Contacts of the helix formed by residues 134 - 156 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H PHE* 3.7 1.6 - - - -
132H LEU* 3.4 4.4 - - - +
133H LYS* 1.3 79.1 - - - +
135H LYS* 1.3 64.2 + - - +
136H ALA 3.4 0.7 + - - -
137H LEU* 3.2 36.0 + - - +
138H SER* 3.1 24.9 + - - -
130I GLU* 3.3 29.3 + - - -
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Residues in contact with LYS 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H VAL* 4.1 19.7 - - + -
103H PHE* 3.2 47.2 - - + -
134H SER* 1.3 69.6 + - - +
136H ALA* 1.3 68.2 + - - +
138H SER* 3.0 13.6 + - - -
139H LEU* 3.0 17.7 + - + +
95I PHE* 3.5 37.6 - - + +
97I ASP* 3.1 32.7 + - - -
130I GLU* 5.1 1.2 + - - -
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Residues in contact with ALA 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134H SER* 3.4 7.3 + - - +
135H LYS* 1.3 79.8 - - - +
137H LEU* 1.3 64.1 + - + +
139H LEU 3.1 0.5 + - - -
140H GLU* 2.9 23.6 + - - +
95I PHE* 3.6 24.5 - - + -
105I VAL 4.6 2.7 - - - +
126I TYR* 3.7 11.6 - - + -
128I VAL* 3.3 37.7 - - + -
130I GLU* 4.0 6.4 + - - +
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Residues in contact with LEU 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132H LEU* 3.9 23.5 - - + +
134H SER* 3.2 27.1 + - - +
136H ALA* 1.3 84.0 - - + +
138H SER* 1.3 62.3 + - - +
140H GLU* 3.8 18.9 - - - +
141H LYS* 3.0 26.0 + - - +
58I GLY* 5.7 10.1 - - - +
128I VAL* 4.7 8.3 - - + -
130I GLU* 3.9 13.2 - - - +
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Residues in contact with SER 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H PHE* 3.5 18.8 + - - +
105H VAL* 3.8 20.6 - - - +
129H SER* 3.1 32.9 + - - -
132H LEU* 3.3 14.5 - - - +
134H SER 3.1 19.8 + - - -
135H LYS 3.0 6.7 + - - -
137H LEU* 1.3 77.3 - - - +
139H LEU* 1.3 61.0 + - - +
142H ALA* 3.3 19.2 + - - +
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Residues in contact with LEU 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93H VAL* 4.2 17.7 - - + -
96H VAL* 3.8 20.4 - - + -
105H VAL* 3.7 25.8 - - + -
107H VAL* 4.8 2.0 - - + -
135H LYS* 3.0 15.6 + - + +
136H ALA 3.7 2.9 - - - +
138H SER* 1.3 73.8 - - - +
140H GLU* 1.3 66.5 + - - +
141H LYS 3.1 1.3 - - - -
142H ALA 3.3 0.5 + - - -
143H ARG* 2.8 34.2 + - + +
94I ASP* 3.4 17.5 - - + +
95I PHE* 3.8 23.8 - - + -
126I TYR* 3.1 29.8 - - + +
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Residues in contact with GLU 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136H ALA 2.9 16.3 + - - +
137H LEU* 3.8 21.1 - - - +
139H LEU* 1.3 75.5 - - - +
141H LYS* 1.3 64.4 + - - +
143H ARG* 4.9 0.2 - - - -
144H LYS* 3.1 65.0 + - + +
126I TYR* 3.7 36.8 - - + +
128I VAL* 4.9 7.1 - - + +
149I ASP* 4.4 2.1 - - - +
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Residues in contact with LYS 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H VAL* 2.9 30.9 + - - +
129H SER* 4.1 12.1 - - - +
132H LEU* 5.0 7.2 - - + -
137H LEU 3.0 17.3 + - - +
138H SER 3.8 4.3 - - - +
139H LEU 3.1 0.2 - - - -
140H GLU* 1.3 79.4 - - - +
142H ALA* 1.3 57.3 + - - +
144H LYS* 4.0 2.2 - - - +
145H GLU* 2.9 64.6 + - - +
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Residues in contact with ALA 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105H VAL* 3.7 12.3 - - + +
107H VAL* 3.7 19.4 - - + +
127H GLY* 3.1 35.4 - - - +
