Contacts of the helix formed by residues 470 - 487 (chain B) in PDB entry 4YJL
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 GLY 470 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B ARG* 3.5 12.3 + - - -
466B MET 3.2 1.6 + - - -
467B ASN* 3.3 11.2 + - - -
468B GLU 3.4 1.6 + - - -
469B LEU* 1.3 78.1 - - - +
471B GLY* 1.3 62.2 + - - +
472B LEU 3.4 2.9 + - - -
473B GLN* 3.6 10.2 + - - +
474B ALA* 3.2 16.8 + - - +
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Residues in contact with GLY 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B LEU* 3.8 23.1 - - - -
466B MET* 2.8 31.6 + - - -
467B ASN* 4.6 1.0 - - - +
469B LEU 3.4 0.6 - - - -
470B GLY* 1.3 69.8 - - - +
472B LEU* 1.3 65.1 + - - +
474B ALA* 3.3 0.9 + - - +
475B ILE* 3.0 34.6 + - - +
508B LEU* 4.3 1.6 - - - -
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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
----------------------------------------------------------
467B ASN* 4.7 4.5 + - - +
470B GLY 3.4 0.8 - - - -
471B GLY* 1.3 74.4 - - - +
473B GLN* 1.3 64.5 + - - +
476B ALA* 2.9 26.2 + - - +
505B LEU* 3.8 19.5 - - + +
508B LEU* 3.9 36.3 - - + +
509B THR* 4.1 15.0 - - + -
515B ASN* 3.5 49.6 - - + +
518B THR* 3.8 27.4 - - + -
519B LEU* 3.9 15.0 - - + +
522B MET* 5.2 0.9 - - - -
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Residues in contact with GLN 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B GLY* 3.6 10.7 + - - +
471B GLY 3.4 0.2 - - - -
472B LEU* 1.3 80.4 - - - +
474B ALA* 1.3 59.1 + - - +
476B ALA* 3.8 1.0 - - - +
477B GLU* 2.8 55.4 + - - +
518B THR* 5.1 10.1 - - + +
522B MET* 4.0 23.5 - - + +
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Residues in contact with ALA 474 (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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410B LEU* 4.3 7.2 - - + +
413B ILE* 3.7 18.4 - - + +
414B ARG* 4.0 34.5 - - + +
417B CYS* 5.0 1.6 - - - -
470B GLY 3.2 15.7 + - - +
471B GLY 3.3 3.6 + - - +
473B GLN* 1.3 80.6 - - - +
475B ILE* 1.3 62.3 + - - +
477B GLU* 3.4 6.5 + - - +
478B LEU* 3.0 24.1 + - - +
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Residues in contact with ILE 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B LEU* 4.6 3.4 - - + -
413B ILE* 3.8 19.7 - - + -
450B VAL* 5.3 4.0 - - + -
453B LEU* 4.0 18.8 - - + -
466B MET* 4.3 11.0 - - - -
471B GLY 3.0 22.4 + - - +
472B LEU 4.0 2.2 - - - +
474B ALA* 1.3 74.4 - - - +
476B ALA* 1.3 57.5 + - - +
478B LEU* 3.5 3.6 + - - +
479B LEU* 3.0 27.2 + - - +
501B ALA* 3.5 40.2 - - + +
504B ALA* 4.0 21.5 - - + -
505B LEU* 3.8 10.1 - - + -
508B LEU* 4.0 14.8 - - + -
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Residues in contact with ALA 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B LEU 2.9 18.6 + - - +
475B ILE* 1.3 74.4 - - - +
477B GLU* 1.3 60.9 + - - +
479B LEU* 3.4 1.5 + - - +
480B GLN* 2.9 29.5 + - - +
505B LEU* 4.0 10.7 - - + +
519B LEU* 3.7 30.7 - - + -
522B MET* 3.8 15.9 - - + -
525B CYS* 3.5 14.7 - - - -
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Residues in contact with GLU 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B ARG* 6.1 0.5 - - - +
417B CYS* 3.9 15.5 - - + +
473B GLN* 2.8 53.5 + - - +
474B ALA* 3.8 6.1 - - - +
476B ALA* 1.3 73.0 - - - +
478B LEU* 1.3 56.8 + - - +
480B GLN* 3.4 13.0 + - - +
481B VAL* 2.8 40.9 + - + +
522B MET* 3.5 16.1 - - + +
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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
----------------------------------------------------------
413B ILE* 4.2 22.9 - - + +
416B TYR* 3.5 33.9 - - + -
417B CYS* 3.5 18.5 - - - -
446B ILE* 3.7 23.1 - - + -
450B VAL* 3.4 33.0 - - + -
474B ALA 3.0 17.0 + - - +
475B ILE 3.7 5.4 - - - +
477B GLU* 1.3 73.4 - - - +
479B LEU* 1.3 65.3 + - - +
481B VAL* 3.4 1.7 + - - +
482B ASP* 3.1 24.1 + - + +
497B LEU* 4.5 10.3 - - + +
501B ALA* 5.0 2.7 - - + -
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Residues in contact with LEU 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B ILE 3.0 17.8 + - - +
