Contacts of the helix formed by residues 69 - 91 (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 TYR 69 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LYS* 4.5 9.5 - - - -
61C TYR* 3.4 35.7 + + - -
65C GLU* 3.4 23.6 - - + -
66C CYS 3.5 7.4 + - - +
67C LYS 3.2 1.4 - - - -
68C GLN* 1.3 77.3 - - + +
70C LYS* 1.3 66.7 + - - +
71C ALA 3.1 2.9 - - - -
72C VAL* 2.8 30.1 + - + +
73C VAL* 3.0 16.7 + - + +
169C PRO* 4.6 1.1 - - + -
174C VAL* 4.0 28.5 - - + -
177C THR* 4.0 34.1 - - + -
179C VAL* 5.6 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C CYS 3.8 3.2 + - - -
67C LYS* 3.0 17.3 + - - +
69C TYR* 1.3 76.7 - - - +
71C ALA* 1.3 63.7 + - - +
73C VAL* 3.2 5.2 + - - +
74C TYR* 3.1 48.9 + - + +
167C TYR* 5.0 6.1 - - + +
169C PRO* 4.0 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C GLN 4.1 11.3 + - - +
70C LYS* 1.3 79.5 - - - +
72C VAL* 1.3 62.8 + - + +
74C TYR* 3.8 10.3 + - - +
75C SER* 3.2 24.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C GLN 4.9 2.0 - - - +
69C TYR* 2.8 34.0 + - + +
71C ALA* 1.3 73.4 - - + +
73C VAL* 1.3 54.9 + - - +
75C SER* 3.1 6.0 + - - -
76C ASN* 2.7 46.3 + - - +
177C THR* 3.8 22.4 - - + -
178C ARG 3.9 0.2 - - - +
179C VAL* 3.7 30.5 - - + -
165D LYS* 5.7 7.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
69C TYR* 3.0 17.7 + - + +
70C LYS* 3.6 8.5 - - - +
72C VAL* 1.3 77.1 - - - +
74C TYR* 1.3 58.7 + - + +
76C ASN* 3.3 8.2 + - - +
77C THR* 2.7 34.2 + - - +
155C TYR* 4.1 25.7 - - + +
162C ILE* 3.6 28.0 - - + -
167C TYR* 3.9 17.0 - - + +
169C PRO* 4.8 5.4 - - + -
173C ASP* 4.2 13.9 - - + +
177C THR* 4.1 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C LYS* 3.1 29.4 + - + +
71C ALA* 3.9 8.3 - - - +
73C VAL* 1.3 76.7 - - + +
75C SER* 1.3 55.1 + - - +
77C THR* 2.9 10.3 + - - -
78C ILE* 2.7 45.0 + - + +
119C MET* 3.8 53.5 - - + +
162C ILE* 3.6 38.2 + - + -
164C GLN 4.8 4.7 + - - -
165C PRO 5.0 4.3 + - - -
167C TYR* 3.8 20.8 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ALA 3.2 16.9 + - - -
72C VAL* 3.1 8.4 + - - -
74C TYR* 1.3 79.1 - - - +
76C ASN* 1.3 55.1 + - - +
78C ILE* 3.3 10.5 + - - +
79C GLN* 2.7 38.2 + - - +
165D LYS* 5.7 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C VAL* 2.7 25.6 + - - +
73C VAL* 3.4 9.0 - - - +
75C SER* 1.3 74.0 - - - +
77C THR* 1.3 57.3 + - - +
79C GLN* 3.3 2.1 + - - +
80C SER* 2.9 35.9 + - - +
149C ASN* 3.7 14.1 + - + +
151C SER* 5.2 0.9 - - - -
155C TYR* 3.6 21.7 - - + -
176C ARG 3.9 0.5 - - - +
177C THR* 3.5 8.9 - - - -
178C ARG* 2.7 55.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C VAL* 2.7 24.6 + - - +
74C TYR* 3.2 9.3 - - - -
76C ASN* 1.3 75.2 - - - +
78C ILE* 1.3 65.8 + - - +
80C SER* 3.4 6.8 + - - -
81C ILE* 3.3 21.4 + - - +
119C MET* 4.8 4.3 - - + +
127C ILE* 4.5 8.7 - - + -
155C TYR* 3.5 28.9 - - + +
156C LEU* 4.0 25.0 - - + +
159C LEU* 4.2 22.0 - - + -
162C ILE* 5.3 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C TYR* 2.7 31.4 + - + +
75C SER* 3.5 8.5 - - - +
77C THR* 1.3 73.1 - - - +
79C GLN* 1.3 64.3 + - - +
81C ILE* 3.1 12.9 - - - +
82C ILE* 3.0 41.7 + - + +
107C LEU* 5.0 3.6 - - + -
111C ALA* 4.0 19.7 - - + -
119C MET* 4.9 6.1 - - + +
123C LEU* 3.9 30.1 - - + -
127C ILE* 4.4 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C SER* 2.7 23.0 + - - +
76C ASN* 3.7 5.2 - - - +
78C ILE* 1.3 74.1 - - - +
80C SER* 1.3 63.0 + - - +
82C ILE* 3.4 10.9 + - - +
83C ALA* 3.1 21.0 + - - +
149C ASN* 4.0 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ASN* 2.9 23.6 + - - +
77C THR* 3.5 7.7 - - - -
78C ILE 3.2 0.2 - - - -
79C GLN* 1.3 74.9 - - - +
81C ILE* 1.3 64.4 + - - +
