Contacts of the helix formed by residues 69 - 77 (chain C) in PDB entry 4JDL
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 PRO 69 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C HIS 4.2 2.9 - - - +
68C ALA* 1.3 92.4 - - + +
70C PRO* 1.3 77.0 - - + +
71C GLU* 3.4 3.4 - - + +
72C SER* 3.4 23.7 + - - +
73C VAL* 3.3 17.5 + - - +
160C GLU 5.4 3.6 - - - +
161C GLY* 4.5 5.6 - - - -
162C THR* 3.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C PRO* 1.3 84.4 - - + +
71C GLU* 1.3 66.3 + - + +
72C SER 3.1 1.6 - - - -
73C VAL* 2.9 3.2 + - + +
74C TRP* 2.7 31.5 + - - +
132C HIS* 3.8 7.0 - - + +
154C LEU* 2.9 29.6 - - + +
161C GLY 3.7 10.8 - - - +
162C THR* 2.5 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C PRO* 3.4 2.9 - - + +
70C PRO* 1.3 86.5 - - + +
72C SER* 1.3 57.8 + - - +
74C TRP* 3.8 6.0 - - + +
75C ALA* 3.1 24.6 + - - +
132C HIS* 3.6 25.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ALA* 4.8 0.9 - - - -
69C PRO* 3.4 34.7 + - - +
71C GLU* 1.3 79.1 - - - +
73C VAL* 1.3 58.0 + - - +
75C ALA* 3.2 19.5 - - - +
76C LEU* 4.1 6.1 - - - +
200C THR* 4.0 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ILE* 3.9 36.8 - - + -
68C ALA 4.2 2.5 - - - +
69C PRO 3.3 15.0 + - - +
70C PRO 2.9 7.5 + - - +
72C SER* 1.3 75.6 - - - +
74C TRP* 1.3 67.2 + - - +
75C ALA 3.1 1.1 - - - -
76C LEU* 3.0 15.3 + - + +
77C VAL* 2.9 31.2 + - + +
154C LEU* 4.1 14.6 - - + -
162C THR* 4.3 7.9 - - + -
164C VAL* 4.3 12.8 - - + -
196C LEU* 4.6 8.7 - - + -
200C THR* 4.3 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C PRO 2.7 11.0 + - - +
71C GLU* 3.9 6.3 - - + +
73C VAL* 1.3 69.9 - - - +
75C ALA* 1.3 68.9 + - - +
77C VAL* 2.7 30.5 + - + -
78C ARG* 3.0 63.4 + - + +
127C LEU* 4.2 11.7 - - + -
128C ASP 3.7 12.8 - - - -
129C GLU* 4.2 7.8 + - - +
132C HIS* 3.4 70.3 + + + +
133C VAL 3.6 13.2 - - - -
134C ILE* 3.4 40.4 - - + -
152C THR 5.3 0.7 - - - -
154C LEU* 4.0 6.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C GLU 3.1 11.9 + - - +
72C SER* 3.2 20.0 - - - +
74C TRP* 1.3 83.5 - - - +
76C LEU* 1.3 62.1 + - + +
78C ARG* 3.6 17.5 - - - +
79C ARG* 3.7 14.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C SER 4.1 14.6 - - - +
73C VAL* 3.0 9.4 + - + +
75C ALA* 1.3 75.7 - - + +
77C VAL* 1.3 58.7 + - - +
78C ARG 3.1 9.5 + - - -
79C ARG* 3.8 15.2 + - - +
84C LYS 5.4 3.3 - - - +
196C LEU* 4.8 22.1 - - + +
199C SER* 3.9 33.2 - - - +
200C THR* 4.3 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C VAL* 2.9 30.5 - - + +
74C TRP* 2.7 24.7 + - + +
76C LEU* 1.3 70.5 - - - +
78C ARG* 1.3 55.2 + - - +
79C ARG 3.8 0.2 - - - -
80C PHE 5.7 0.2 - - - -
134C ILE* 3.3 41.7 - - + +
152C THR* 4.1 20.2 - - + -
154C LEU* 4.5 9.2 - - + -
164C VAL* 6.0 0.7 - - + -
193C LEU* 5.9 0.7 - - + -
196C LEU* 3.7 29.8 - - + -
----------------------------------------------------------
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