Contacts of the helix formed by residues 503 - 518 (chain B) in PDB entry 1JPP
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 503 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458B GLU* 3.5 34.0 + - - +
501B PRO 4.5 8.5 + - - -
502B SER* 1.3 76.0 + - - +
504B TRP* 1.3 64.9 + - - +
505B PRO* 3.5 8.3 - - + -
506B LEU* 3.5 3.6 + - - +
507B ILE* 2.9 29.5 + - - +
562B GLU* 3.1 28.4 + - - +
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Residues in contact with TRP 504 (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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503B HIS* 1.3 68.2 - - - +
505B PRO* 1.3 71.6 - - + +
507B ILE* 3.2 25.6 + - + +
508B LYS* 3.0 25.3 + - - +
539B LEU* 4.9 16.6 - - + -
542B ARG* 3.1 37.3 - - + +
543B ALA* 5.3 4.9 - - + -
561B VAL* 3.8 31.3 - - + +
562B GLU* 3.0 28.5 + - + +
564B VAL* 3.5 19.0 - - + +
566B MET* 4.1 25.8 - - + +
569B ILE* 4.2 35.9 - - + -
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Residues in contact with PRO 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B GLU* 4.0 23.1 - - - +
503B HIS* 3.7 8.1 - - + -
504B TRP* 1.3 94.5 - - + +
506B LEU* 1.3 59.5 + - - +
508B LYS* 3.7 8.1 + - + +
509B ALA* 3.7 17.5 + - - +
562B GLU* 3.5 32.3 - - + +
563B GLY* 5.6 0.4 - - - -
564B VAL* 3.8 10.7 - - + -
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Residues in contact with LEU 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B GLU* 3.7 37.9 - - + +
461B THR* 3.9 16.6 - - - +
462B GLU* 3.8 38.5 + - + +
465B ILE* 4.8 4.9 - - + -
497B LEU* 4.1 21.1 - - + +
502B SER* 3.7 21.8 - - - +
503B HIS 3.5 7.2 + - - +
504B TRP 3.2 0.4 - - - -
505B PRO* 1.3 77.6 - - - +
507B ILE* 1.3 65.1 + - - +
508B LYS 3.2 0.6 + - - -
509B ALA* 3.5 5.2 + - + +
510B THR* 3.1 32.6 + - - +
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Residues in contact with ILE 507 (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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497B LEU 4.4 7.9 - - - +
498B LEU* 4.2 19.1 - - + +
499B HIS 5.8 1.1 - - - -
500B PRO* 6.5 0.7 - - + -
502B SER* 4.0 23.3 - - - +
503B HIS 2.9 28.8 + - - +
504B TRP* 3.2 29.8 + - + +
506B LEU* 1.3 73.9 - - - +
508B LYS* 1.3 68.2 + - - +
510B THR* 3.3 6.9 + - - -
511B VAL* 3.3 22.1 + - + +
535B ARG* 5.6 1.3 - - - +
539B LEU* 3.9 31.6 - - + -
569B ILE* 5.2 3.8 - - + -
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Residues in contact with LYS 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B ARG* 4.9 12.5 + - - +
504B TRP 3.0 17.0 + - - +
505B PRO* 3.7 8.6 + - + +
506B LEU 3.2 0.2 - - - -
507B ILE* 1.3 76.2 - - - +
509B ALA* 1.3 64.9 + - - +
510B THR 3.2 0.9 + - - -
511B VAL* 3.2 16.0 + - - +
512B GLY* 3.3 8.7 + - - -
564B VAL* 4.3 21.7 - - + +
568B GLU* 4.5 24.6 + - + +
569B ILE* 4.1 22.4 - - + +
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Residues in contact with ALA 509 (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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462B GLU* 5.3 2.7 - - + +
465B ILE* 3.9 14.7 - - + +
466B CYS* 4.1 27.8 - - - +
469B ARG* 4.2 21.2 - - - +
505B PRO 3.7 8.8 + - - +
506B LEU* 3.5 10.2 + - + +
507B ILE 3.4 0.4 - - - -
508B LYS* 1.3 81.1 - - - +
510B THR* 1.3 57.3 + - - +
512B GLY* 3.4 1.9 + - - -
513B LEU* 3.1 23.9 + - - +
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Residues in contact with THR 510 (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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465B ILE* 4.1 20.1 - - + +
494B VAL* 3.3 39.5 - - + +
497B LEU* 4.4 15.6 - - + +
498B LEU* 4.1 17.7 - - + -
506B LEU* 3.1 17.0 + - - +
507B ILE* 3.3 9.6 + - - -
508B LYS 3.2 1.2 - - - -
509B ALA* 1.3 73.1 - - - +
511B VAL* 1.3 66.4 + - - +
512B GLY 3.1 1.6 - - - -
513B LEU* 3.1 2.3 + - + +
514B ILE* 3.0 25.4 + - + +
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Residues in contact with VAL 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B LEU* 4.1 17.0 - - + -
507B ILE* 3.3 17.7 + - + +
