Contacts of the helix formed by residues 503 - 518 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458A GLU* 3.5 34.4 + - - +
501A PRO 4.6 9.1 + - - -
502A SER* 1.3 76.9 + - - +
504A TRP* 1.3 66.2 + - - +
505A PRO* 3.6 8.5 - - + -
506A LEU* 3.5 3.9 + - - +
507A ILE* 2.9 29.7 + - - +
562A GLU* 3.4 26.7 + - - +
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Residues in contact with TRP 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503A HIS* 1.3 73.3 - - - +
505A PRO* 1.3 71.0 - - + +
507A ILE* 3.3 26.0 + - + +
508A LYS* 3.0 26.0 + - - +
539A LEU* 4.9 16.4 - - + -
542A ARG* 3.2 34.7 - - + +
543A ALA* 5.3 4.9 - - + -
561A VAL* 3.9 25.8 - - + +
562A GLU* 3.0 33.3 + - + +
564A VAL* 3.5 18.5 - - + +
566A MET* 4.0 26.0 - - + +
569A ILE* 4.1 39.0 - - + -
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Residues in contact with PRO 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A GLU* 4.0 23.4 - - - +
503A HIS* 3.7 8.3 - - + -
504A TRP* 1.3 96.2 - - + +
506A LEU* 1.3 60.4 + - - +
508A LYS* 3.6 16.5 - - + +
509A ALA* 3.6 9.5 + - - +
562A GLU* 3.5 20.9 - - + +
563A GLY 5.8 0.4 - - - -
564A VAL* 3.8 15.7 - - + -
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Residues in contact with LEU 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A GLU* 3.7 39.0 - - + +
461A THR* 3.9 15.7 - - - +
462A GLU* 3.8 38.3 + - + +
465A ILE* 4.8 8.5 - - + -
497A LEU* 4.1 20.2 - - + +
502A SER* 4.0 18.6 - - - +
503A HIS* 3.5 7.9 + - - +
504A TRP 3.2 0.4 - - - -
505A PRO* 1.3 76.8 - - - +
507A ILE* 1.3 65.7 + - - +
508A LYS 3.1 2.4 + - - -
509A ALA* 3.2 11.9 + - + +
510A THR* 3.1 26.8 + - - +
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Residues in contact with ILE 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497A LEU 4.3 7.9 - - - +
498A LEU* 4.1 21.5 - - + +
499A HIS 5.8 0.4 - - - -
500A PRO* 6.1 0.4 - - + -
502A SER* 4.1 24.5 - - - +
503A HIS 2.9 29.0 + - - +
504A TRP* 3.8 29.2 - - + +
506A LEU* 1.3 75.3 - - - +
508A LYS* 1.3 62.4 + - - +
510A THR* 3.5 7.1 + - - -
511A VAL* 3.4 24.9 + - + +
535A ARG* 5.5 1.1 - - - +
539A LEU* 3.9 30.1 - - + -
569A ILE* 5.4 3.8 - - + -
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Residues in contact with LYS 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469A ARG* 4.5 14.2 + - - +
504A TRP 3.0 16.9 + - - +
505A PRO* 3.6 9.0 - - + +
506A LEU 3.1 0.4 - - - -
507A ILE* 1.3 78.6 - - - +
509A ALA* 1.3 63.7 + - - +
511A VAL* 3.5 6.0 + - - +
512A GLY* 3.5 14.4 + - - -
564A VAL* 4.2 18.8 - - + -
568A GLU* 4.7 25.4 + - + +
569A ILE* 3.8 25.5 - - + +
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Residues in contact with ALA 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A GLU* 5.2 2.5 - - + +
465A ILE* 3.8 14.0 - - + +
466A CYS* 3.9 28.9 - - - +
469A ARG* 4.1 19.2 - - - +
505A PRO 3.6 8.6 + - - +
506A LEU* 3.2 11.5 + - + +
508A LYS* 1.3 80.5 - - - +
510A THR* 1.3 59.9 + - - +
512A GLY* 3.4 2.6 + - - -
513A LEU* 3.1 24.3 + - - +
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Residues in contact with THR 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465A ILE* 4.1 19.0 - - + +
494A VAL* 3.2 39.5 - - + +
497A LEU* 4.3 16.3 - - + +
498A LEU* 4.2 17.7 - - + -
506A LEU* 3.1 22.0 + - - +
507A ILE* 3.5 6.1 + - - -
508A LYS 3.3 0.2 - - - -
509A ALA* 1.3 73.1 - - - +
511A VAL* 1.3 66.1 + - - +
512A GLY 3.1 2.0 - - - -
513A LEU* 3.3 2.5 + - + +
514A ILE* 3.1 25.7 + - + +
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Residues in contact with VAL 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A LEU* 4.0 17.5 - - + -
507A ILE* 3.4 20.2 + - + +
508A LYS* 3.9 9.4 - - - +
