Contacts of the helix formed by residues 149 - 161 (chain C) in PDB entry 3CQ6
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 149 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C SER 4.5 2.9 + - - +
142C ARG* 4.5 2.6 - - - +
143C GLY* 4.2 23.0 - - - +
147C ARG 3.3 3.6 + - - -
148C ILE* 1.3 70.4 - - - +
150C MET* 1.3 60.1 + - - +
151C ASP* 3.3 16.6 + - - +
152C VAL* 2.8 49.7 + - + +
153C ALA* 2.8 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C ILE* 3.3 27.2 + - - +
149C ASP* 1.3 72.2 + - - +
151C ASP* 1.3 63.9 + - - +
153C ALA* 3.1 2.6 + - + -
154C LEU* 2.9 57.7 + - + +
178C THR* 5.2 1.3 - - - -
182C ASP* 3.5 60.6 - - - +
185C ARG* 3.8 26.2 - - + +
186C ILE* 4.0 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 151 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C ASP* 3.3 8.3 + - - +
150C MET* 1.3 77.2 - - - +
152C VAL* 1.3 62.6 + - - +
154C LEU* 4.2 3.5 - - - +
155C GLU* 3.1 27.5 + - - +
185C ARG* 4.5 11.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C VAL* 4.3 14.1 - - + -
141C SER 4.0 14.8 - - - +
149C ASP* 2.8 46.0 + - + +
151C ASP* 1.3 75.2 - - - +
153C ALA* 1.3 60.8 + - + +
155C GLU* 3.5 15.1 - - - +
156C GLU* 2.9 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C PHE* 3.6 32.2 - - + -
140C VAL* 4.5 2.9 - - - -
148C ILE* 3.9 15.7 - - + -
149C ASP 2.8 13.4 + - - +
150C MET* 3.1 15.0 + - + +
152C VAL* 1.3 80.5 - - - +
154C LEU* 1.3 58.5 + - + +
156C GLU* 3.9 2.1 - - - +
157C ILE* 3.0 35.3 + - - +
186C ILE* 5.0 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 154 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C MET* 2.9 27.3 + - + +
151C ASP* 4.3 3.8 - - - +
153C ALA* 1.3 72.9 - - - +
155C GLU* 1.3 66.1 + - - +
157C ILE* 3.4 1.6 + - + +
158C ARG* 3.0 57.0 + - - +
185C ARG* 3.5 66.9 - - + +
186C ILE* 3.8 11.0 - - + +
189C VAL* 3.6 17.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C ASP 3.1 18.2 + - - +
152C VAL* 3.5 21.0 + - - +
154C LEU* 1.3 77.1 - - - +
156C GLU* 1.3 65.6 + - - +
158C ARG* 3.3 11.0 + - - +
159C ALA* 3.0 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C LEU* 4.3 2.9 - - + +
138C ILE* 5.4 0.2 - - + -
140C VAL* 3.5 33.2 - - + -
152C VAL* 2.9 30.9 + - - +
153C ALA 3.9 2.5 - - - +
155C GLU* 1.3 85.2 - - - +
157C ILE* 1.3 60.1 + - - +
159C ALA* 4.4 6.8 - - - +
160C LYS* 3.0 64.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 157 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C LEU* 4.3 17.0 - - + -
119C PHE* 4.1 14.1 - - + -
153C ALA 3.0 24.3 + - - +
154C LEU* 3.9 3.6 - - - +
156C GLU* 1.3 72.7 - - - +
158C ARG* 1.3 61.5 + - - +
161C GLN* 2.9 31.0 + - - -
162C PRO* 3.3 16.4 - - + +
165C VAL* 4.3 11.2 - - + -
186C ILE* 3.9 31.4 - - + -
189C VAL* 3.6 40.2 - - + +
190C ALA* 3.8 9.9 - - + +
191C PRO* 4.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 158 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C LEU* 3.0 45.5 + - - +
155C GLU* 3.5 8.6 - - - +
157C ILE* 1.3 77.3 - - - +
159C ALA* 1.3 62.4 + - - +
161C GLN* 3.1 25.7 + - - +
189C VAL* 3.4 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 159 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C GLU* 3.0 18.3 + - + +
156C GLU* 3.8 13.2 - - - +
158C ARG* 1.3 77.2 - - - +
160C LYS* 1.3 71.6 + - + +
161C GLN* 3.9 2.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 160 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C THR* 4.9 3.5 + - - +
117C LEU* 4.7 2.2 - - + -
138C ILE* 3.9 45.5 - - + +
156C GLU* 3.0 45.5 + - + +
159C ALA* 1.3 84.7 - - + +
161C GLN* 1.3 73.0 + - - +
162C PRO* 3.4 7.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 161 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C THR* 4.6 1.2 + - - -
157C ILE 2.9 20.5 + - - -
158C ARG* 3.1 29.9 + - - +
159C ALA 4.7 2.9 - - - +
160C LYS* 1.3 80.0 - - - +
162C PRO* 1.3 69.0 - - - +
163C ASP* 3.6 5.9 + - - +
189C VAL 4.4 10.6 + - - +
191C PRO* 3.4 29.0 - - + +
----------------------------------------------------------
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