Contacts of the helix formed by residues 519 - 537 (chain B) in PDB entry 1JEY
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 PRO 519 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B HIS* 3.0 32.1 - - + +
189B GLY* 4.9 1.3 - - - -
463B LEU* 4.3 1.3 - - + -
476B LEU* 3.3 39.3 - - + +
477B PHE* 4.2 10.1 - - + -
518B PRO* 1.3 90.8 - - + +
520B ALA* 1.3 66.7 + - - +
521B GLU* 2.9 14.1 + - + +
522B VAL* 2.9 33.9 + - + +
523B THR* 3.4 4.2 + - - -
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Residues in contact with ALA 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B PRO* 5.8 5.8 - - + +
184B ARG* 5.0 23.1 - - + +
188B HIS 4.2 2.2 + - - -
518B PRO 3.3 4.4 + - - -
519B PRO* 1.3 71.2 - - - +
521B GLU* 1.3 68.5 + - + +
523B THR* 3.4 9.4 + - - -
524B THR* 2.9 30.1 + - - +
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Residues in contact with GLU 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B GLY* 5.5 12.2 - - - +
476B LEU* 6.3 2.9 - - + -
519B PRO* 4.5 13.0 - - + +
520B ALA* 1.3 84.1 - - + +
522B VAL* 1.3 63.5 + - + +
524B THR* 3.3 5.2 + - - -
525B LYS* 3.1 34.9 + - - +
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Residues in contact with VAL 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A MET 4.1 17.3 - - - +
460B SER 4.3 7.0 - - - +
461B MET* 3.8 33.7 - - + +
462B SER 3.8 17.0 - - - +
463B LEU* 4.0 7.0 - - + -
476B LEU* 4.9 7.9 - - + -
518B PRO* 4.4 6.3 - - + -
519B PRO* 2.9 33.8 + - + +
521B GLU* 1.3 77.9 - - + +
523B THR* 1.3 63.3 + - - +
525B LYS* 3.4 5.5 + - - +
526B SER* 3.3 22.3 + - - -
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Residues in contact with THR 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B PRO* 3.7 22.2 + - - +
519B PRO 3.4 9.7 + - - -
520B ALA* 3.8 10.1 - - - -
522B VAL* 1.3 77.9 - - - +
524B THR* 1.3 58.1 + - - +
526B SER* 2.9 11.1 + - - +
527B GLN* 2.6 38.8 + - - +
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Residues in contact with THR 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B ALA* 2.9 20.8 + - - +
521B GLU* 3.7 5.3 - - - -
523B THR* 1.3 78.4 - - - +
525B LYS* 1.3 61.9 + - - +
527B GLN* 3.3 23.9 + - + +
528B ILE 5.0 0.2 + - - -
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Residues in contact with LYS 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B ASP 5.5 2.6 + - - -
460B SER* 3.6 37.6 + - - +
521B GLU* 3.1 27.2 + - - +
522B VAL* 3.4 2.4 + - - +
524B THR* 1.3 77.3 - - + +
526B SER* 1.3 61.6 + - - +
527B GLN 3.4 0.3 + - - -
528B ILE* 4.2 1.9 + - - +
529B PRO* 3.2 15.9 - - - +
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Residues in contact with SER 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B LEU* 4.4 0.4 - - - -
460B SER* 3.4 11.0 + - - -
461B MET* 3.3 44.7 - - - +
522B VAL 3.3 5.9 + - - -
523B THR* 2.9 18.9 + - - +
525B LYS* 1.3 77.7 - - - +
527B GLN* 1.3 61.9 + - - +
528B ILE 3.4 0.2 - - - -
529B PRO* 3.1 3.0 - - - +
530B LEU* 2.7 42.1 + - - +
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Residues in contact with GLN 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ASN* 5.6 2.6 + - - -
523B THR* 2.6 33.8 + - - +
524B THR* 3.3 23.1 - - + +
525B LYS 3.3 0.6 - - - -
526B SER* 1.3 82.2 + - - +
528B ILE* 1.3 67.6 + - + +
530B LEU* 3.2 14.7 + - - +
531B SER* 2.9 22.7 + - - -
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Residues in contact with ILE 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B THR 5.0 0.2 + - - -
525B LYS 4.2 2.1 + - - +
527B GLN* 1.3 76.5 - - + +
529B PRO* 1.3 76.8 - - + +
531B SER* 2.8 30.0 + - - +
532B LYS* 3.0 33.4 + - - +
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Residues in contact with PRO 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B ALA 4.9 2.4 - - - +