509A ALA 3.4 0.2 - - - -
510A THR* 1.3 77.9 - - - +
512A GLY* 1.3 62.4 + - - +
514A ILE* 3.5 8.6 + - - +
515A ARG* 3.2 21.1 + - - +
536A LEU* 4.3 14.6 - - + -
539A LEU* 4.9 2.0 - - + -
569A ILE* 6.1 3.8 - - + -
572A GLY* 3.8 35.0 - - - +
573A CYS* 4.0 16.2 - - - +
576A ALA* 4.7 7.8 - - + +
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Residues in contact with GLY 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469A ARG* 3.8 32.0 + - - -
508A LYS 3.5 5.3 + - - -
509A ALA 3.4 5.0 + - - -
510A THR 3.1 0.8 - - - -
511A VAL* 1.3 79.7 - - - +
513A LEU* 1.3 62.5 + - - +
515A ARG* 3.5 12.6 + - - +
516A ASN* 3.2 21.0 + - - -
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Residues in contact with LEU 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A ILE* 3.9 33.4 - - + +
468A LEU* 4.2 23.8 - - + +
469A ARG* 4.2 20.8 - - + +
472A THR* 4.1 17.9 - - + +
485A VAL* 5.9 2.5 - - + -
494A VAL* 4.3 19.7 - - + -
509A ALA 3.1 13.4 + - - +
510A THR 3.6 8.3 - - - +
512A GLY* 1.3 75.2 - - - +
514A ILE* 1.3 64.2 + - - +
516A ASN* 3.3 5.4 + - - +
517A LEU* 3.2 43.3 + - + +
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Residues in contact with ILE 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494A VAL* 4.1 21.8 - - + -
495A VAL* 4.5 12.6 - - + -
498A LEU* 3.8 32.3 - - + -
510A THR* 3.1 18.4 + - + +
511A VAL* 3.8 8.1 - - - +
512A GLY 3.3 0.2 - - - -
513A LEU* 1.3 74.2 - - - +
515A ARG* 1.3 65.1 + - - +
517A LEU* 3.4 10.7 + - + +
518A ALA* 3.3 22.2 + - + +
527A LEU* 4.6 19.6 - - + +
532A ALA* 5.0 7.6 - - + -
536A LEU* 4.8 19.3 - - + -
576A ALA* 5.1 5.6 - - + -
580A LEU* 5.6 6.3 - - + -
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Residues in contact with ARG 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511A VAL 3.2 14.1 + - - +
512A GLY* 3.9 10.5 - - - +
513A LEU 3.3 0.4 - - - -
514A ILE* 1.3 77.6 - - - +
516A ASN* 1.3 69.6 + - - +
518A ALA* 3.4 16.4 + - - +
519A LEU* 4.0 8.7 + - + +
571A GLU* 3.7 24.5 + - - -
572A GLY* 4.2 11.0 + - - +
575A GLY* 3.5 43.7 + - - +
576A ALA* 4.8 11.4 - - - +
579A ILE* 4.4 16.1 - - + +
612A ARG* 4.8 8.5 - - - +
613A VAL* 4.6 11.9 - - - +
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Residues in contact with ASN 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469A ARG* 3.5 32.7 + - - +
472A THR* 3.6 30.4 + - - +
473A SER* 4.5 8.5 + - - -
482A GLN* 3.6 11.1 - - - +
512A GLY 3.2 17.8 + - - -
513A LEU 3.3 5.8 + - - +
514A ILE 3.3 0.4 - - - -
515A ARG* 1.3 84.2 - - - +
517A LEU* 1.3 62.3 + - - +
519A LEU* 3.0 33.7 + - + +
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Residues in contact with LEU 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472A THR* 4.5 5.2 - - + -
482A GLN* 4.2 20.6 - - - +
485A VAL* 4.1 35.0 - - + -
491A LEU* 4.4 21.1 - - + -
494A VAL* 4.7 12.1 - - + -
513A LEU* 3.2 42.5 + - + +
514A ILE* 3.7 11.7 - - + +
515A ARG 3.4 0.2 - - - -
516A ASN* 1.3 78.9 - - - +
518A ALA* 1.3 60.1 + - - +
519A LEU 3.2 2.0 + - - -
520A CYS* 3.6 3.5 + - - +
523A ASN* 3.0 34.3 + - - +
527A LEU* 4.6 12.1 - - + -
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Residues in contact with ALA 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514A ILE* 3.3 10.1 + - + +
515A ARG* 3.6 11.9 - - - +
516A ASN 3.1 1.4 - - - -
517A LEU* 1.3 73.6 - - - +
519A LEU* 1.3 56.9 + - - +
520A CYS 3.1 7.2 - - - -
523A ASN* 5.0 1.3 - - - -
524A HIS* 3.2 29.3 - - - +
527A LEU* 4.5 8.9 - - + +
576A ALA 5.3 1.6 - - - +
579A ILE* 3.7 23.4 - - + +
580A LEU* 4.2 26.7 - - + +
582A ARG* 5.6 0.2 - - - -
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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