Contacts of the helix formed by residues 133 - 142 (chain C) in PDB entry 2IK8
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 133 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C PHE* 3.3 15.4 - - - +
96C GLY* 2.7 23.7 + - - -
97C ASP* 3.1 25.5 + - - +
100C ARG* 3.5 31.1 + - - +
129C ARG 3.4 3.2 + - - -
130C LEU 3.2 14.3 + - - +
132C LYS* 1.3 78.2 - - - +
134C SER* 1.3 61.1 + - - +
135C GLY 3.3 8.0 + - - -
136C VAL* 3.1 12.2 + - + +
137C GLN* 2.9 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C GLY* 3.3 19.9 - - - -
132C LYS 3.4 4.8 + - - -
133C ASP* 1.3 74.6 + - - +
135C GLY* 1.3 59.4 + - - +
137C GLN* 3.1 10.5 + - - +
138C ALA* 2.8 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C MET* 3.5 15.4 - - - +
93C ILE* 3.6 8.1 - - - +
94C ASP 3.4 20.6 - - - -
95C PHE 4.4 0.4 - - - -
96C GLY 3.8 2.4 - - - +
133C ASP* 3.3 8.8 + - - -
134C SER* 1.3 80.3 + - - +
136C VAL* 1.3 61.8 + - - +
138C ALA* 4.1 6.3 - - - -
139C CYS* 3.2 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ILE* 4.1 17.9 - - + -
84C ILE* 3.6 20.2 - - + +
85C ILE* 5.5 1.8 - - + -
88C MET* 3.5 23.6 - - + -
95C PHE* 3.9 17.3 - - + -
130C LEU* 3.1 35.9 - - + +
131C TRP* 4.4 11.7 - - + -
133C ASP* 3.1 12.5 + - + +
135C GLY* 1.3 75.5 - - - +
137C GLN* 1.3 59.6 + - - +
138C ALA 3.3 0.2 - - - -
139C CYS* 4.6 0.7 - - - -
140C PHE* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C TRP* 2.8 62.4 + - - +
132C LYS 4.6 4.0 - - - +
133C ASP 2.9 16.6 + - - +
134C SER* 3.1 12.8 + - - +
136C VAL* 1.3 76.1 - - - +
138C ALA* 1.3 63.1 - - - +
140C PHE* 3.4 14.8 + - - +
141C ASN* 3.1 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ILE* 4.2 15.9 - - + -
134C SER 2.8 13.1 + - - +
135C GLY* 3.6 13.7 - - - +
136C VAL 3.3 0.2 - - - -
137C GLN* 1.3 76.1 - - - +
139C CYS* 1.3 63.3 + - - +
141C ASN* 3.1 21.2 + - - +
142C ARG* 3.2 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ILE* 3.3 20.0 - - + -
87C ALA* 3.3 35.4 - - - -
88C MET* 3.7 22.7 - - + -
91C LEU* 4.2 2.2 - - - -
93C ILE* 3.5 22.3 - - + +
135C GLY 3.2 6.4 + - - +
136C VAL 3.9 0.2 - - - +
138C ALA* 1.3 75.5 - - - +
140C PHE* 1.3 64.1 + - - +
142C ARG* 3.0 11.9 + - - +
143C SER 3.4 2.9 + - - -
146C TYR* 2.7 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ILE* 4.0 6.0 - - + +
131C TRP* 3.8 33.4 - + + -
136C VAL 3.0 20.1 + - - +
137C GLN* 3.6 14.1 - - - +
138C ALA 3.2 0.2 - - - -
139C CYS* 1.3 75.3 - - - +
141C ASN* 1.3 75.1 + - - +
142C ARG 3.0 1.4 + - - -
143C SER* 3.0 23.7 + - - -
146C TYR* 3.6 5.8 - - - -
148C LEU* 3.5 30.1 - - + -
152C ALA* 4.2 12.8 - - + -
153C ALA* 3.6 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C GLN* 3.1 22.5 + - - +
138C ALA* 3.1 12.8 + - - +
140C PHE* 1.3 87.7 - - - +
142C ARG* 1.3 61.2 + - + +
143C SER* 3.4 2.1 + - - -
144C ARG* 5.2 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LEU* 4.2 30.1 + - + +
93C ILE* 3.9 27.0 - - - +
138C ALA* 3.2 12.5 + - - +
139C CYS 3.0 12.2 + - - +
141C ASN* 1.3 77.9 - - + +
143C SER* 1.3 57.1 + - - +
144C ARG* 2.9 15.2 + - - -
145C GLU* 2.9 62.0 + - - +
146C TYR* 3.9 3.0 - - - -
----------------------------------------------------------
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