Contacts of the helix formed by residues 442 - 455 (chain A) in PDB entry 1JPW
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 442 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406A VAL* 4.2 4.0 - - - -
439A CYS 4.0 3.4 + - - -
440A GLN 3.3 7.3 + - - -
441A VAL* 1.3 76.9 - - - +
443A GLY* 1.3 64.7 + - - +
444A ILE 3.4 2.4 + - - -
445A GLU* 3.6 9.7 + - - +
446A ALA* 3.2 22.9 + - - +
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Residues in contact with GLY 443 (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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406A VAL* 4.2 12.2 - - - +
409A LEU* 6.1 0.2 - - - -
438A VAL* 2.9 36.8 + - - -
439A CYS 4.4 1.6 + - - -
441A VAL 3.4 1.6 + - - -
442A GLY* 1.3 76.2 - - - +
444A ILE* 1.3 56.3 + - - +
446A ALA* 3.4 2.0 + - - +
447A LEU* 2.9 40.2 + - - +
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Residues in contact with ILE 444 (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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438A VAL* 4.6 0.8 + - - +
439A CYS* 4.6 18.1 + - + +
442A GLY 3.5 0.8 - - - -
443A GLY* 1.3 69.6 - - - +
445A GLU* 1.3 68.9 + - - +
447A LEU* 3.1 2.6 + - - +
448A VAL* 2.8 29.0 + - + +
468A LEU* 4.0 16.1 - - + +
471A LEU* 4.4 18.6 - - + -
472A THR* 5.1 2.2 - - + -
481A ALA* 4.3 19.3 - - + -
484A ALA* 4.1 17.5 - - + +
485A VAL* 3.5 49.1 - - + +
488A HIS* 4.3 8.1 - - + +
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Residues in contact with GLU 445 (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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442A GLY* 3.6 9.6 + - - +
443A GLY 3.6 0.2 - - - -
444A ILE* 1.3 78.7 - - - +
446A ALA* 1.3 56.9 + - - +
448A VAL* 3.4 3.8 + - - +
449A ARG* 2.9 47.2 + - + +
488A HIS* 3.8 48.1 + - + +
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Residues in contact with ALA 446 (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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406A VAL* 4.2 14.8 - - + +
409A LEU* 3.5 20.0 - - + +
442A GLY 3.2 17.4 + - - +
443A GLY 3.7 3.4 - - - +
444A ILE 3.1 0.4 - - - -
445A GLU* 1.3 79.1 - - - +
447A LEU* 1.3 57.9 + - - +
449A ARG* 3.5 25.0 + - - +
450A THR* 2.6 34.0 + - - -
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Residues in contact with LEU 447 (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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409A LEU* 3.9 21.3 - - + -
421A ALA* 5.3 2.2 - - - -
424A LEU* 4.6 14.4 - - + -
438A VAL* 4.3 5.4 - - + -
443A GLY* 2.9 23.0 + - - +
446A ALA* 1.3 74.8 - - - +
448A VAL* 1.3 59.2 + - - +
450A THR* 2.9 23.6 + - - -
451A VAL* 3.1 13.2 + - - +
464A ALA* 4.2 18.0 - - + +
467A ALA* 3.9 25.1 - - + -
468A LEU* 3.5 25.6 - - + -
471A LEU* 3.5 32.8 - - + -
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Residues in contact with VAL 448 (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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444A ILE* 2.8 27.2 + - + +
445A GLU* 3.6 7.2 - - - +
447A LEU* 1.3 76.3 - - - +
449A ARG* 1.3 64.0 + - - +
451A VAL* 3.2 19.1 + - - +
452A LEU* 3.2 23.2 + - + +
468A LEU* 4.1 12.3 - - + -
485A VAL* 3.9 28.9 - - + +
488A HIS* 3.8 16.4 - - + +
489A TYR 4.1 3.6 - - - +
490A GLY* 3.7 23.6 - - - +
493A VAL* 5.0 2.5 - - + -
494A VAL* 6.1 0.4 - - + -