128H VAL* 3.8 9.4 - - - +
138H SER 3.3 15.0 + - - +
139H LEU 3.3 0.9 + - - +
141H LYS* 1.3 78.6 - - - +
143H ARG* 1.3 56.9 + - - +
146H ALA* 2.9 28.4 + - - +
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Residues in contact with ARG 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H GLN* 2.7 63.4 + - - +
93H VAL* 3.3 29.4 - - - +
107H VAL* 4.2 12.6 - - + -
139H LEU* 2.8 28.1 + - + +
140H GLU* 4.3 2.9 - - - +
142H ALA* 1.3 72.2 - - - +
144H LYS* 1.3 64.1 + - + +
147H VAL* 3.3 15.6 + - - +
92I ASN* 4.7 3.8 - - - +
94I ASP* 2.6 45.0 + - - -
108I CYS* 3.4 23.3 - - - -
110I PHE* 4.6 3.6 - - - -
124I VAL* 4.5 7.9 - - + -
126I TYR* 3.7 22.9 - - + -
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Residues in contact with LYS 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140H GLU* 3.1 48.3 + - + +
141H LYS* 4.0 1.8 - - - +
143H ARG* 1.3 74.4 - - + +
145H GLU* 1.3 66.8 + - - +
147H VAL* 3.2 2.8 + - - +
148H THR* 3.1 25.1 + - - -
124I VAL* 4.4 11.2 - - + +
126I TYR* 4.2 9.0 - - + +
149I ASP* 2.7 37.4 + - - -
153I ARG* 3.2 48.3 + - - +
156I ARG* 5.8 2.0 - - - +
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Residues in contact with GLU 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H TYR 4.3 3.5 - - - +
127H GLY* 3.9 10.0 - - - -
128H VAL* 3.6 11.1 + - - +
141H LYS* 2.9 63.8 + - - +
144H LYS* 1.3 76.3 - - - +
146H ALA* 1.3 65.8 + - - +
147H VAL 3.0 0.5 + - - -
148H THR* 3.2 6.0 + - - -
149H ASP* 2.8 25.3 + - - +
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Residues in contact with ALA 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107H VAL* 3.4 20.6 - - + +
109H ALA* 3.8 17.5 - - + +
125H GLY* 3.2 11.6 - - - -
126H TYR* 3.5 6.7 - - - -
127H GLY* 3.2 21.7 - - - +
142H ALA 2.9 20.5 + - - +
143H ARG 3.7 4.7 - - - +
144H LYS 3.3 0.2 - - - -
145H GLU* 1.3 75.3 - - - +
147H VAL* 1.3 57.5 + - - +
150H GLY* 2.9 22.5 + - - -
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Residues in contact with VAL 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H HIS* 5.2 6.7 - - + -
88H ILE* 3.7 23.8 - - + -
91H GLN* 3.7 8.5 - - - +
109H ALA* 4.1 12.3 - - + -
111H VAL* 3.6 7.2 - - + +
143H ARG 3.3 5.6 + - - +
144H LYS 3.2 8.4 + - - +
145H GLU 3.1 0.8 - - - -
146H ALA* 1.3 73.8 - - - +
148H THR* 1.3 65.2 + - - +
150H GLY* 2.9 4.0 + - - -
151H LEU* 2.8 27.8 + - + +
122I GLU 4.9 2.5 - - - +
123I ASP* 3.6 27.1 - - - +
124I VAL* 3.0 32.1 - - + -
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Residues in contact with THR 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H GLY* 4.1 25.8 - - - +
72H ILE* 6.5 0.9 - - + -
144H LYS 3.1 12.4 + - - -
145H GLU* 3.8 8.5 - - - -
147H VAL* 1.3 79.1 - - - +
149H ASP* 1.3 63.6 + - - +
151H LEU* 3.1 10.2 + - + +
152H LYS* 2.8 34.4 + - + +
123I ASP* 5.4 0.9 + - - -
153I ARG* 3.7 13.3 + - - -
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Residues in contact with ASP 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140G GLU* 5.1 1.1 - - - -
144G LYS* 2.6 34.9 + - - -
125H GLY* 3.4 2.1 - - - -
126H TYR 2.9 32.5 + - - +
145H GLU* 2.8 21.1 + - + +
148H THR* 1.3 72.9 - - - +
150H GLY* 1.3 58.7 + - - +
152H LYS* 3.4 18.2 + - - +
153H ARG* 2.9 35.2 + - - +
156H ARG* 5.1 4.3 + - - -
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Residues in contact with GLY 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H VAL* 3.9 16.0 - - - +
