Contacts of the helix formed by residues 532 - 546 (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 ALA 532 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495A VAL* 4.1 25.4 - - + -
498A LEU* 5.1 1.6 - - + -
514A ILE* 5.0 9.4 - - + -
527A LEU* 3.5 24.9 + - + +
528A ARG 4.1 0.6 + - - -
530A GLN 3.9 0.2 - - - -
531A GLY* 1.3 75.8 - - - +
533A ILE* 1.3 58.8 + - + +
534A PRO* 3.4 0.4 - - - +
535A ARG* 3.1 5.0 + - - +
536A LEU* 2.8 50.6 + - + +
580A LEU* 5.6 3.1 - - + -
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Residues in contact with ILE 533 (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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527A LEU 6.0 0.2 - - - -
528A ARG* 4.5 19.5 - - + +
532A ALA* 1.3 77.4 - - + +
534A PRO* 1.3 69.5 - - + +
536A LEU* 3.2 8.4 + - - +
537A VAL* 3.1 34.5 + - + +
577A LEU* 4.1 9.4 - - + -
580A LEU* 4.0 22.7 - - + -
586A ASN* 3.7 44.0 - - + +
589A VAL* 4.3 17.9 - - + -
590A ILE* 3.7 25.6 - - + -
593A LEU* 4.8 2.2 - - + -
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Residues in contact with PRO 534 (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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528A ARG 5.5 1.1 - - - +
531A GLY* 3.8 23.8 - - - +
532A ALA 3.5 1.1 - - - +
533A ILE* 1.3 95.4 - - + +
535A ARG* 1.3 58.5 + - + +
537A VAL* 4.0 2.4 + - - +
538A GLN* 3.5 21.3 + - - +
589A VAL* 5.3 7.0 - - + -
593A LEU* 4.6 17.7 - - + -
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Residues in contact with ARG 535 (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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495A VAL* 5.5 1.1 - - + +
498A LEU* 3.5 43.2 + - + -
499A HIS* 3.7 37.6 + - + +
500A PRO* 3.9 19.4 - - - +
507A ILE* 5.5 1.8 - - - +
531A GLY 4.2 10.1 - - - +
532A ALA* 3.1 9.2 + - - +
534A PRO* 1.3 78.8 - - + +
536A LEU* 1.3 67.0 + - - +
537A VAL 3.3 0.4 - - - -
538A GLN* 2.7 46.4 + - - +
539A LEU* 3.1 48.7 + - + +
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Residues in contact with LEU 536 (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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498A LEU* 4.5 17.7 - - + -
511A VAL* 4.3 24.9 - - + -
514A ILE* 4.8 13.2 - - + -
532A ALA* 2.8 28.4 + - + +
533A ILE* 3.2 4.9 + - - +
535A ARG* 1.3 75.0 - - - +
537A VAL* 1.3 64.6 + - - +
539A LEU* 3.4 9.1 + - + +
540A LEU* 3.3 17.5 + - - +
573A CYS* 3.8 20.6 - - - +
576A ALA* 4.0 28.0 - - + -
577A LEU* 4.4 15.9 - - + -
580A LEU* 4.3 20.4 - - + -
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Residues in contact with VAL 537 (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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533A ILE* 3.1 20.6 + - + +
534A PRO 4.2 4.0 - - - +
536A LEU* 1.3 76.6 - - - +
538A GLN* 1.3 64.0 + - - +
540A LEU* 3.0 27.3 + - + +
541A VAL* 3.3 16.0 + - + +
577A LEU* 4.3 24.7 - - + -
590A ILE* 5.5 2.2 - - + -
593A LEU* 4.2 23.3 - - + +
595A THR* 4.1 25.6 - - + -
598A LEU* 6.2 1.8 - - + -
599A PHE* 6.2 0.2 - - + -
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Residues in contact with GLN 538 (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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499A HIS* 5.9 0.3 - - - -
534A PRO 3.5 14.0 + - - +
535A ARG* 2.7 40.8 + - - +
536A LEU 3.3 0.4 - - - -
537A VAL* 1.3 81.4 - - - +
539A LEU* 1.3 62.7 + - - +
541A VAL* 3.5 18.8 + - + +
542A ARG* 3.7 7.8 + - - +
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Residues in contact with LEU 539 (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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498A LEU* 4.3 19.3 - - + +