456B ALA* 4.3 12.1 - - + +
457B LEU* 3.9 23.6 - - + +
460B SER* 3.8 25.6 - - - +
525B LYS 3.2 15.0 - - - +
526B SER 3.1 9.2 - - - +
528B ILE* 1.3 97.1 - - + +
530B LEU* 1.3 61.6 + - - +
532B LYS* 3.2 10.5 + - + +
533B ILE* 3.1 25.8 + - - +
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Residues in contact with LEU 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LEU* 3.9 23.8 - - + +
264A ASN* 3.9 27.1 - - + +
267A ILE* 3.1 32.9 - - + +
457B LEU* 3.7 23.3 - - + -
461B MET* 3.7 20.0 - - + -
526B SER* 2.7 31.9 + - - +
527B GLN* 3.5 15.7 - - - +
529B PRO* 1.3 73.5 - - - +
531B SER* 1.3 63.3 + - - +
533B ILE* 3.1 5.0 + - + +
534B LYS 3.0 18.5 + - - -
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Residues in contact with SER 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B GLN 2.9 11.7 + - - -
528B ILE* 2.8 22.1 + - - +
530B LEU* 1.3 77.0 - - - +
532B LYS* 1.3 66.4 + - - +
534B LYS* 3.3 12.0 + - - +
535B THR* 3.0 22.3 + - - +
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Residues in contact with LYS 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B ALA* 4.8 7.9 - - + -
528B ILE* 3.0 35.9 + - + +
529B PRO* 3.2 10.5 + - + +
531B SER* 1.3 85.4 + - - +
533B ILE* 1.3 57.6 + - - +
535B THR* 3.4 7.4 + - - -
536B LEU* 3.1 43.4 + - + +
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Residues in contact with ILE 533 (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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263A LEU* 4.4 8.5 - - + -
267A ILE* 4.1 25.5 - - + +
381A LEU* 4.5 5.6 - - + -
453B ALA* 3.7 25.6 - - + +
454B VAL* 4.2 9.4 - - + -
457B LEU* 3.2 48.7 - - + -
529B PRO 3.1 12.4 + - - +
530B LEU* 3.1 8.7 + - + +
532B LYS* 1.3 76.9 - - - +
534B LYS* 1.3 59.7 + - - +
536B LEU* 4.5 1.1 - - - -
537B PHE* 2.9 49.7 + - + +
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Residues in contact with LYS 534 (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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266A ASP* 4.0 39.8 + - + +
267A ILE* 3.9 18.8 - - + -
530B LEU 3.0 12.7 + - - +
531B SER* 3.3 12.3 + - - +
533B ILE* 1.3 78.4 - - - +
535B THR* 1.3 61.0 + - + +
537B PHE 3.9 14.0 - - - +
538B PRO* 5.1 1.9 - - - +
539B LEU* 6.5 0.4 - - - -
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Residues in contact with THR 535 (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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531B SER* 3.0 21.1 - - - +
532B LYS* 3.7 7.8 + - - +
533B ILE 3.2 0.4 - - - -
534B LYS* 1.3 78.1 - - + +
536B LEU* 1.3 71.3 + - - +
537B PHE 5.0 0.2 - - - -
538B PRO* 4.9 4.5 - - - +
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Residues in contact with LEU 536 (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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449B ALA* 3.6 32.3 - - + +
450B GLN* 2.8 28.8 + - + +
453B ALA* 3.4 31.9 - - + -
532B LYS* 3.1 25.2 + - + +
535B THR* 1.3 87.6 + - - +
537B PHE* 1.3 67.3 + - + +
538B PRO* 3.3 8.1 - - - +
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Residues in contact with PHE 537 (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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267A ILE* 6.0 0.4 - - + +
377A GLY 5.4 1.1 - - - +
380A THR* 3.8 14.6 - - + -
381A LEU* 3.6 46.7 - - + -
384A ALA* 4.1 4.5 - - + -
446B PRO* 4.7 0.2 - - + -
450B GLN* 3.1 68.0 - - + -
453B ALA* 4.6 0.4 - - + -
454B VAL* 3.7 20.4 - - + -
533B ILE* 2.9 40.0 + - + +
534B LYS* 3.9 11.8 - - - +
535B THR 4.9 0.2 - - - -
536B LEU* 1.3 82.0 - - + +
538B PRO* 1.3 69.2 - - - +
539B LEU* 3.3 14.0 + - + +
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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