Contacts of the helix formed by residues 470 - 485 (chain B) in PDB entry 1JQI
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 ASP 470 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B HIS* 3.0 24.4 + - - -
458B MET* 4.2 1.9 + - - +
459B ASP* 3.9 10.8 - - - +
469B LEU* 1.3 82.4 - - - +
471B TYR* 1.3 63.9 + - - +
472B LEU* 4.0 1.9 - - - +
473B ALA* 3.0 21.0 + - - +
474B TYR* 3.0 24.5 + - - +
712B ASP* 3.2 27.6 - - + +
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Residues in contact with TYR 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B ASP* 3.5 37.2 + - + -
470B ASP* 1.3 69.2 - - - +
472B LEU* 1.3 60.5 + - - +
473B ALA 3.3 0.2 - - - -
474B TYR* 3.4 30.8 - + + +
475B SER* 2.9 28.9 + - - -
496B ASN* 4.6 4.0 + - + -
497B SER* 2.8 29.6 + - - -
501B GLY* 5.6 0.5 - - - -
646B MET* 3.4 48.5 - - + +
649B ILE* 4.0 23.6 - - + -
708B ALA* 3.6 18.1 - - + +
711B LYS* 4.0 17.9 - - + -
712B ASP* 2.9 17.3 + - - +
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Residues in contact with LEU 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B LEU* 5.0 10.8 - - + -
411B PRO* 5.1 6.1 - - + -
414B HIS* 3.5 28.3 - - + +
470B ASP* 3.3 6.3 - - - +
471B TYR* 1.3 75.4 - - - +
473B ALA* 1.3 62.7 + - - +
475B SER* 3.4 1.4 + - - -
476B ILE* 3.0 36.3 + - + +
705B TRP* 4.0 37.7 - - + -
708B ALA* 3.8 8.4 - - + +
709B MET* 4.0 24.0 - - + -
712B ASP* 3.2 15.9 + - - +
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Residues in contact with ALA 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B HIS* 3.6 20.6 + - + +
417B LEU* 3.8 10.8 - - + +
458B MET* 3.5 6.7 - - + +
469B LEU* 3.9 24.7 - - + -
470B ASP* 3.0 21.8 + - - +
472B LEU* 1.3 75.6 - - - +
474B TYR* 1.3 55.8 + - - +
476B ILE* 3.4 5.2 + - - +
477B ALA* 2.8 37.4 + - - +
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Residues in contact with TYR 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B MET* 3.8 25.0 - - + +
459B ASP* 5.7 0.9 - - + +
470B ASP 3.0 14.6 + - - +
471B TYR* 3.4 42.4 - + + +
473B ALA* 1.3 76.7 - - - +
475B SER* 1.3 58.9 + - - +
477B ALA* 3.8 0.7 - - - +
478B LEU* 2.8 50.2 + - + +
492B MET* 4.3 5.2 - - + -
493B SER* 2.9 36.6 + - - -
496B ASN* 3.4 35.7 - - + -
497B SER* 2.9 24.7 + - - -
649B ILE* 5.3 2.2 - - + -
650B GLY* 4.0 14.8 - - - -
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Residues in contact with SER 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B TYR 2.9 18.9 + - - -
472B LEU 3.6 5.2 - - - -
474B TYR* 1.3 79.6 - - - +
476B ILE* 1.3 62.5 + - - +
478B LEU* 3.3 0.6 + - - -
479B GLU* 3.0 24.5 + - - +
649B ILE* 4.7 4.3 - - - -
653B SER* 2.9 28.5 + - - -
656B LEU* 5.0 1.7 - - - +
704B THR* 3.4 18.9 - - - +
705B TRP* 3.7 15.4 + - - -
708B ALA* 4.5 10.3 - - - -
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Residues in contact with ILE 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B TYR* 5.5 0.7 - - - +
410B LEU* 3.6 31.2 - - + -
414B HIS* 4.1 17.9 - - + +
417B LEU* 4.1 5.6 - - + -
418B ARG* 3.8 40.8 - - + +
472B LEU* 3.0 27.8 + - + +
473B ALA* 3.7 4.9 - - - +
475B SER* 1.3 82.4 - - - +
477B ALA* 1.3 63.2 + - - +
479B GLU* 3.4 7.4 + - - +
480B GLU* 3.3 21.6 + - + +
705B TRP* 3.7 29.4 - - + +
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Residues in contact with ALA 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B LEU* 3.5 21.3 - - + -
421B CYS* 3.6 19.0 - - - +
455B LEU* 4.0 4.3 - - + -
458B MET* 3.6 23.3 - - + -
473B ALA 2.8 20.8 + - - +
476B ILE* 1.3 73.8 - - - +
478B LEU* 1.3 61.6 + - - +
480B GLU* 3.3 4.0 + - - +
481B ILE* 3.1 28.8 + - - +
492B MET* 4.3 1.6 - - + -
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Residues in contact with LEU 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B TYR* 2.8 50.2 + - + +
475B SER 3.8 3.1 - - - +
477B ALA* 1.3 70.8 - - - +
