Contacts of the helix formed by residues 469 - 480 (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 SER 469 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B GLU* 4.4 17.2 + - - -
445E ASP* 2.7 22.3 + - - -
467E GLY 3.9 0.2 - - - -
468E ASP* 1.3 82.5 - - - +
470E ASP* 1.3 66.1 + - - +
471E LEU* 3.5 11.8 + - - +
472E GLY 3.1 4.7 + - - -
492E PRO* 3.2 16.2 + - - +
493E PHE* 3.1 20.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 470 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B LEU* 5.0 5.2 - - + -
549B GLU* 5.6 0.2 + - - -
469E SER* 1.3 72.9 - - - +
471E LEU* 1.3 67.4 + - - +
472E GLY 2.9 0.7 + - - -
473E MET 2.9 3.1 + - - -
474E HIS* 2.9 23.0 + - - +
492E PRO 3.6 3.7 + - - +
493E PHE* 3.9 4.0 - - - -
494E GLY* 2.5 43.1 + - - +
495E ASP 4.3 1.9 + - - -
496E LYS* 2.9 42.7 + - + -
497E ALA* 3.5 27.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 471 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B LYS* 6.3 5.4 - - - +
525B LEU* 4.5 13.2 - - + +
528B GLN* 4.4 19.1 - - + +
445E ASP* 3.6 12.1 - - + +
449E GLU* 6.0 0.4 - - - +
469E SER* 3.5 15.4 + - - +
470E ASP* 1.3 75.5 - - - +
472E GLY* 1.3 63.7 + - - +
474E HIS* 3.0 15.2 + - + -
475E HIS* 3.0 54.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 472 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445E ASP* 3.8 15.7 + - - -
448E PHE* 3.3 38.7 - - - +
469E SER 3.1 9.8 + - - -
470E ASP 2.9 2.8 + - - -
471E LEU* 1.3 82.3 - - - +
473E MET* 1.3 61.1 + - - +
474E HIS 3.2 0.3 + - - -
475E HIS* 3.6 3.4 + - - +
476E VAL* 3.5 12.8 + - - +
493E PHE* 4.1 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 473 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470E ASP 2.9 5.6 + - - +
472E GLY* 1.3 73.7 - - - +
474E HIS* 1.3 66.6 + - - +
476E VAL* 3.1 6.8 + - - +
477E LEU* 3.1 38.7 + - + +
486E LEU* 4.7 6.7 - - + -
488E ILE* 4.0 18.8 - - + -
493E PHE* 3.7 31.2 - - + -
494E GLY 4.1 3.8 - - - +
497E ALA* 3.5 26.5 - - + -
498E LEU* 3.9 21.8 - - + +
511E LEU* 4.6 4.3 - - - -
513E MET* 3.5 42.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 474 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B LEU* 3.8 32.9 - - + +
528B GLN* 4.5 11.2 + - + +
529B LYS* 4.3 36.0 + - + -
470E ASP 2.9 11.8 + - - +
471E LEU* 3.3 17.9 - - + +
472E GLY 2.9 1.0 - - - -
473E MET* 1.3 81.9 - - - +
475E HIS* 1.4 62.6 + - - +
476E VAL 3.0 0.7 + - - -
477E LEU* 3.1 0.9 + - - +
478E SER* 2.8 46.1 + - - -
497E ALA* 3.9 8.2 - - + +
500E ALA* 5.1 1.3 - - + -
501E ASN* 3.0 37.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 475 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B GLN* 4.4 17.2 + - - -
445E ASP* 4.4 6.8 - - + +
448E PHE 3.5 17.5 - - - +
449E GLU* 3.3 48.1 + - + +
452E GLY* 3.3 15.0 - - - -
471E LEU* 3.0 58.7 + - + +
472E GLY* 4.0 2.9 - - - +
474E HIS* 1.4 76.2 - + - +
476E VAL* 1.3 57.8 + - - +
478E SER* 4.0 6.9 + - - -
479E GLY* 3.0 21.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 476 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448E PHE* 3.8 26.9 - - + +
451E ILE* 4.2 16.2 - - + -
452E GLY* 4.7 0.7 - - - -
461E LEU* 4.2 15.7 - - + -
472E GLY 3.5 13.4 + - - +
473E MET* 3.1 9.3 + - - +
474E HIS 3.0 1.6 + - - -
475E HIS* 1.3 77.2 - - - +
477E LEU* 1.3 67.3 + - - +
480E CYS* 3.1 45.7 + - - +
483E LEU* 4.1 18.6 - - + +
486E LEU* 4.1 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 477 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473E MET* 3.1 43.2 + - + +
476E VAL* 1.3 76.6 - - - +
478E SER* 1.3 60.8 + - - +
483E LEU* 4.0 12.1 - - + -
486E LEU* 3.9 21.8 - - + -
497E ALA 4.0 19.3 - - - +
498E LEU* 4.9 3.1 - - + +
501E ASN* 3.7 28.7 + - + +
504E LYS* 3.4 35.4 - - + +
505E LEU* 4.5 14.1 - - + -
508E MET* 4.2 16.8 - - + -
511E LEU* 4.9 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 478 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B LYS* 6.0 0.7 - - - -
474E HIS* 2.8 30.6 + - - -
475E HIS* 4.3 5.4 + - - -
477E LEU* 1.3 80.3 - - - +
479E GLY* 1.3 58.7 + - - +
480E CYS 3.6 0.2 - - - -
481E ASP* 5.0 3.6 - - - +
501E ASN* 3.5 19.1 - - - +
504E LYS* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 479 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452E GLY 3.1 23.5 - - - +
456E LYS* 2.6 30.4 + - - +
475E HIS 3.0 14.0 + - - -
478E SER* 1.3 78.8 + - - +
480E CYS* 1.3 59.5 + - - +
481E ASP* 2.9 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 480 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451E ILE* 3.9 26.9 - - - -
455E ALA 4.0 11.4 - - - +
458E MET* 3.7 29.4 - - + +
476E VAL* 3.1 30.4 + - - +
477E LEU 4.3 1.0 + - - -
478E SER 3.6 1.4 - - - -
479E GLY* 1.3 73.7 - - - +
481E ASP* 1.3 65.8 + - - +
482E SER 2.8 5.3 + - - -
483E LEU* 2.9 27.0 + - + +
504E LYS* 3.1 13.1 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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