Contacts of the helix formed by residues 420 - 431 (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 LEU 420 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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384E MET* 4.2 10.8 - - + +
385E THR* 4.0 8.3 - - - -
386E ASN* 3.0 33.6 - - - +
389E LEU* 4.2 4.3 - - + -
406E ILE* 3.3 34.3 - - + -
411E ALA 4.6 4.3 - - - +
412E PRO 5.3 0.4 - - - -
413E ASP* 4.0 25.8 - - + +
419E PRO* 1.3 68.3 - - - +
421E ASP* 1.3 63.3 + - - +
422E ILE 3.3 2.9 - - - -
423E GLY* 3.1 10.0 + - - -
424E PHE* 3.1 28.0 + - + -
440E SER 3.7 11.0 - - - +
441E GLY* 4.2 3.4 - - - -
442E LEU 3.0 15.3 + - - +
443E LEU* 3.9 10.1 - - + -
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Residues in contact with ASP 421 (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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419E PRO* 3.1 13.3 - - + +
420E LEU* 1.3 76.0 - - - +
422E ILE* 1.3 54.9 + - + +
425E GLY 2.7 30.1 + - - -
443E LEU* 3.3 9.4 - - - +
444E THR* 2.5 53.7 + - - +
446E LYS* 3.3 17.1 - - + +
447E VAL* 3.7 24.2 - - - +
450E TYR* 3.3 14.3 - - + +
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Residues in contact with ILE 422 (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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386E ASN* 3.3 39.5 - - + +
390E ILE* 4.3 14.7 - - + +
418E GLU* 5.8 2.9 - - - +
419E PRO 4.7 1.3 - - - +
421E ASP* 1.3 79.2 - - + +
423E GLY* 1.3 56.0 + - - +
425E GLY* 3.5 1.0 - - - -
426E ALA* 2.9 29.3 + - - +
450E TYR* 3.9 23.3 - - + +
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Residues in contact with GLY 423 (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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386E ASN* 3.1 26.1 + - - -
389E LEU* 3.2 36.2 - - - +
390E ILE* 4.5 3.4 - - - -
420E LEU 3.1 4.5 + - - -
422E ILE* 1.3 77.5 - - - +
424E PHE* 1.3 61.7 + - - +
426E ALA* 3.3 10.0 + - - +
427E ILE* 3.5 9.2 + - - +
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Residues in contact with PHE 424 (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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389E LEU* 4.0 12.1 - - + -
402E PHE* 4.1 23.1 - + - -
404E LEU* 3.5 28.0 - - + -
420E LEU* 3.1 35.5 + - + +
423E GLY* 1.3 73.2 - - - +
425E GLY* 1.3 69.9 + - - +
426E ALA 2.9 2.1 + - - -
427E ILE* 2.9 19.5 + - + +
428E VAL* 3.2 13.6 + - - +
437E LEU* 4.4 14.0 - - + +
438E SER 4.5 1.1 - - - -
439E LEU* 3.4 36.1 - - + -
440E SER 3.3 24.2 - - - -
443E LEU* 3.8 12.3 - - + -
447E VAL* 3.8 17.7 - - + -
451E ILE* 5.9 2.0 - - + -
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Residues in contact with GLY 425 (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 2.7 13.1 + - - -
422E ILE 3.5 2.9 - - - -
424E PHE* 1.3 79.3 - - - +
426E ALA* 1.3 60.4 + - - -
428E VAL* 3.4 4.8 + - - +
429E GLU* 3.0 25.4 + - - +
447E VAL* 4.3 1.8 - - - +
450E TYR* 3.3 38.6 - - - +
451E ILE* 6.4 0.2 - - - -
454E TYR* 4.8 1.4 - - - -
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Residues in contact with ALA 426 (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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390E ILE* 3.7 33.4 - - + -
393E ALA* 3.7 4.9 - - + -
394E ARG* 6.2 0.7 - - - +
422E ILE 2.9 18.9 + - - +
423E GLY 3.6 7.0 - - - +
424E PHE 2.9 2.2 + - - -
425E GLY* 1.3 70.8 - - - +
427E ILE* 1.3 69.4 + - - +
429E GLU* 4.3 5.2 - - - -
430E HIS* 2.8 39.9 + - + +
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Residues in contact with ILE 427 (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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389E LEU* 3.3 42.4 - - + +
392E ILE* 5.1 3.1 - - + -
393E ALA* 3.8 19.1 - - + +
399E MET* 6.2 0.2 - - + -
402E PHE* 3.5 39.3 - - + -
423E GLY 3.5 11.5 + - - +
424E PHE* 2.9 11.5 + - + +
426E ALA* 1.3 79.9 - - - +
428E VAL* 1.3 57.6 + - + +
431E CYS* 3.0 40.8 + - - +
434E LEU* 3.9 21.3 - - + -
437E LEU* 4.5 7.6 - - + -
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Residues in contact with VAL 428 (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 3.2 9.3 + - - +
425E GLY 3.8 8.1 - - - +
426E ALA 3.0 0.6 - - - -
427E ILE* 1.3 76.6 - - + +
429E GLU* 1.3 69.4 + - - +
431E CYS 4.1 11.0 + - - +
432E LYS* 4.9 1.7 + - - +
434E LEU* 4.1 14.4 - - + -
437E LEU* 4.1 26.0 - - + -
450E TYR* 3.6 22.0 - - + +
451E ILE* 4.1 8.5 - - + +
454E TYR* 3.4 38.3 - - + +
455E ALA* 3.4 27.4 - - + +
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Residues in contact with GLU 429 (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 3.0 19.0 + - - +
426E ALA* 3.8 5.2 - - - +
428E VAL* 1.3 83.3 - - - +
430E HIS* 1.3 81.9 + - + +
432E LYS* 3.3 24.1 - - - +
454E TYR* 3.7 48.3 + - + -
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Residues in contact with HIS 430 (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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393E ALA* 3.6 26.9 - - + +
394E ARG* 3.5 49.9 + - + +
397E PRO* 3.5 20.8 - - + +
426E ALA* 2.8 32.7 + - + +
429E GLU* 1.3 104.4 + - + +
431E CYS* 1.3 56.6 + - - +
432E LYS* 3.4 15.5 + - - +
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Residues in contact with CYS 431 (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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393E ALA* 4.5 10.5 - - - -
396E ARG 3.6 21.5 - - - -
397E PRO* 3.6 10.1 - - - +
399E MET* 3.7 27.4 - - + +
427E ILE* 3.0 33.5 + - - +
428E VAL 4.1 7.1 - - - +
429E GLU 3.6 0.6 - - - -
430E HIS* 1.3 76.3 - - - +
432E LYS* 1.3 54.5 + - - +
433E ASP 3.0 6.1 - - - -
434E LEU* 2.8 32.1 + - + +
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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