Contacts of the helix formed by residues 58 - 63 (chain D) in PDB entry 6P19
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 CYS 58 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D PRO* 4.3 1.1 - - - -
52D GLU 3.4 16.2 - - - +
54D ASP* 3.0 26.2 - - - +
55D GLY* 3.3 29.7 + - - +
56D LEU 3.7 0.4 - - - -
57D PHE* 1.3 73.0 - - - +
59D ALA* 1.3 57.8 + - - +
60D ARG* 3.5 32.1 - - - -
61D ILE* 2.9 34.9 + - + +
62D PHE* 3.0 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D PRO* 4.1 17.5 - - + +
52D GLU 4.3 1.6 + - - -
57D PHE 3.2 5.6 + - - +
58D CYS* 1.3 72.4 - - - +
60D ARG* 1.3 58.6 + - - +
61D ILE 3.2 0.2 - - - -
62D PHE* 4.3 2.5 - - - +
63D GLY* 2.9 43.6 + - - +
64D PRO* 5.1 0.4 - - + -
65D VAL* 4.2 12.3 - - + -
71D LEU* 3.9 26.2 - - + -
90D VAL* 3.4 13.0 - - + +
98D ARG* 5.6 1.3 - - - +
101D ARG* 4.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D PHE 4.5 3.3 - - - +
52D GLU 5.4 0.9 - - - +
53D ARG* 3.2 62.2 - - + +
54D ASP* 2.4 40.6 + - - +
58D CYS* 3.2 12.1 - - - -
59D ALA* 1.3 77.2 - - + +
61D ILE* 1.3 63.9 + - + +
71D LEU* 5.5 3.4 - - + -
88D CYS 3.3 18.8 + - - +
89D GLY* 4.6 13.8 - - - +
90D VAL* 3.8 14.1 - - + +
91D GLU 5.8 0.2 + - - -
101D ARG* 4.1 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D PHE* 3.3 28.1 - - + +
36D GLY* 3.3 29.2 - - - +
37D GLU 3.4 28.7 - - - +
38D VAL* 3.9 10.1 - - + +
54D ASP* 4.5 8.1 - - - +
55D GLY 5.1 0.4 - - - +
58D CYS* 2.9 28.3 + - + +
60D ARG* 1.3 83.2 - - + +
62D PHE* 1.3 82.8 + - + +
63D GLY 3.4 0.9 - - - -
101D ARG* 2.8 22.1 + - - -
102D MET 4.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D VAL* 5.6 5.6 - - + -
55D GLY 4.8 3.6 - - - -
56D LEU* 4.0 20.6 - - - -
57D PHE 4.1 0.7 - - - -
58D CYS 3.0 25.0 + - - +
59D ALA* 4.0 0.4 - - - -
61D ILE* 1.3 97.4 - - + +
63D GLY* 1.3 62.0 + - - +
97D VAL 4.0 0.3 - - - +
98D ARG* 3.4 30.9 - - - +
101D ARG* 3.6 24.2 - - + +
102D MET* 3.5 5.2 - - - -
103D GLY* 3.4 35.4 - - - -
244D VAL* 4.1 14.8 - - + -
245D LEU 4.5 2.7 - - - -
247D PRO* 3.6 37.7 - - + -
250D ARG* 4.2 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D ALA* 2.9 31.9 + - - +
62D PHE* 1.3 78.8 - - - +
64D PRO* 1.3 77.9 - - - +
90D VAL* 5.3 1.6 - - - -
91D GLU 4.7 3.8 - - - -
97D VAL* 4.2 1.3 - - - -
98D ARG* 4.3 2.1 - - - -
101D ARG* 3.1 26.9 - - - +
----------------------------------------------------------
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