479B GLU* 1.3 64.9 + - - +
481B ILE* 4.5 0.9 - - + -
482B SER* 2.9 41.7 + - - +
489B GLY* 3.2 30.5 - - - +
492B MET* 4.0 24.0 - - + +
493B SER* 3.7 9.4 - - - -
650B GLY* 3.2 29.6 - - - +
653B SER* 3.9 9.9 - - - -
654B GLN* 4.4 2.2 - - + +
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Residues in contact with GLU 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B TYR* 4.4 8.0 + - - -
422B ARG* 5.5 0.7 + - - -
475B SER* 3.0 16.8 + - - +
476B ILE* 3.7 7.4 - - - +
477B ALA 3.3 0.2 - - - -
478B LEU* 1.3 77.2 - - - +
480B GLU* 1.3 77.2 + - - +
482B SER 3.3 1.2 + - - -
483B ARG* 3.0 22.2 + - + +
653B SER* 3.5 18.5 + - - +
656B LEU* 4.0 17.0 - - + +
657B GLY* 3.5 20.4 - - - +
660B GLN* 4.4 11.5 - - + +
701B ARG* 2.9 46.6 + - - +
705B TRP* 4.7 5.2 + - - -
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Residues in contact with GLU 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B TYR* 4.9 3.6 + - - -
418B ARG* 3.7 38.9 - - + +
421B CYS* 3.7 21.1 - - + -
422B ARG* 3.1 55.7 + - - +
425B ALA* 3.4 17.7 - - - +
476B ILE* 3.3 14.5 + - - +
477B ALA 3.3 1.8 + - - +
479B GLU* 1.3 90.1 - - - +
481B ILE* 1.3 63.5 + - - +
483B ARG* 3.4 21.9 + - - +
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Residues in contact with ILE 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B CYS* 4.3 13.9 - - + +
424B PHE* 3.9 28.7 - - + -
425B ALA* 4.4 2.5 - - + -
429B LEU* 3.7 18.2 - - + +
450B MET* 4.0 9.2 - - + -
455B LEU* 4.0 19.3 - - + -
477B ALA 3.1 18.1 + - - +
478B LEU* 3.8 5.2 - - + +
480B GLU* 1.3 76.2 - - - +
482B SER* 1.3 57.9 + - - +
484B GLY* 2.9 18.0 + - - -
485B CYS 3.0 10.7 + - - +
488B THR* 3.9 19.1 - - + -
489B GLY* 4.1 13.7 - - - +
492B MET* 4.1 17.5 - - - -
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Residues in contact with SER 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B LEU* 2.9 22.5 + - - +
479B GLU 3.3 3.6 + - - -
481B ILE* 1.3 74.2 - - - +
483B ARG* 1.3 64.0 + - - +
484B GLY 3.4 0.3 + - - -
485B CYS* 3.5 22.9 + - - -
486B ALA* 3.6 6.0 + - - -
489B GLY* 3.6 13.0 - - - -
654B GLN* 3.3 48.1 - - - +
657B GLY* 4.1 7.7 - - - -
658B ILE* 4.2 5.0 + - - +
661B ALA* 5.5 0.2 - - - +
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Residues in contact with ARG 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B ARG* 3.0 44.9 + - - +
425B ALA* 5.8 3.8 - - + +
426B GLU* 3.0 29.6 + - - +
430B VAL* 5.1 2.6 - - - +
479B GLU* 3.0 13.3 + - - +
480B GLU* 3.5 17.4 + - - +
481B ILE 3.1 0.4 - - - -
482B SER* 1.3 79.4 - - - +
484B GLY* 1.3 61.0 + - - +
657B GLY* 3.4 16.6 - - - +
660B GLN* 3.6 27.1 - - - -
661B ALA* 3.6 28.9 - - + +
664B ASP* 2.8 22.4 + - - +
757B TYR* 4.9 6.2 + - - -
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Residues in contact with GLY 484 (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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425B ALA* 4.2 6.7 - - - +
429B LEU* 4.0 11.4 - - - -
430B VAL* 3.9 29.2 + - - +
433B ALA* 3.5 19.1 - - - +
480B GLU 3.5 3.4 + - - -
481B ILE 2.9 8.4 + - - -
483B ARG* 1.3 82.2 - - - +
485B CYS* 1.3 61.6 + - - +
756B ARG* 4.3 3.6 + - - -
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Residues in contact with CYS 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B LEU* 4.3 13.0 - - + +
433B ALA* 4.4 14.4 - - + -
436B LEU* 4.0 22.0 - - + -
481B ILE 3.0 11.0 + - - +
482B SER* 3.5 5.4 - - - -
483B ARG 3.5 0.8 - - - -
484B GLY* 1.3 79.8 - - - +
486B ALA* 1.3 66.4 + - - +
487B SER* 3.6 14.4 - - - -
488B THR* 3.4 36.0 - - - +
489B GLY 3.2 15.9 + - - -
611B ALA* 5.1 0.2 - - - -
756B ARG* 4.9 4.3 - - - +
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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
------------------------------------------------------------
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