Contacts of the helix formed by residues 134 - 157 (chain C) in PDB entry 1KN0
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 SER 134 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C PHE* 3.6 1.6 - - - -
132C LEU* 4.0 4.4 - - - +
133C LYS* 1.3 79.3 - - - +
135C LYS* 1.3 64.6 + - - +
136C ALA 3.5 0.5 + - - -
137C LEU* 3.3 33.1 + - - +
138C SER* 3.1 25.1 + - - -
130D GLU* 3.1 34.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C VAL* 4.1 20.4 - - + -
103C PHE* 3.4 46.3 - - + -
105C VAL* 5.9 0.2 - - + -
133C LYS 3.7 0.2 + - - -
134C SER* 1.3 70.8 + - - +
136C ALA* 1.3 68.6 + - - +
138C SER* 3.0 5.4 + - - -
139C LEU* 3.0 25.7 + - + +
95D PHE* 3.5 37.0 - - + +
97D ASP* 2.8 34.1 + - - -
130D GLU* 5.1 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C SER* 3.4 6.9 + - - +
135C LYS* 1.3 80.6 - - - +
137C LEU* 1.3 64.6 + - + +
139C LEU* 3.1 0.5 + - - -
140C GLU* 2.9 21.8 + - - +
95D PHE* 3.3 25.0 - - + -
105D VAL 4.5 1.8 - - - +
126D TYR* 3.6 14.4 - - + -
128D VAL* 3.4 38.1 - - + -
130D GLU* 4.3 6.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LEU* 3.8 27.1 - - + +
134C SER* 3.3 26.6 + - - +
136C ALA* 1.3 83.0 - - + +
138C SER* 1.3 62.8 + - - +
140C GLU* 3.6 18.3 + - - +
141C LYS* 3.1 24.4 + - - +
58D GLY* 5.7 9.4 - - - +
128D VAL* 4.7 9.6 - - + -
130D GLU* 3.6 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C PHE* 3.6 18.3 + - - +
105C VAL* 3.9 20.4 - - - -
129C SER* 3.1 33.8 + - - -
132C LEU* 3.3 15.1 - - - +
134C SER 3.1 19.1 + - - -
135C LYS 3.0 6.3 + - - -
137C LEU* 1.3 75.7 - - - +
139C LEU* 1.3 62.5 + - - +
141C LYS 3.5 0.7 + - - -
142C ALA* 3.1 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C VAL* 4.4 15.5 - - + -
96C VAL* 3.8 20.4 - - + -
105C VAL* 3.5 30.3 - - + -
107C VAL* 5.0 1.6 - - + -
135C LYS* 3.0 15.2 + - + +
136C ALA 3.7 2.5 - - - +
138C SER* 1.3 73.8 - - - +
140C GLU* 1.3 68.3 + - - +
141C LYS 3.0 1.6 - - - -
142C ALA* 2.9 2.4 + - - -
143C ARG* 2.8 31.6 + - + +
94D ASP* 3.4 24.5 - - + +
95D PHE* 3.7 19.5 - - + -
126D TYR* 3.2 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C ALA 2.9 11.8 + - - +
137C LEU* 3.9 20.8 - - - +
139C LEU* 1.3 75.6 - - - +
141C LYS* 1.3 64.2 + - - +
143C ARG* 4.9 0.7 - - - -
144C LYS* 3.0 59.6 + - + +
126D TYR* 3.4 51.0 - - + +
128D VAL* 5.0 6.2 - - + +
149D ASP* 4.4 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C VAL* 2.8 31.4 + - - +
129C SER* 3.9 14.3 - - - +
132C LEU* 5.1 6.3 - - + -
137C LEU 3.1 19.0 + - - +
138C SER 3.6 4.9 - - - +
139C LEU 3.0 0.8 - - - -
140C GLU* 1.3 79.4 - - - +
142C ALA* 1.3 57.4 + - - +
144C LYS* 4.0 2.6 - - - +
145C GLU* 2.9 63.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C VAL* 3.8 26.7 - - + +
107C VAL* 3.9 9.0 - - + +
127C GLY* 3.2 34.8 - - - +
128C VAL* 4.0 5.8 - - - +
138C SER 3.1 12.4 + - - +
139C LEU 2.9 3.6 + - - +
141C LYS* 1.3 78.1 - - - +
