Contacts of the helix formed by residues 119 - 129 (chain C) in PDB entry 4I6N
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 ASP 119 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A MSE 5.5 0.2 + - - -
62A LYS 4.4 2.0 + - - -
64A VAL* 3.5 29.8 - - + +
179A ARG* 3.4 22.9 - - + +
180A ALA* 2.7 33.0 + - - +
181A ALA* 3.3 21.0 + - - +
118C LEU* 1.3 76.8 - - - +
120C SER* 1.3 60.7 + - - +
121C ALA* 3.0 19.7 + - - +
122C SER* 3.0 13.9 + - - +
123C ARG* 2.9 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ALA* 3.8 15.9 - - - +
76C PHE* 3.0 48.5 + - - +
78C GLN* 3.1 15.8 + - - -
118C LEU 3.7 1.2 + - - -
119C ASP* 1.3 76.1 + - - +
121C ALA* 1.3 61.4 + - - +
123C ARG* 3.4 12.9 + - - +
124C GLY 3.1 17.5 + - - -
180C ALA 4.0 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLN* 3.9 3.8 - - - +
178A LEU 3.9 14.6 - - - +
179A ARG* 4.6 0.4 - - - -
180A ALA* 3.9 2.4 - - - +
-2C LEU* 3.8 21.7 - - + +
78C GLN* 3.5 26.2 - - - +
80C VAL* 3.9 9.0 - - + +
119C ASP* 3.0 15.6 + - - +
120C SER* 1.3 76.2 - - - +
122C SER* 1.3 59.8 + - - +
124C GLY* 3.2 3.1 + - - -
125C LEU* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLU 5.0 0.3 + - - -
60A MSE 2.8 55.8 + - - +
118C LEU* 4.0 12.6 - - - -
119C ASP* 3.0 20.4 + - - +
121C ALA* 1.3 77.7 - - - +
123C ARG* 1.3 66.1 + - - +
125C LEU* 3.2 3.5 + - - +
126C CYS* 3.0 28.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL* 5.8 1.0 - - - +
74C VAL 4.5 5.1 + - - -
75C TYR* 3.7 30.3 - - - +
76C PHE* 2.7 51.0 + - - +
77C SER* 3.7 12.1 - - - -
111C PHE* 3.6 7.4 - - - -
115C THR* 2.9 39.8 + - - +
116C TYR* 2.9 23.6 + - - -
117C ASP* 4.8 0.8 - - - +
118C LEU* 3.1 20.0 + - + +
119C ASP 2.9 15.1 + - - +
120C SER* 3.6 16.2 + - - +
121C ALA 3.4 0.2 - - - -
122C SER* 1.3 76.6 - - - +
124C GLY* 1.3 58.3 + - - +
126C CYS* 3.2 4.7 + - - +
127C LEU* 2.9 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C SER* 3.8 0.6 - - - -
78C GLN 3.0 27.4 - - - -
80C VAL* 4.1 4.0 + - - -
88C GLN* 3.5 15.1 + - - -
120C SER 3.1 9.7 + - - -
121C ALA 3.2 2.0 + - - -
122C SER 3.2 0.4 - - - -
123C ARG* 1.3 77.7 - - - +
125C LEU* 1.3 59.1 + - - +
127C LEU* 3.3 2.8 + - - +
128C THR* 2.8 29.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A MSE 3.5 36.1 - - + -
-2C LEU* 3.8 19.5 - - + +
1C MSE 4.1 24.7 - - + +
2C ALA* 4.0 16.8 - - + -
80C VAL* 3.8 17.8 - - + +
121C ALA 3.0 13.0 + - - +
122C SER 3.2 7.6 + - - +
124C GLY* 1.3 72.6 - - - +
126C CYS* 1.3 67.0 + - - +
128C THR* 3.2 3.2 + - - -
129C ASN* 3.0 45.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A MSE 6.5 0.7 - - - -
111C PHE* 3.7 14.9 - - + -
114C PHE* 4.4 15.7 - - + -
115C THR* 3.9 18.8 - - + -
118C LEU* 4.1 13.0 - - - -
122C SER* 3.0 19.2 + - - -
123C ARG 3.2 7.6 + - - +
125C LEU* 1.3 78.3 - - - +
127C LEU* 1.3 61.3 + - - +
129C ASN* 3.3 5.8 + - - +
130C SER* 3.1 21.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C TRP* 3.5 28.4 - - + -
77C SER* 4.4 4.5 - - - +
84C ALA* 4.4 8.5 - - + -
88C GLN* 3.8 44.0 - - + +
91C ILE* 3.9 39.9 - - + -
111C PHE* 3.5 20.1 - - + -
123C ARG 2.9 9.5 + - - +
124C GLY 3.6 7.2 - - - +
125C LEU 3.3 0.2 - - - -
126C CYS* 1.3 76.5 - - - +
128C THR* 1.3 67.2 + - - +
130C SER* 3.2 17.7 + - - -
133C ILE* 4.3 12.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ALA* 3.8 28.9 - - + -
3C GLU* 4.0 9.2 - - - +
4C GLY 4.0 1.3 - - - +
6C TRP* 3.3 38.9 + - - +
80C VAL* 4.0 12.0 + - - +
81C ILE* 4.0 20.0 - - + +
84C ALA* 5.1 0.9 - - - +
88C GLN* 4.8 2.4 + - - -
124C GLY 2.8 22.2 + - - -
125C LEU* 3.6 8.7 - - - -
126C CYS 3.2 0.2 - - - -
127C LEU* 1.3 81.4 - - - +
129C ASN* 1.3 61.2 + - - +
130C SER 4.5 1.2 - - - +
134C ARG* 4.5 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MSE 3.4 18.3 + - - +
2C ALA* 3.5 1.9 - - - -
3C GLU* 2.6 36.8 + - - +
125C LEU* 3.0 31.9 + - - +
126C CYS* 3.6 6.0 - - - +
127C LEU 3.2 0.2 - - - -
128C THR* 1.3 77.3 - - - +
130C SER* 1.3 60.4 + - - +
131C GLU* 3.3 21.4 + - - +
----------------------------------------------------------
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