83C ALA* 3.0 21.4 + - - +
84C ILE* 3.3 4.1 + - - +
148C LEU* 3.2 15.5 - - - +
149C ASN* 3.5 16.6 + - - +
151C SER 4.9 0.3 - - - -
152C ALA* 3.5 37.4 + - - +
155C TYR* 5.6 0.9 - - - -
156C LEU* 4.5 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C THR 3.3 10.3 + - - +
78C ILE* 3.1 22.2 - - - +
80C SER* 1.3 78.5 - - - +
82C ILE* 1.3 63.2 + - - +
84C ILE* 3.3 12.9 + - + -
85C ILE* 3.1 38.4 + - + +
107C LEU* 3.8 19.5 - - + -
127C ILE* 4.2 21.8 - - + -
130C LEU* 4.1 22.2 - - + -
131C TRP* 4.6 8.7 - - + +
136C VAL* 4.1 26.2 - - + -
156C LEU* 4.5 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ILE* 3.0 37.4 + - + +
79C GLN* 3.5 11.0 - - - +
80C SER 3.1 0.2 - - - -
81C ILE* 1.3 76.8 - - - +
83C ALA* 1.3 64.1 - - - +
85C ILE* 3.2 3.3 + - - +
86C ARG* 3.0 55.9 + - - +
107C LEU* 3.7 21.3 - - + -
108C PHE* 3.7 24.8 - - + -
111C ALA* 4.2 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C GLN 3.1 11.0 + - - +
80C SER 3.0 12.0 + - - +
82C ILE* 1.3 75.8 - - - +
84C ILE* 1.3 57.5 + - - +
86C ARG* 3.1 11.5 + - - +
87C ALA* 2.9 28.8 + - - +
146C TYR* 4.3 8.4 - - + -
147C GLN 3.7 23.6 - - - +
148C LEU* 3.8 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C SER 3.6 15.3 - - - +
81C ILE* 3.3 18.1 + - + +
82C ILE 3.3 1.0 - - - -
83C ALA* 1.3 75.1 - - - +
85C ILE* 1.3 57.3 + - - +
88C MET* 3.0 28.1 + - + +
131C TRP* 4.2 15.0 - - + -
136C VAL* 3.6 35.2 - - + +
139C CYS* 3.3 17.2 - - + -
140C PHE* 4.0 21.8 - - + +
146C TYR* 3.6 22.0 - - - +
148C LEU* 3.6 17.5 - - + -
152C ALA* 5.3 0.2 - - + -
156C LEU* 4.6 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ILE* 3.1 17.9 + - + +
82C ILE 3.7 4.7 - - - +
84C ILE* 1.3 73.9 - - - +
86C ARG* 1.3 68.5 + - - +
88C MET* 3.3 25.3 + - - +
89C GLY 3.6 4.0 + - - -
95C PHE* 5.1 7.0 - - + -
104C ALA* 4.2 20.6 - - + -
107C LEU* 3.2 34.5 - - + -
108C PHE* 3.7 22.2 - - + -
130C LEU* 3.4 27.8 - - + -
136C VAL* 5.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ILE* 3.0 39.8 + - - +
83C ALA* 3.4 10.2 - - - +
85C ILE* 1.3 79.7 - - - +
87C ALA* 1.3 63.3 + - - +
88C MET 3.3 0.3 + - - -
89C GLY* 3.4 2.6 + - - -
90C ARG* 3.2 50.7 + - - +
108C PHE* 4.2 19.6 - - + -
135D GLU* 5.3 6.6 + - - -
158D LYS* 6.3 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ALA 2.9 14.7 + - - +
85C ILE 3.3 0.2 - - - -
86C ARG* 1.3 78.0 - - - +
88C MET* 1.3 56.1 + - - +
90C ARG* 2.9 11.9 + - - +
91C LEU* 2.6 39.4 + - + +
139C CYS* 3.3 17.9 - - - -
146C TYR* 3.3 39.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ILE 3.0 20.9 + - - +
85C ILE* 3.5 15.3 - - - +
86C ARG 3.2 0.8 - - - -
87C ALA* 1.3 74.2 - - - +
89C GLY* 1.3 57.5 + - - +
92C LYS* 2.9 7.6 + - - -
93C ILE* 2.6 49.4 + - + +
94C ASP 3.4 26.5 - - - +
95C PHE* 3.5 38.8 - - + -
135C GLY 3.5 15.0 - - - +
136C VAL* 3.5 25.4 - - - -
139C CYS* 3.7 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ILE 3.6 4.0 + - - -
86C ARG 3.4 5.6 + - - -
87C ALA 3.2 0.2 - - - -
88C MET* 1.3 76.7 - - - +
90C ARG* 1.3 64.6 + - - +
92C LYS* 3.0 14.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ARG* 3.2 43.4 + - - +
87C ALA* 2.9 11.4 + - - +
89C GLY* 1.3 76.6 - - - +
91C LEU* 1.3 65.9 + - + +
92C LYS* 3.4 1.9 + - - +
146C TYR* 5.9 6.7 - - - +
135D GLU* 3.0 33.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ALA* 2.6 25.9 + - + +
90C ARG* 1.3 76.6 - - + +
92C LYS* 1.3 70.1 + - - +
93C ILE* 3.6 14.8 + - + +
139C CYS* 4.2 7.6 - - - -
142C ARG* 4.2 30.4 + - + +
145C GLU* 3.4 38.8 - - + +
146C TYR* 4.0 30.1 - - + -
----------------------------------------------------------
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