143C ARG* 1.3 64.3 + - - +
146C ALA* 3.0 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C GLN* 2.7 63.5 + - - +
93C VAL* 3.4 29.5 - - + +
107C VAL* 4.2 12.3 - - + -
139C LEU* 2.8 26.5 + - + +
140C GLU* 4.3 3.1 - - - +
142C ALA* 1.3 72.2 - - - +
144C LYS* 1.3 64.6 + - + +
146C ALA 3.6 0.2 + - - -
147C VAL* 3.4 14.9 + - - +
92D ASN* 4.6 6.3 - - - +
94D ASP* 2.5 36.1 + - - -
108D CYS* 3.5 24.1 - - - -
110D PHE* 4.3 5.1 - - - -
124D VAL* 3.8 9.3 - - + +
126D TYR* 3.8 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C GLU* 3.0 48.6 + - + +
141C LYS* 4.0 2.7 - - - +
143C ARG* 1.3 76.8 - - + +
145C GLU* 1.3 67.3 + - + +
147C VAL* 3.2 3.6 + - - +
148C THR* 3.1 24.2 + - - -
124D VAL* 4.3 10.3 - - + +
125D GLY 5.9 0.2 - - - -
126D TYR* 4.2 7.9 - - + +
149D ASP* 2.6 40.9 + - - -
153D ARG* 3.4 46.3 + - - +
156D ARG* 5.7 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C TYR 4.2 1.9 - - - +
127C GLY* 3.8 11.8 - - - -
128C VAL* 3.6 10.9 + - - +
141C LYS* 2.9 63.2 + - - +
144C LYS* 1.3 78.4 - - + +
146C ALA* 1.3 56.0 + - - +
148C THR* 3.8 6.3 - - - +
149C ASP* 2.7 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C GLN* 4.1 0.2 - - - +
107C VAL* 3.7 14.6 - - + +
108C CYS 4.0 2.7 - - - -
109C ALA* 3.8 23.5 - - + +
125C GLY* 3.3 9.9 - - - -
126C TYR 3.5 5.4 - - - +
127C GLY* 3.4 20.3 - - - +
142C ALA 3.0 20.4 + - - +
143C ARG 3.8 4.7 - - - +
144C LYS 3.3 0.2 - - - -
145C GLU* 1.3 74.9 - - - +
147C VAL* 1.3 58.6 + - - +
150C GLY* 2.8 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C HIS* 5.0 7.4 - - + -
88C ILE* 3.7 27.1 - - + -
91C GLN* 3.7 9.4 - - - +
109C ALA* 4.0 12.6 - - + -
111C VAL* 3.7 7.3 - - + +
143C ARG 3.4 5.6 + - - +
144C LYS 3.2 7.5 + - - +
146C ALA* 1.3 74.8 - - - +
148C THR* 1.3 68.8 + - - +
150C GLY* 3.0 1.9 + - - -
151C LEU* 2.8 23.1 + - + +
122D GLU 4.8 2.5 - - - +
123D ASP* 3.7 24.9 - - - +
124D VAL* 3.1 30.5 - - + -
153D ARG* 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C GLY* 4.1 26.7 - - - +
144C LYS 3.1 14.0 + - - -
145C GLU* 3.9 6.1 - - - -
147C VAL* 1.3 79.4 - - - +
149C ASP* 1.3 63.7 + - - +
151C LEU* 3.3 9.0 + - + +
152C LYS* 2.9 35.2 + - + +
123D ASP* 5.4 1.0 + - - -
153D ARG* 3.7 14.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLU* 5.2 0.9 - - - -
144B LYS* 2.7 33.9 + - - -
125C GLY* 3.4 2.1 - - - -
126C TYR 2.9 29.8 + - - +
145C GLU 2.7 23.0 + - - +
146C ALA 3.6 3.6 - - - +
148C THR* 1.3 74.5 - - - +
150C GLY* 1.3 63.2 + - - +
152C LYS* 3.4 18.9 + - - +
153C ARG* 3.0 29.6 + - - +
156C ARG* 5.2 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C VAL* 3.7 16.5 - - - +
123C ASP* 4.3 3.9 - - - +
124C VAL 4.0 3.6 - - - -
125C GLY* 3.3 22.6 - - - -
146C ALA 2.8 12.9 + - - -
147C VAL 3.0 4.0 + - - -
149C ASP* 1.3 76.6 - - - +
151C LEU* 1.3 55.3 + - - +
153C ARG* 3.1 4.3 + - - +
