Contacts of the helix formed by residues 502 - 508 (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 ALA 502 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498E LEU 3.2 8.5 + - - +
499E LEU* 3.3 14.8 + - + +
500E ALA 3.5 0.6 - - - -
501E ASN* 1.3 77.3 - - - +
503E SER* 1.3 61.4 + - - +
505E LEU* 2.6 40.1 + - - +
506E GLU 3.9 1.6 + - - -
526E LEU* 3.6 25.4 - - + -
529E LYS* 4.0 23.6 - - + -
530E MET* 4.1 9.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 503 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501E ASN 3.3 0.6 - - - -
502E ALA* 1.3 80.2 - - - +
504E LYS* 1.4 65.5 + - - +
505E LEU 2.9 1.4 + - - -
506E GLU* 3.4 23.5 + - - +
507E THR* 4.3 4.5 + - - +
529E LYS* 5.3 4.4 - - - +
530E MET* 4.3 17.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 504 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477E LEU* 3.4 37.4 + - + +
478E SER 6.0 0.2 - - - -
480E CYS 3.1 30.7 + - - -
481E ASP* 3.8 15.0 + - - +
483E LEU* 4.2 15.4 + - - +
501E ASN* 3.4 21.6 + - + +
502E ALA 3.1 1.2 + - - -
503E SER* 1.4 78.8 + - - +
505E LEU* 1.3 57.5 + - + +
507E THR* 2.8 51.5 + - + +
508E MET* 3.8 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 505 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477E LEU* 4.5 12.6 - - + -
498E LEU* 3.9 22.9 - - + +
501E ASN 3.8 8.7 - - - +
502E ALA* 2.6 33.5 + - - +
504E LYS* 1.3 71.9 - - - +
506E GLU* 1.4 53.3 - - - +
507E THR 3.2 0.2 - - - -
508E MET* 3.2 45.2 + - - +
510E SER* 5.9 0.7 - - - -
511E LEU* 3.8 33.9 - - + +
526E LEU* 4.0 18.4 - - + -
533E LEU* 3.9 17.6 - - + +
558E ILE* 4.3 13.0 - - + -
559E TYR* 5.8 0.3 - - - -
560E ARG* 4.5 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 506 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D TRP* 3.5 39.4 + - + -
502E ALA 3.9 1.2 + - - -
503E SER* 3.4 19.0 + - - +
505E LEU* 1.4 75.0 - - - +
507E THR* 1.3 59.3 + - + +
508E MET 3.5 0.7 - - - -
530E MET* 4.7 18.8 - - - +
532E LYS* 3.8 23.7 + - - +
533E LEU* 4.2 15.9 - - + +
560E ARG* 2.8 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 507 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481E ASP 5.7 0.2 + - - -
483E LEU 3.9 7.8 + - - +
484E ARG* 5.1 3.3 - - - +
503E SER 4.4 4.9 - - - +
504E LYS* 2.8 50.5 + - + +
506E GLU* 1.3 76.6 - - + +
508E MET* 1.3 58.3 + - - +
560E ARG* 3.2 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 508 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477E LEU* 4.2 7.0 - - + -
483E LEU* 3.2 49.1 - - + +
484E ARG* 3.5 7.9 - - - +
486E LEU* 3.6 18.8 - - + +
504E LYS* 3.8 27.8 - - + +
505E LEU* 3.2 33.0 + - + +
506E GLU 3.5 0.2 - - - -
507E THR* 1.3 84.3 - - - +
509E ARG* 1.3 65.1 + - - +
510E SER 3.6 25.8 - - - +
511E LEU* 4.6 0.9 - - + -
560E ARG* 3.2 23.2 + - - +
----------------------------------------------------------
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