476B ALA* 3.6 5.6 - - - +
478B LEU* 1.3 79.0 - - - +
480B GLN* 1.3 62.9 + - - +
482B ASP* 3.4 3.0 + - - +
483B CYS* 3.0 39.3 + - - -
497B LEU* 5.5 2.2 - - + -
498B ARG* 3.6 42.8 - - + +
501B ALA* 4.2 8.1 - - + -
502B GLY* 4.3 15.7 - - - +
505B LEU* 4.0 17.0 - - + -
525B CYS* 5.2 2.9 - - - -
528B ALA* 5.9 1.6 - - + -
529B LEU* 3.5 32.1 - - + +
532B GLN* 5.4 0.2 - - + -
544B ILE* 4.6 6.7 - - + -
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Residues in contact with GLN 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B ALA 2.9 15.5 + - - +
477B GLU* 3.4 17.7 - - - +
478B LEU 3.3 0.2 - - - -
479B LEU* 1.3 77.0 - - - +
481B VAL* 1.3 64.9 + - + +
483B CYS* 3.2 2.8 + - - +
484B GLU* 2.9 55.7 + - + +
522B MET* 4.8 4.0 - - - +
524B GLY* 3.4 18.2 - - - +
525B CYS* 3.3 34.1 + - - +
528B ALA* 4.3 11.0 - - + -
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Residues in contact with VAL 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B TYR* 4.6 7.9 - - + -
417B CYS* 3.8 25.8 - - + +
420B CYS* 3.7 21.3 - - + -
477B GLU* 2.8 26.2 + - + +
478B LEU* 3.7 4.9 - - - +
479B LEU 3.4 0.2 - - - -
480B GLN* 1.3 76.9 - - + +
482B ASP* 1.3 59.2 + - - +
484B GLU* 3.9 7.1 - - - +
485B MET* 3.0 56.2 + - + +
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Residues in contact with ASP 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B TYR* 4.8 7.0 + - + -
441B PRO* 3.6 24.4 - - + +
478B LEU* 3.1 16.5 + - + +
479B LEU 4.0 2.5 - - - +
481B VAL* 1.3 78.8 - - - +
483B CYS* 1.3 62.5 + - - +
485B MET* 4.6 4.2 - - - +
486B TYR* 3.1 32.5 + - - -
494B SER* 2.7 28.3 + - - -
497B LEU* 4.1 22.0 - - + +
498B ARG* 2.9 29.8 + - + +
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Residues in contact with CYS 483 (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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479B LEU* 3.0 45.6 + - - +
480B GLN 3.7 2.9 - - - +
482B ASP* 1.3 75.2 - - - +
484B GLU* 1.3 58.7 + - - +
487B GLY* 2.9 18.2 + - - -
498B ARG* 3.5 13.7 - - - +
528B ALA* 3.7 14.4 - - + -
532B GLN* 3.3 32.8 - - - +
801B EDO 2.8 36.8 + - - +
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Residues in contact with GLU 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B GLN* 5.9 1.0 + - - -
480B GLN* 2.9 52.6 + - + +
481B VAL* 3.9 7.3 - - - +
483B CYS* 1.3 76.0 - - - +
485B MET* 1.3 66.7 + - + +
487B GLY* 4.2 2.8 + - - -
524B GLY* 4.1 9.4 - - - +
527B ARG* 5.2 2.9 + - - -
528B ALA* 5.2 4.3 - - + -
801B EDO 4.7 8.3 - - - +
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Residues in contact with MET 485 (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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416B TYR* 4.4 3.8 - - - +
420B CYS* 3.3 36.3 - - + -
423B TRP* 4.1 20.2 - - + -
438B MET* 3.3 33.2 - - + +
439B PRO* 3.4 39.7 - - + +
481B VAL* 3.0 30.9 + - + +
482B ASP* 4.1 1.6 - - - +
484B GLU* 1.3 79.9 - - + +
486B TYR* 1.3 72.3 + - + +
487B GLY 3.6 0.2 - - - -
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Residues in contact with TYR 486 (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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416B TYR* 4.7 0.2 - - - -
438B MET* 3.7 29.0 + - + +
439B PRO 2.5 33.4 + - - -
440B ALA* 3.5 12.1 - - + +
441B PRO* 4.1 14.8 - - + -
482B ASP* 3.1 26.8 + - - +
485B MET* 1.3 97.1 - - + +
487B GLY* 1.3 65.9 + - - +
488B LEU 3.7 0.5 + - - -
489B THR* 3.0 30.6 + - + +
494B SER* 5.0 3.6 - - - +
498B ARG* 3.9 4.3 - - - +
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Residues in contact with GLY 487 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B CYS 2.9 19.1 + - - -
484B GLU 4.2 3.0 + - - -
485B MET 3.6 1.4 - - - -
486B TYR* 1.3 78.4 - - - +
488B LEU* 1.3 58.2 + - - -
489B THR 3.0 4.9 + - - -
498B ARG* 2.8 27.2 + - - -
801B EDO 3.2 14.4 - - - -
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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