154C ALA* 2.8 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C VAL* 5.7 0.4 - - + -
72C ILE* 4.7 16.6 - - + -
84C TRP* 3.9 18.4 - - + -
86C HIS* 3.5 38.6 - - + +
111C VAL* 3.7 13.4 - - + +
113C VAL* 3.5 24.5 - - + -
147C VAL* 2.8 18.2 + - + +
148C THR* 3.7 9.4 - - + +
150C GLY* 1.3 71.1 - - - +
152C LYS* 1.3 64.9 + - + +
154C ALA* 3.2 2.2 + - - +
155C LEU* 2.9 39.7 + - + +
123D ASP* 6.0 0.4 - - - +
157D SER* 4.9 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ARG* 6.1 0.8 - - - +
65C TYR* 4.3 15.8 - - - +
66C ILE* 3.0 31.8 + - + +
67C GLU* 5.0 0.4 - - - +
68C GLY* 4.4 11.8 - - - +
71C VAL* 3.8 33.8 - - + +
148C THR* 2.9 29.9 + - + +
149C ASP* 3.8 19.4 + - - +
151C LEU* 1.3 78.9 - - + +
153C ARG* 1.3 65.5 + - + +
155C LEU* 3.3 2.1 + - - +
156C ARG* 3.1 38.2 + - - +
162C LEU 4.5 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LYS* 3.5 69.9 + - - +
147B VAL* 5.0 0.2 - - - +
148B THR* 3.7 13.7 + - - -
123C ASP* 3.2 38.2 + - + +
124C VAL 2.8 25.5 + - - +
149C ASP* 3.0 19.9 + - - +
150C GLY 3.7 3.1 - - - +
152C LYS* 1.3 77.3 - - + +
154C ALA* 1.3 62.1 + - - +
156C ARG* 3.5 52.3 + - - +
157C SER* 4.0 4.7 + - - -
167C LEU* 5.9 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C VAL 4.1 13.0 - - - +
113C VAL* 3.5 26.0 - - + -
121C HIS* 3.8 21.1 - - - +
122C GLU 4.9 1.3 - - - -
123C ASP* 3.8 12.3 - - - +
150C GLY 2.8 16.5 + - - +
151C LEU* 3.7 2.2 - - - +
152C LYS 3.2 0.2 - - - -
153C ARG* 1.3 75.2 - - - +
155C LEU* 1.3 65.2 + - - +
157C SER* 3.2 23.7 + - - -
158C PHE* 4.4 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C VAL* 3.4 33.0 - - + -
72C ILE* 5.3 0.7 - - - +
75C ALA* 4.4 17.5 - - + -
79C PHE* 4.8 3.6 - - + -
84C TRP* 4.2 18.2 - - + -
113C VAL* 3.7 25.4 - - + -
151C LEU* 2.9 41.4 + - + +
152C LYS 3.9 3.4 - - - +
154C ALA* 1.3 74.1 - - - +
156C ARG* 1.3 67.0 + - - +
158C PHE* 2.9 28.8 + - + +
162C LEU* 3.5 25.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE* 4.7 4.5 - - + -
144B LYS* 5.7 1.6 - - - +
65C TYR* 6.4 0.2 - - - +
149C ASP* 5.2 4.4 + - - -
152C LYS* 3.1 28.3 + - + +
153C ARG* 3.6 50.7 - - - +
154C ALA 3.2 0.6 - - - -
155C LEU* 1.3 76.2 - - - +
157C SER* 1.3 62.7 + - - +
158C PHE 3.0 1.9 + - - -
159C GLY 3.0 16.3 + - - +
162C LEU 3.7 12.1 + - - +
163C GLY* 3.7 23.3 - - - -
164C ASN* 3.4 22.5 - - + +
166C ILE* 3.9 18.7 - - - +
167C LEU* 3.4 36.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 157 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE* 3.4 26.2 - - - +
76B ASN* 3.2 23.7 + - - +
84B TRP* 3.9 6.0 - - - -
86B HIS* 3.4 18.2 + - - -
151B LEU* 5.1 0.9 - - - +
121C HIS* 3.4 31.8 - - - -
123C ASP* 4.8 2.6 + - - -
153C ARG 4.0 6.4 + - - -
154C ALA* 3.2 16.1 + - - -
155C LEU 3.0 1.2 - - - -
156C ARG* 1.3 77.8 - - - +
158C PHE* 1.3 56.7 + - - +
----------------------------------------------------------
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