Contacts of the helix formed by residues 59 - 67 (chain W) in PDB entry 5JPQ
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 59 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54W TRP* 5.9 2.0 - - - -
55W ASN 3.1 12.8 + - - -
56W ALA 3.3 7.5 - - - +
58W ARG* 1.3 80.2 - - - +
60W LYS* 1.3 64.7 + - - +
61W LEU* 3.1 2.0 - - - -
62W ALA* 3.0 23.6 + - - +
63W GLY 3.0 9.7 + - - -
89W THR* 5.3 2.5 - - - -
90W THR* 4.3 28.7 - - - +
93W HIS* 5.9 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56W ALA 5.0 1.1 - - - -
58W ARG 3.8 4.8 + - - -
59W SER* 1.3 71.2 - - - +
61W LEU* 1.3 58.4 + - - +
63W GLY* 3.7 3.2 - - - +
64W ALA* 2.9 28.2 + - - +
90W THR* 5.2 3.4 - - - -
153W ASP* 6.1 3.8 - - + -
180W VAL* 5.5 11.4 - - + -
220W ASP* 6.0 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59W SER* 3.1 4.1 - - - -
60W LYS* 1.3 77.8 - - - +
62W ALA* 1.3 64.4 + - - +
64W ALA* 3.2 8.2 + - - +
65W ILE* 3.0 21.1 + - - +
90W THR* 5.3 9.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27W LEU* 5.2 7.0 - - + -
54W TRP* 4.0 22.7 - - + +
56W ALA* 3.9 19.4 - - + +
59W SER* 3.0 19.1 + - - +
61W LEU* 1.3 73.9 - - - +
63W GLY* 1.3 65.9 + - - +
65W ILE* 3.1 9.1 + - - +
66W LEU* 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 63 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56W ALA* 4.1 17.6 - - - +
59W SER 3.0 13.0 + - - -
60W LYS* 3.7 4.5 - - - -
61W LEU 3.2 0.4 - - - -
62W ALA* 1.3 76.4 - - - +
64W ALA* 1.3 61.4 + - - +
66W LEU* 3.3 5.9 + - - +
67W LYS* 3.1 23.6 + - - +
216W LEU* 5.7 8.9 - - - -
219W TYR* 4.6 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 64 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60W LYS 2.9 18.0 + - - +
61W LEU* 3.5 8.3 - - - +
63W GLY* 1.3 74.4 - - - +
65W ILE* 1.3 65.4 + - - +
67W LYS* 3.2 14.7 + - - +
68W GLY 3.4 0.9 + - - -
69W LEU* 3.3 25.6 + - + +
214W ILE* 5.2 11.2 - - + +
216W LEU* 5.8 3.9 - - - +
225W ILE* 4.9 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 65 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61W LEU 3.0 12.4 + - - +
62W ALA* 3.1 12.3 + - - +
64W ALA* 1.3 75.9 - - - +
66W LEU* 1.3 53.8 + - - +
68W GLY* 2.8 27.5 + - - -
69W LEU* 3.5 12.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56W ALA* 5.2 8.1 - - + -
62W ALA 3.0 15.2 + - - +
63W GLY* 3.3 6.9 + - - +
65W ILE* 1.3 75.2 - - - +
67W LYS* 1.3 56.2 + - - +
68W GLY 3.3 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 67 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63W GLY 3.1 14.9 + - - +
64W ALA* 3.2 10.1 + - - +
65W ILE 3.0 1.6 + - - -
66W LEU* 1.3 75.2 - - - +
68W GLY* 1.3 61.5 + - - +
214W ILE* 4.9 14.6 - - + +
215W ASN 4.5 16.6 - - - +
216W LEU* 5.6 2.7 - - - -
217W ASP 5.8 2.5 - - - +
----------------------------------------------------------
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