Contacts of the helix formed by residues 444 - 455 (chain E) in PDB entry 2P1N
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 444 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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419E PRO* 3.6 23.3 - - + -
421E ASP* 2.5 28.3 + - - +
442E LEU* 5.3 4.7 - - + -
443E LEU* 1.3 77.0 - - - +
445E ASP* 1.3 66.9 + - - +
446E LYS* 2.7 12.5 + - - +
447E VAL* 3.0 20.6 + - - +
448E PHE* 3.6 1.6 - - - -
467E GLY* 4.0 4.7 - - - -
468E ASP* 3.2 22.0 - - - +
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Residues in contact with ASP 445 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444E THR* 1.3 73.8 - - - +
446E LYS* 1.3 63.7 + - - +
448E PHE* 2.9 22.1 + - - +
449E GLU* 3.1 10.9 + - - +
467E GLY* 3.6 2.4 - - - -
468E ASP* 2.6 39.3 + - - +
469E SER* 2.7 37.3 + - - +
471E LEU* 3.6 15.8 - - + +
472E GLY* 3.8 15.0 + - - +
475E HIS* 4.4 4.1 - - + -
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Residues in contact with LYS 446 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421E ASP* 3.3 20.9 - - + +
444E THR* 2.7 11.1 + - - +
445E ASP* 1.3 74.4 - - - +
447E VAL* 1.3 65.0 + - - +
449E GLU* 2.9 51.8 + - - +
450E TYR* 3.1 49.5 + - + +
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Residues in contact with VAL 447 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421E ASP* 3.7 22.1 - - - +
424E PHE* 3.8 29.8 - - + -
425E GLY 4.3 2.9 - - - +
439E LEU* 3.8 16.8 - - + -
443E LEU* 3.8 23.3 - - + -
444E THR 3.0 16.3 + - - +
446E LYS* 1.3 79.9 - - - +
448E PHE* 1.3 74.7 + - + +
450E TYR* 3.2 9.8 + - - +
451E ILE* 2.7 40.1 + - + +
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Residues in contact with PHE 448 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439E LEU* 5.3 1.3 - - + -
444E THR 3.6 9.0 - - - -
445E ASP* 2.9 9.1 + - - +
447E VAL* 1.3 93.0 - - + +
449E GLU* 1.3 61.2 + - - +
451E ILE* 3.1 17.3 + - + +
452E GLY* 2.8 25.5 + - - -
461E LEU* 5.1 5.6 - - + -
463E VAL* 3.9 40.2 - - + -
466E ALA* 4.0 7.4 - - + -
467E GLY* 3.6 32.5 - - - -
472E GLY* 3.3 28.3 - - - +
473E MET* 5.4 0.2 - - - -
475E HIS* 3.5 8.7 - - - +
476E VAL* 3.8 22.0 - - + +
488E ILE* 6.3 0.2 - - + -
493E PHE* 3.9 20.0 - + - -
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Residues in contact with GLU 449 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445E ASP 3.1 6.7 + - - +
446E LYS* 2.9 49.0 + - - +
448E PHE* 1.3 78.6 - - - +
450E TYR* 1.3 61.7 + - + +
452E GLY* 3.3 2.1 + - - -
453E THR* 2.9 43.2 + - + +
471E LEU* 6.0 0.3 - - - +
475E HIS* 3.3 37.2 + - + +
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Residues in contact with TYR 450 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421E ASP* 3.3 25.7 - - + +
422E ILE* 3.9 19.6 - - + +
425E GLY* 3.3 33.9 - - - -
428E VAL* 3.6 5.3 - - + +
446E LYS* 3.1 56.4 + - + +
447E VAL* 3.4 7.4 - - - +
449E GLU* 1.3 77.6 - - + +
451E ILE* 1.3 70.2 + - + +
452E GLY 3.0 1.6 - - - -
453E THR* 4.6 2.2 - - + -
454E TYR* 2.9 48.3 + + + -
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Residues in contact with ILE 451 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424E PHE* 6.0 2.0 - - + +
428E VAL* 4.1 15.0 - - + -
437E LEU* 3.9 27.4 - - + -
439E LEU* 4.0 20.0 - - + -
447E VAL* 2.7 27.3 + - + +
448E PHE* 3.6 20.4 - - + +
450E TYR* 1.3 76.9 - - + +
452E GLY* 1.3 57.8 + - - +
455E ALA* 2.9 29.6 + - + +
458E MET* 3.7 30.3 - - + -
461E LEU* 4.1 15.3 - - + -
476E VAL* 4.2 5.6 - - + -
480E CYS* 3.9 11.1 - - - -
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Residues in contact with GLY 452 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448E PHE 2.8 12.9 + - - -
449E GLU 3.7 2.5 - - - -
450E TYR 3.0 0.4 - - - -
451E ILE* 1.3 78.9 - - - +
453E THR* 1.3 58.4 + - - +
456E LYS* 2.9 23.9 + - - +
475E HIS* 3.3 28.0 - - - -
479E GLY* 3.1 15.2 - - - +
480E CYS* 4.4 4.9 - - - -
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Residues in contact with THR 453 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449E GLU* 2.9 29.9 + - + +
450E TYR* 4.5 3.6 - - + -
452E GLY* 1.3 78.5 - - - +
454E TYR* 1.3 84.7 + - + +
456E LYS* 3.8 17.0 - - - +
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Residues in contact with TYR 454 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425E GLY 4.8 0.7 - - - -
428E VAL* 3.4 32.1 - - + +
429E GLU* 3.7 50.2 + - + -
432E LYS* 5.4 8.1 - - - +
450E TYR* 2.9 41.1 + + + -
453E THR* 1.3 92.9 - - + +
455E ALA* 1.3 59.3 + - - +
456E LYS* 3.1 13.0 + - - +
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Residues in contact with ALA 455 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428E VAL* 3.4 31.0 - - + +
432E LYS 6.2 0.2 - - - -
434E LEU* 5.6 3.6 - - + +
451E ILE* 2.9 18.0 + - + +
453E THR 3.8 0.4 - - - -
454E TYR* 1.3 76.9 - - - +
456E LYS* 1.3 57.7 + - - +
457E LYS 3.1 10.7 + - - -
458E MET* 3.2 39.1 + - + +
480E CYS* 4.0 14.0 - - - -
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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