Contacts of the helix formed by residues 444 - 455 (chain A) in PDB entry 2JOA
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 SER 444 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389A SER* 3.2 25.4 - - - +
411A GLY 4.2 1.1 - - - -
412A ALA* 4.4 2.9 - - - -
443A VAL* 1.3 83.4 - - - +
445A ALA* 1.3 67.3 + - - +
446A ASN* 2.9 32.7 + - - -
447A ASP* 2.9 21.7 + - - +
448A VAL* 3.2 12.5 + - - +
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Residues in contact with ALA 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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387A MET* 3.2 41.5 - - - +
388A MET 3.5 25.2 + - - -
389A SER* 3.5 10.3 - - - +
412A ALA* 4.5 0.7 - - - -
444A SER* 1.3 73.9 - - - +
446A ASN* 1.3 64.0 + - - +
448A VAL* 2.9 14.5 + - - -
449A SER 2.9 11.8 + - - -
5B TRP* 3.7 17.0 - - + +
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Residues in contact with ASN 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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389A SER* 5.1 3.4 - - - -
444A SER* 2.9 21.9 + - - -
445A ALA* 1.3 78.0 - - - +
447A ASP* 1.3 92.4 + - - +
449A SER* 4.0 2.4 - - - -
450A ASP* 2.9 23.7 + - - +
3B ARG* 5.9 4.2 - - - +
5B TRP* 3.4 34.1 - - + -
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Residues in contact with ASP 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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441A SER 4.7 5.7 - - - +
442A VAL* 3.5 18.4 - - + -
443A VAL* 2.9 30.5 - - - +
444A SER* 2.9 13.0 + - - +
446A ASN* 1.3 95.0 + - - +
448A VAL* 1.3 51.5 + - - +
450A ASP* 2.5 25.5 - - - +
451A VAL* 2.7 27.9 - - + +
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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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383A ILE* 5.7 2.0 - - + -
387A MET* 3.7 13.0 - - + -
412A ALA* 3.3 27.8 - - + -
434A ILE* 4.9 15.3 - - + -
437A ILE* 5.1 11.4 - - + -
442A VAL* 3.1 27.4 - - + -
444A SER 3.4 4.7 - - - +
445A ALA* 2.9 7.5 + - - +
447A ASP* 1.3 75.2 - - - +
449A SER* 1.3 65.7 + - - +
451A VAL* 3.2 8.0 + - - +
452A ILE* 3.0 43.0 + - + +
460A MET* 6.0 2.7 - - - -
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Residues in contact with SER 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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380A LYS* 3.9 7.8 - - - -
387A MET* 3.9 5.1 - - - +
445A ALA 2.9 6.5 + - - -
446A ASN 4.0 1.8 - - - -
447A ASP 3.4 0.2 - - - -
448A VAL* 1.3 76.8 - - - +
450A ASP* 1.3 65.3 + - - +
452A ILE* 2.8 26.9 + - - +
453A LYS* 3.1 29.8 + - - +
5B TRP* 3.5 37.1 - - - -
7B VAL* 3.8 14.7 - - - +
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Residues in contact with ASP 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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440A GLN* 5.3 0.2 - - - +
446A ASN 2.9 16.5 + - - +
447A ASP* 2.5 29.5 - - - +
449A SER* 1.3 78.9 - - - +
451A VAL* 1.3 70.8 + - - +
453A LYS* 3.1 20.3 - - + +
454A ARG* 2.6 50.9 + - + +
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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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437A ILE* 3.0 43.5 - - + -
438A ASN* 3.3 18.2 - - - +
440A GLN* 3.4 17.3 - - + +
442A VAL* 4.9 3.8 - - + -
447A ASP* 2.7 28.3 - - + +
448A VAL* 3.3 9.9 - - - +
449A SER 3.0 0.6 - - - -
450A ASP* 1.3 86.8 + - - +
452A ILE* 1.3 59.5 + - - +
454A ARG* 4.1 4.7 - - - -
455A GLU* 2.6 34.8 + - + +
458A LEU* 3.9 0.6 - - + +
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Residues in contact with ILE 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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381A LYS* 3.2 24.9 - - + +
383A ILE* 3.7 27.1 - - + -
387A MET* 4.7 1.6 - - + -
437A ILE* 5.2 1.1 - - + -
448A VAL* 3.1 40.4 - - + +
449A SER* 2.8 6.1 + - - +
451A VAL* 1.3 77.3 - - + +
453A LYS* 1.3 57.0 + - - +
455A GLU 3.4 11.8 - - - +
458A LEU* 3.8 20.9 - - + -
475A PRO* 3.6 28.3 - - + +
7B VAL* 3.5 32.5 - - + -
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Residues in contact with LYS 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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379A MET* 5.6 4.4 - - + -
380A LYS* 3.4 58.8 - - - +
381A LYS* 3.9 13.4 - - - +
449A SER* 3.1 26.5 + - - +
450A ASP* 3.1 28.1 - - + +
452A ILE* 1.3 76.5 - - - +
454A ARG* 1.3 62.4 + - + +
455A GLU 5.0 0.4 - - - -
5B TRP* 5.8 2.0 - - - -
7B VAL* 6.3 0.4 - - - -
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Residues in contact with ARG 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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440A GLN* 4.1 17.9 - - - +
450A ASP* 2.6 31.9 + - + +
451A VAL* 3.9 4.5 - - - +
453A LYS* 1.3 76.6 - - + +
455A GLU* 1.3 79.8 + - + +
456A SER* 4.0 1.4 + - - -
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Residues in contact with GLU 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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381A LYS* 5.4 0.4 - - - -
438A ASN* 3.2 44.5 - - - +
440A GLN* 4.0 7.8 + - - +
451A VAL* 2.6 23.7 + - + +
452A ILE 3.4 10.3 - - - +
453A LYS 5.1 0.2 - - - -
454A ARG* 1.3 111.0 + - + +
456A SER* 1.3 61.4 + - - +
457A THR* 3.8 8.5 - - - +
458A LEU* 3.0 21.5 - - + +
475A PRO* 4.3 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
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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