508B LYS* 3.2 11.3 + - - +
510B THR* 1.3 77.9 - - - +
512B GLY* 1.3 62.5 + - - +
514B ILE* 3.4 8.8 + - - +
515B ARG* 3.2 21.3 + - - +
536B LEU* 4.2 17.3 - - + -
539B LEU* 4.9 2.9 - - + -
569B ILE* 5.6 7.0 - - + +
572B GLY* 3.8 35.4 - - - +
573B CYS* 4.0 17.3 - - - +
576B ALA* 4.9 3.9 - - + +
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Residues in contact with GLY 512 (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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469B ARG* 3.8 30.3 + - - -
508B LYS 3.3 8.1 + - - -
509B ALA 3.4 4.4 + - - -
510B THR 3.1 0.6 - - - -
511B VAL* 1.3 79.5 - - - +
513B LEU* 1.3 62.3 + - - +
515B ARG* 3.5 13.1 + - - +
516B ASN* 3.3 20.4 + - - +
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Residues in contact with LEU 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B ILE* 3.7 39.7 - - + +
468B LEU* 4.3 37.2 - - + +
469B ARG* 4.3 10.3 - - + +
472B THR* 4.3 7.6 - - + +
485B VAL* 5.8 2.7 - - + -
494B VAL* 4.3 19.5 - - + -
509B ALA 3.1 13.4 + - - +
510B THR 3.1 8.3 + - - +
512B GLY* 1.3 77.1 - - - +
514B ILE* 1.3 63.1 + - - +
516B ASN* 3.5 3.7 + - - +
517B LEU* 3.2 42.1 + - + +
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Residues in contact with ILE 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B VAL* 4.1 19.1 - - + +
495B VAL* 4.7 11.0 - - + -
498B LEU* 3.9 30.5 - - + -
510B THR* 3.0 26.0 + - + +
511B VAL* 3.8 8.1 - - - +
513B LEU* 1.3 76.2 - - - +
515B ARG* 1.3 67.6 + - - +
517B LEU* 3.5 9.4 + - + +
518B ALA* 3.3 20.6 + - + +
527B LEU* 4.6 21.2 - - + +
532B ALA* 5.0 8.1 - - + -
536B LEU* 4.8 20.6 - - + -
576B ALA* 5.1 6.1 - - + -
580B LEU* 5.6 5.8 - - + -
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Residues in contact with ARG 515 (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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511B VAL 3.2 13.3 + - - +
512B GLY* 3.5 10.9 + - - +
513B LEU 3.3 0.4 - - - -
514B ILE* 1.3 80.5 - - - +
516B ASN* 1.3 68.2 + - - +
518B ALA* 3.4 15.3 + - - +
519B LEU* 4.0 8.3 + - + +
571B GLU* 3.6 35.0 + - - -
572B GLY* 4.1 12.7 + - - +
575B GLY* 3.8 36.1 + - - +
576B ALA* 4.6 11.2 - - - +
579B ILE* 4.6 13.6 - - + +
612B ARG* 4.9 12.5 - - - +
613B VAL* 4.8 6.1 - - - +
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Residues in contact with ASN 516 (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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469B ARG* 3.5 34.4 + - - +
472B THR* 3.6 30.3 + - - +
473B SER* 4.7 7.2 - - - -
482B GLN* 3.6 10.4 - - - +
512B GLY 3.3 17.8 + - - +
513B LEU* 3.5 4.7 + - - +
514B ILE 3.3 0.4 - - - -
515B ARG* 1.3 85.0 - - - +
517B LEU* 1.3 63.5 + - - +
519B LEU* 2.9 34.9 + - + +
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Residues in contact with LEU 517 (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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472B THR* 4.4 5.2 - - + -
482B GLN* 4.2 21.5 - - - +
485B VAL* 3.9 37.5 - - + -
491B LEU* 4.5 19.5 - - + -
494B VAL* 4.7 11.2 - - + -
513B LEU* 3.2 41.4 + - + +
514B ILE* 3.8 10.5 - - + +
515B ARG 3.4 0.2 - - - -
516B ASN* 1.3 78.8 - - + +
518B ALA* 1.3 57.3 + - - +
519B LEU 3.1 4.3 + - - -
520B CYS* 3.5 4.5 + - - +
523B ASN* 3.1 32.2 + - - +
527B LEU* 4.7 12.3 - - + -
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Residues in contact with ALA 518 (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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514B ILE* 3.3 10.9 + - + +
515B ARG* 3.6 12.6 - - - +
516B ASN 3.1 1.6 + - - -
517B LEU* 1.3 74.0 - - - +
519B LEU* 1.3 56.1 + - - +
520B CYS 3.1 8.7 - - - -
523B ASN* 5.0 1.8 - - - -
524B HIS* 3.2 28.3 - - - +
527B LEU* 4.5 8.9 - - + +
576B ALA 5.2 1.8 - - - +
579B ILE* 3.6 22.8 - - + +
580B LEU* 4.2 26.9 - - + +
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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
------------------------------------------------------------
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