Contacts of the helix formed by residues 115 - 127 (chain C) in PDB entry 1M6X
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 115 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LYS* 3.6 30.6 + - - +
114C SER* 1.3 80.8 - - - +
116C ILE* 1.3 68.0 + - - +
117C THR* 2.5 31.9 + - - +
118C ASP* 3.0 29.2 + - - +
119C ILE* 2.9 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 4.7 10.1 - - + -
44A MET* 6.6 0.4 - - + -
45A ILE* 3.7 22.4 - - + -
92A SER* 2.9 54.3 - - - +
93A LEU* 3.8 4.3 - - + +
95A LYS* 5.3 4.9 - - + +
96A LEU* 4.4 32.5 - - + +
114C SER 4.3 0.2 - - - -
115C ASP* 1.3 72.2 + - - +
117C THR* 1.3 54.6 + - + +
119C ILE* 2.7 18.0 + - + +
120C VAL* 2.6 52.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 6.2 0.9 - - + -
96A LEU* 4.4 20.2 - - + -
115C ASP* 2.5 22.5 + - - +
116C ILE* 1.3 77.4 - - + +
118C ASP* 1.3 63.8 + - - +
120C VAL* 3.8 8.4 - - - +
121C SER* 2.9 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C SER* 6.1 0.7 - - - -
115C ASP* 3.2 29.1 + - + +
116C ILE 2.9 0.4 - - - -
117C THR* 1.3 83.8 + - - +
119C ILE* 1.3 69.8 + - + +
121C SER* 2.6 22.3 + - - -
122C SER* 2.8 13.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A MET* 3.9 24.5 - - + +
45A ILE* 4.1 18.6 - - + +
48A ASN* 3.9 21.8 - - - +
49A GLY* 3.4 30.5 - - - +
114C SER* 4.1 12.3 - - - -
115C ASP 3.1 22.2 - - - +
116C ILE* 2.7 16.2 + - + +
118C ASP* 1.3 71.8 - - + +
120C VAL* 1.3 58.0 + - + +
122C SER* 3.1 10.1 - - - -
123C LEU* 2.8 39.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PRO* 4.0 4.9 - - + -
13A LYS* 3.9 23.8 - - + +
16A VAL* 3.3 36.3 - - + -
40A TYR* 6.3 2.2 - - + -
41A LEU* 5.3 2.7 - - + -
44A MET* 6.5 0.7 - - + -
116C ILE* 2.6 45.7 + - + +
117C THR* 3.8 7.4 - - - +
119C ILE* 1.3 72.1 - - + +
121C SER* 1.3 52.5 + - - +
123C LEU* 2.6 35.6 + - + +
124C GLN* 2.6 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C THR 2.9 13.4 + - - -
118C ASP* 2.6 24.4 + - - -
120C VAL* 1.3 78.2 - - - +
122C SER* 1.3 53.6 + - - +
124C GLN* 3.1 11.3 + - - +
125C LEU* 2.7 35.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
118C ASP 2.8 14.3 + - - -
119C ILE* 3.1 13.9 - - - -
121C SER* 1.3 76.5 + - - +
123C LEU* 1.3 59.1 + - - +
125C LEU* 3.1 14.3 - - - +
126C GLN* 3.0 42.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PRO* 3.5 13.4 - - + +
40A TYR* 3.2 25.6 - - + +
44A MET* 3.7 26.2 - - + -
49A GLY* 3.3 32.5 - - - +
119C ILE* 2.8 25.6 + - + +
120C VAL* 2.6 17.8 + - + +
122C SER* 1.3 68.6 - - - +
124C GLN* 1.3 53.3 + - - +
125C LEU 2.9 5.1 + - - -
126C GLN* 3.0 25.5 + - - +
127C PHE* 2.7 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PRO* 3.5 5.8 - - - +
12A PRO* 3.4 24.6 - - + +
13A LYS* 2.9 61.7 + - + +
120C VAL 2.6 15.4 + - - +
121C SER* 3.4 14.8 - - - +
123C LEU* 1.3 70.8 - - - +
125C LEU* 1.3 58.4 + - - +
127C PHE* 3.7 11.8 - - - +
128C GLU* 3.0 39.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
121C SER 2.7 12.9 + - - +
122C SER* 3.1 16.4 - - - +
124C GLN* 1.3 75.8 - - - +
126C GLN* 1.3 67.5 + - + +
128C GLU* 3.0 31.6 + - - +
129C SER* 3.6 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLY* 4.8 5.5 + - - +
263A GLY 6.2 0.2 - - - +
264A ASN 5.2 4.9 - - - +
122C SER* 3.0 30.1 + - - +
123C LEU* 3.3 33.6 - - - +
125C LEU* 1.3 75.5 - - + +
127C PHE* 1.3 64.3 + - - +
128C GLU 2.9 1.6 + - - -
129C SER* 3.1 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A CYS 4.0 15.5 - - - -
9A LYS* 3.8 11.9 - - - -
10A THR 3.8 14.1 - - - -
11A PRO* 3.5 35.4 - - + -
12A PRO* 3.5 21.5 - - + -
264A ASN* 4.2 21.1 - - + +
123C LEU 2.7 21.0 + - - +
124C GLN* 3.7 14.4 - - - +
126C GLN* 1.3 72.8 - - - +
128C GLU* 1.3 61.9 + - + +
129C SER 4.5 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