Contacts of the helix formed by residues 441 - 448 (chain A) in PDB entry 2JB2
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 THR 441 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429A TRP* 4.1 14.6 - - + +
430A ALA 3.6 19.5 + - - +
431A GLY* 3.6 22.7 - - - +
432A SER* 3.8 14.6 - - - +
440A ALA* 1.3 77.4 - - - +
442A PRO* 1.3 75.5 - - + +
443A GLU* 3.7 11.4 + - - -
444A TYR* 3.3 22.8 + - - +
445A GLU* 3.1 22.0 + - - +
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Residues in contact with PRO 442 (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 ALA 4.5 0.9 - - - +
441A THR* 1.3 89.8 - - + +
443A GLU* 1.3 69.4 + - - +
445A GLU* 3.4 15.3 + - - +
446A LYS* 2.9 30.0 + - - +
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Residues in contact with GLU 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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311A THR* 4.9 5.9 - - + +
312A ALA* 3.7 26.4 - - + +
315A ALA* 3.5 32.8 - - + +
429A TRP* 4.0 5.8 - - + -
430A ALA 4.2 7.9 - - - +
441A THR* 3.2 10.1 + - - -
442A PRO* 1.3 95.4 - - - +
444A TYR* 1.3 64.6 + - - +
446A LYS* 3.4 2.8 + - - +
447A LEU* 3.2 29.3 + - - +
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Residues in contact with TYR 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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429A TRP* 3.7 31.4 - + + -
440A ALA* 3.6 25.6 - - + -
441A THR* 3.3 22.9 + - - +
443A GLU* 1.3 74.9 - - - +
445A GLU* 1.3 69.5 + - - +
447A LEU* 3.1 12.8 + - - +
448A LEU* 3.4 21.8 + - + +
460A HIS 3.3 26.9 - - - -
461A LEU* 3.7 9.7 - - + +
462A SER* 3.2 39.9 - - - -
463A ASN* 3.7 7.0 + - - -
465A ILE* 5.4 0.2 - - + -
196B GLY* 2.7 37.4 + - - -
197B LEU* 4.4 0.4 - - + -
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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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440A ALA* 4.0 23.3 - - + +
441A THR 3.1 12.8 + - - +
442A PRO* 3.6 19.8 - - - +
444A TYR* 1.3 76.0 - - - +
446A LYS* 1.3 64.3 + - - +
448A LEU* 3.2 27.0 + - + +
449A GLU* 4.0 8.7 + - - +
197B LEU* 4.0 23.4 - - + +
199B PHE* 6.0 0.2 - - - -
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Residues in contact with LYS 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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308A ASP* 3.2 39.0 + - + +
309A VAL* 4.1 18.0 - - + +
312A ALA* 4.3 14.8 - - + -
442A PRO 2.9 17.6 + - - +
443A GLU* 3.6 9.0 - - - +
444A TYR 3.3 0.2 - - - -
445A GLU* 1.3 75.9 - - - +
447A LEU* 1.3 58.5 + - + +
449A GLU* 3.1 38.4 + - + +
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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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295A PRO* 5.8 0.2 - - + -
309A VAL* 3.9 23.1 - - + +
312A ALA* 3.6 31.6 - - + +
313A LEU* 3.7 21.5 - - + +
429A TRP* 3.7 17.9 - - + -
443A GLU 3.2 17.2 + - - +
444A TYR 3.1 7.5 + - - +
446A LYS* 1.3 74.6 - - - +
448A LEU* 1.3 63.9 + - - +
449A GLU 3.3 4.0 + - - +
456A PHE* 3.8 52.9 + - + +
460A HIS* 5.9 1.1 - - + -
461A LEU* 3.9 17.9 - - + +
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Residues in contact with LEU 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 TYR* 3.4 20.6 - - + +
445A GLU* 3.2 13.3 + - - +
447A LEU* 1.3 75.5 - - - +
449A GLU* 1.3 66.2 + - - +
450A PRO* 3.8 3.8 - - - +
455A TYR* 5.5 4.0 - - - -
456A PHE 5.8 1.1 - - - -
461A LEU* 4.1 28.0 - - + +
478A VAL* 6.2 0.2 - - - +
481A HIS* 5.1 11.8 + - + -
196B GLY* 3.6 35.9 - - - -
197B LEU* 3.6 32.5 - - + -
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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