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Residues in contact with ARG 449 (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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406A VAL 5.5 0.6 + - - -
409A LEU 4.5 3.0 + - - -
410A GLY* 3.8 32.5 - - - +
445A GLU* 2.9 31.1 + - - +
446A ALA* 3.7 26.0 + - - +
448A VAL* 1.3 77.7 - - - +
450A THR* 1.3 58.9 + - - +
452A LEU* 3.7 10.4 - - + +
453A ARG* 3.0 46.5 + - + +
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Residues in contact with THR 450 (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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409A LEU* 3.6 28.0 + - + +
417A VAL* 3.8 17.2 - - + +
421A ALA* 4.9 0.4 - - + -
446A ALA 2.6 19.2 + - - -
447A LEU* 2.9 14.2 + - - -
449A ARG* 1.3 79.1 + - - +
451A VAL* 1.3 61.8 + - - +
453A ARG* 3.9 7.7 - - - +
454A ALA* 3.0 22.7 + - - +
460A ILE* 3.5 27.8 - - + -
464A ALA* 4.4 11.4 - - + -
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Residues in contact with VAL 451 (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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447A LEU 3.1 13.8 + - - +
448A VAL* 3.2 10.5 + - - +
450A THR* 1.3 72.7 - - - +
452A LEU* 1.3 67.7 + - - +
454A ALA* 3.1 11.8 + - - +
455A GLY* 3.2 10.8 + - - +
461A THR* 3.9 18.2 - - + +
464A ALA* 4.4 12.1 - - + -
465A ILE* 4.1 25.1 - - + -
468A LEU* 4.6 6.3 - - + -
493A VAL* 3.3 34.4 - - + +
494A VAL* 6.2 0.4 - - + -
497A LEU* 3.7 20.6 - - + -
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Residues in contact with LEU 452 (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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448A VAL* 3.2 23.5 + - + +
449A ARG* 3.7 13.2 - - + +
451A VAL* 1.3 82.1 - - - +
453A ARG* 1.3 63.9 + - - +
454A ALA 3.1 1.6 + - - -
455A GLY* 3.3 10.2 + - - -
489A TYR* 4.9 9.0 - - + +
492A PRO* 6.3 1.6 - - + -
493A VAL* 3.6 34.8 - - + -
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Residues in contact with ARG 453 (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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409A LEU 3.1 20.8 + - - -
410A GLY* 4.0 7.9 + - - -
411A SER 2.7 30.9 + - - -
412A ASP* 4.1 13.5 + - - +
414A ILE* 4.6 16.8 - - + +
417A VAL* 3.8 17.4 - - - +
449A ARG* 3.0 29.7 + - + +
450A THR* 3.9 7.4 - - - +
452A LEU* 1.3 78.9 - - - +
454A ALA* 1.3 60.0 + - - +
455A GLY* 3.7 0.3 + - - -
457A ARG* 4.7 5.0 + - - -
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Residues in contact with ALA 454 (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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450A THR 3.0 18.8 + - - +
451A VAL 3.5 4.9 - - - +
452A LEU 3.1 0.6 - - - -
453A ARG* 1.3 79.2 - - - +
455A GLY* 1.3 62.7 + - - +
457A ARG* 2.9 35.5 + - - +
460A ILE* 3.7 39.5 - - + -
461A THR* 3.9 11.9 - - + -
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Residues in contact with GLY 455 (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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451A VAL 3.2 9.3 + - - +
452A LEU 3.3 9.3 + - - -
453A ARG 3.5 0.6 + - - -
454A ALA* 1.3 75.6 - - - +
456A ASP* 1.3 60.0 + - - -
457A ARG* 3.6 3.0 + - - -
461A THR* 3.6 16.1 - - - +
497A LEU* 4.7 8.8 - - - +
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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