYS* 2.7 26.3 + - - -
402B CYS 2.9 12.5 + - - -
404B ARG 3.3 1.2 - - - -
405B TYR* 1.3 79.1 - - - +
407B LEU* 1.3 65.3 + - - +
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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