123H ASP* 4.4 3.4 - - - +
124H VAL 4.0 4.5 - - - -
125H GLY* 3.2 22.6 - - - -
146H ALA 2.9 8.9 + - - -
147H VAL 2.9 7.8 + - - -
149H ASP* 1.3 78.2 - - - +
151H LEU* 1.3 62.7 + - - +
153H ARG* 3.2 3.1 + - - +
154H ALA* 2.9 23.2 + - - +
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Residues in contact with LEU 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71H VAL* 5.6 1.1 - - + -
72H ILE* 4.8 16.4 - - + -
84H TRP* 3.9 19.3 - - + -
86H HIS* 3.7 37.7 - - + +
111H VAL* 3.7 9.9 - - + +
113H VAL* 3.6 19.7 - - + -
147H VAL* 2.8 16.3 + - + +
148H THR* 3.1 13.4 + - + +
150H GLY* 1.3 72.3 - - - +
152H LYS* 1.3 65.6 + - + +
154H ALA* 3.2 2.4 + - - +
155H LEU* 3.0 42.0 + - + +
123I ASP* 6.1 0.2 - - - +
157I SER* 5.1 2.7 - - - +
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Residues in contact with LYS 152 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H ARG* 6.2 0.2 - - - +
65H TYR* 4.3 14.8 - - - +
66H ILE* 2.9 33.3 + - + +
67H GLU* 4.8 0.2 - - - +
68H GLY* 4.3 11.6 - - - +
71H VAL* 3.7 35.7 - - + -
148H THR* 2.8 34.6 + - + +
149H ASP* 3.8 20.4 + - - +
151H LEU* 1.3 74.7 - - + +
153H ARG* 1.3 62.6 + - + +
154H ALA 3.2 0.3 + - - -
155H LEU* 3.3 3.5 + - - +
156H ARG* 3.1 36.9 + - + +
162H LEU 4.7 1.7 - - - +
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Residues in contact with ARG 153 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G LYS* 3.5 68.6 + - - +
148G THR* 3.8 12.9 + - - -
123H ASP* 3.2 38.7 + - + +
124H VAL 2.9 25.9 + - - +
149H ASP* 2.9 20.7 + - - +
150H GLY 3.8 3.6 - - - +
152H LYS* 1.3 76.9 - - - +
154H ALA* 1.3 62.2 + - - +
156H ARG* 3.7 52.9 - - - +
157H SER* 4.0 4.7 + - - -
167H LEU* 5.8 0.2 - - - +
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Residues in contact with ALA 154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H VAL 4.1 12.3 - - - +
113H VAL* 3.3 27.6 - - + -
121H HIS* 3.8 20.4 - - - +
122H GLU 5.0 1.1 - - - -
123H ASP* 3.9 10.1 - - - +
150H GLY 2.9 15.8 + - - +
151H LEU* 3.4 3.1 - - - +
152H LYS 3.1 0.2 - - - -
153H ARG* 1.3 77.5 - - - +
155H LEU* 1.3 65.2 + - - +
157H SER* 3.0 24.0 + - - -
158H PHE* 4.4 1.9 + - - -
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Residues in contact with LEU 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71H VAL* 3.4 39.3 - - + +
72H ILE* 5.6 0.4 - - - -
75H ALA* 4.3 7.9 - - + -
79H PHE* 4.7 3.4 - - + -
84H TRP* 4.2 16.8 - - + -
113H VAL* 3.7 24.9 - - + -
151H LEU* 3.0 39.4 + - + +
152H LYS 3.8 3.8 - - - +
154H ALA* 1.3 71.1 - - - +
156H ARG* 1.3 67.4 + - - +
157H SER 2.9 2.5 - - - -
158H PHE* 2.8 36.5 + - + +
162H LEU* 3.6 23.9 - - + +
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Residues in contact with ARG 156 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G ILE* 4.5 4.7 - - + -
144G LYS* 5.8 1.6 - - - +
65H TYR* 6.4 0.2 - - - +
149H ASP* 5.1 5.7 + - - -
152H LYS* 3.1 27.1 + - + +
153H ARG* 3.7 52.4 - - - +
154H ALA 3.2 0.6 - - - -
155H LEU* 1.3 76.6 - - - +
157H SER* 1.3 62.3 + - - +
158H PHE 3.1 1.0 + - - -
159H GLY 3.2 10.6 + - - -
162H LEU 3.8 12.7 + - - +
163H GLY* 3.5 26.9 - - - +
164H ASN* 3.4 24.4 - - + +
166H ILE* 4.0 17.6 - - - +
167H LEU* 3.4 36.4 - - + +
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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