504A TRP* 4.9 19.8 - - + -
507A ILE* 3.9 27.8 - - + -
511A VAL* 4.9 3.1 - - + -
535A ARG* 3.1 51.0 + - + +
536A LEU* 3.8 9.6 - - - +
537A VAL 3.2 0.4 - - - -
538A GLN* 1.3 76.6 - - - +
540A LEU* 1.3 65.9 + - - +
541A VAL 3.3 0.3 + - - -
542A ARG* 3.6 7.5 + - + +
543A ALA* 3.4 22.9 + - - +
569A ILE* 4.6 7.4 - - + +
573A CYS* 4.2 16.8 - - - -
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Residues in contact with LEU 540 (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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536A LEU 3.3 9.6 + - - +
537A VAL* 3.0 17.8 + - + +
539A LEU* 1.3 79.7 - - - +
541A VAL* 1.3 61.5 + - - +
543A ALA* 3.5 3.8 + - - +
544A HIS* 3.1 22.5 + - + +
569A ILE 5.3 0.7 - - - -
570A VAL* 3.7 42.6 - - + +
573A CYS* 4.1 14.3 - - + -
574A THR* 4.0 11.4 - - - +
577A LEU* 4.8 11.9 - - + -
598A LEU* 3.7 27.1 - - + -
599A PHE* 4.6 18.8 - - + -
602A LEU* 5.1 4.7 - - + -
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Residues in contact with VAL 541 (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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537A VAL* 3.5 22.2 - - + +
538A GLN* 3.7 9.6 - - - +
539A LEU 3.2 0.6 - - - -
540A LEU* 1.3 76.5 - - - +
542A ARG* 1.3 65.2 + - - +
543A ALA 3.0 1.6 + - - -
544A HIS* 3.1 21.8 + - - +
545A GLN* 3.8 21.3 + - - +
598A LEU* 4.6 16.8 - - + -
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Residues in contact with ARG 542 (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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504A TRP* 3.2 38.7 - - + +
538A GLN 3.7 7.6 + - - +
539A LEU* 3.6 10.3 + - + +
541A VAL* 1.3 79.8 - - - +
543A ALA* 1.3 58.6 + - - +
545A GLN* 4.3 7.3 + - - +
546A ASP* 3.5 38.5 + - - +
566A MET* 5.3 0.6 - - - -
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Residues in contact with ALA 543 (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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504A TRP* 5.3 3.8 - - + -
539A LEU 3.4 15.2 + - - +
540A LEU* 3.7 2.5 - - - +
541A VAL 3.0 0.8 - - - -
542A ARG* 1.3 79.0 - - - +
544A HIS* 1.3 66.9 + - - +
545A GLN 3.2 1.4 + - - -
546A ASP 3.7 7.4 + - - +
566A MET* 3.6 37.2 - - - +
569A ILE* 3.9 21.3 - - + -
570A VAL* 3.7 20.0 - - + +
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Residues in contact with HIS 544 (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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540A LEU* 3.1 13.1 + - + +
541A VAL* 3.1 14.1 + - - +
543A ALA* 1.3 77.8 - - - +
545A GLN* 1.3 72.3 + - + +
546A ASP 4.0 2.8 - - - +
570A VAL* 4.0 13.2 - - + +
598A LEU* 4.1 28.6 - - + +
601A GLN* 4.7 21.1 + - + -
602A LEU* 4.3 22.7 - - + +
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Residues in contact with GLN 545 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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541A VAL* 3.8 26.4 + - - +
542A ARG* 4.7 6.4 - - - +
543A ALA 3.2 0.6 - - - -
544A HIS* 1.3 86.3 - - + +
546A ASP* 1.3 73.8 + - - +
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Residues in contact with ASP 546 (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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542A ARG* 3.5 40.1 + - - +
543A ALA 3.7 8.2 + - - +
544A HIS 4.0 2.4 - - - +
545A GLN* 1.3 89.6 - - - +
561A VAL* 4.9 12.7 - - + +
566A MET* 3.6 34.8 - - + +
567A GLU* 5.6 1.4 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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