Contacts of the helix formed by residues 142 - 165 (chain A) in PDB entry 4KYI
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 PRO 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A PRO 3.8 7.2 - - - +
141A ILE* 1.3 89.9 - - + +
143A PRO* 1.3 66.9 - - + +
144A GLU* 4.7 6.7 - - + +
145A GLN* 3.1 25.0 + - + +
146A GLN* 2.6 32.7 + - - +
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Residues in contact with PRO 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ILE 4.7 0.2 - - - +
142A PRO* 1.3 82.4 - - + +
144A GLU* 1.3 59.8 + - + +
145A GLN 3.0 4.5 - - - -
146A GLN* 3.1 33.5 + - + +
147A MET* 4.4 1.2 + - - +
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Residues in contact with GLU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A PRO* 5.0 6.7 - - + -
143A PRO* 1.3 78.1 - - + +
145A GLN* 1.3 74.6 + - + +
146A GLN 3.5 0.2 - - - -
147A MET* 5.0 3.3 + - - +
148A ASN* 4.6 8.7 - - - +
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Residues in contact with GLN 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ILE* 3.2 13.8 - - + +
142A PRO* 3.1 32.2 + - + +
143A PRO 3.0 0.6 - - - -
144A GLU* 1.3 94.6 + - - +
146A GLN* 1.3 65.8 + - - +
147A MET 3.3 3.6 + - - -
148A ASN* 3.6 8.7 + - - +
149A TYR* 3.6 13.7 + - - +
223A GLU* 3.2 48.2 + - - +
224A LEU* 3.4 25.5 - - + +
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Residues in contact with GLN 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A PRO* 6.2 0.4 - - - +
141A ILE* 2.8 36.9 + - + +
142A PRO 2.6 15.0 + - - +
143A PRO* 3.1 21.1 + - + +
145A GLN* 1.3 80.0 - - - +
147A MET* 1.3 65.2 + - - +
149A TYR* 3.8 4.9 + - - +
150A GLY* 3.6 12.5 + - - -
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Residues in contact with MET 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A PRO 4.4 1.6 + - - +
144A GLU 5.0 3.3 - - - +
145A GLN 3.3 0.8 - - - +
146A GLN* 1.3 77.3 - - - +
148A ASN* 1.3 67.9 + - - +
150A GLY* 2.7 25.5 + - - -
151A ILE* 3.2 32.9 + - + +
220A ARG* 5.7 2.2 - - - -
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Residues in contact with ASN 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A GLU 4.6 8.4 + - - +
145A GLN* 3.6 11.4 + - - +
146A GLN 3.6 0.6 - - - -
147A MET* 1.3 88.6 - - - +
149A TYR* 1.3 61.5 + - - +
151A ILE* 3.7 2.9 + - - +
152A LEU* 3.3 29.3 + - - +
220A ARG* 3.9 40.3 + - + +
223A GLU* 3.5 27.9 + - - -
224A LEU* 3.6 19.7 - - + -
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Residues in contact with TYR 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A LEU* 4.1 24.5 + - + -
137A VAL* 5.2 7.0 - - + -
139A GLN* 3.4 24.0 + - + -
141A ILE* 4.1 35.2 - - + -
145A GLN 3.6 9.7 + - - +
146A GLN 4.0 7.9 - - - +
147A MET 3.0 0.8 + - - -
148A ASN* 1.3 77.8 - - - +
150A GLY* 1.3 65.8 + - - +
152A LEU* 4.1 2.4 - - - +
153A LYS* 2.6 65.5 + - + +
224A LEU* 3.8 26.8 - - + +
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Residues in contact with GLY 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A GLN 3.6 6.8 + - - -
147A MET 2.7 16.0 + - - -
149A TYR* 1.3 76.3 - - - +
151A ILE* 1.3 55.1 + - - -
153A LYS* 3.3 6.2 + - - +
154A GLN* 2.9 31.3 + - - +
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Residues in contact with ILE 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A MET* 3.2 33.3 + - + +
148A ASN 4.2 4.5 - - - +
149A TYR 3.5 0.2 - - - -
150A GLY* 1.3 73.7 - - - +
152A LEU* 1.3 63.8 + - - +
154A GLN* 3.2 13.9 + - - +
155A LYS* 3.1 51.6 + - - +
209A GLU* 3.7 18.6 - - + +
217A ASP* 4.8 1.1 - - - +
220A ARG* 3.5 42.8 - - - +
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Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A MET* 4.9 2.9 - - + -
134A LEU* 3.9 18.2 - - + -
148A ASN 3.3 18.3 + - - +
149A TYR 4.1 2.0 - - - +
150A GLY 3.4 0.6 - - - -
151A ILE* 1.3 77.5 - - + +
153A LYS* 1.3 63.0 + - - +
155A LYS* 3.4 5.0 + - - +
156A ILE* 3.2 31.9 + - + +
213A LEU* 4.7 7.2 - - + +
217A ASP* 3.3 43.1 - - + +
220A ARG* 4.1 12.1 - - + -
221A LEU* 3.7 45.3 - - + +
224A LEU* 4.4 9.2 - - + -
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Residues in contact with LYS 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LYS* 4.7 16.7 - - - +
134A LEU* 4.4 22.3 + - + +
135A GLU* 6.3 0.6 - - - +
149A TYR* 2.6 66.7 + - + +
150A GLY* 3.6 6.1 - - - +
152A LEU* 1.3 77.4 - - - +
154A GLN* 1.3 62.0 + - - +
156A ILE* 3.8 7.6 + - + +
157A ALA* 3.3 21.1 + - - +
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Residues in contact with GLN 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A GLY 2.9 12.8 + - - +
151A ILE* 3.2 18.4 + - - +
153A LYS* 1.3 78.2 - - - +
155A LYS* 1.3 63.9 + - + +
157A ALA* 3.3 8.9 - - + +
158A LEU* 3.2 20.7 + - + +
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Residues in contact with LYS 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ILE* 3.1 22.6 + - + +
152A LEU* 3.9 4.5 - - - +
153A LYS 3.3 0.2 - - - -
154A GLN* 1.3 76.4 - - + +
156A ILE* 1.3 66.5 + - - +
158A LEU* 3.0 18.6 + - - +
159A TYR* 3.0 20.2 + - + -
209A GLU* 3.0 25.7 + - - -
210A ASN 2.9 22.9 + - - +
211A PRO* 4.0 13.5 - - + +
212A ARG 3.0 23.7 + - - +
213A LEU* 4.1 14.1 - - + -
214A THR* 4.0 4.8 - - - +
217A ASP* 2.9 38.2 + - - +
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Residues in contact with ILE 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A MET* 3.8 16.2 - - + +
130A MET* 4.2 7.0 - - + +
131A LYS* 3.7 46.0 - - + +
134A LEU* 4.0 18.8 - - + -
152A LEU* 3.2 19.4 + - + +
153A LYS* 4.2 9.0 - - + +
154A GLN 3.5 0.2 - - - -
155A LYS* 1.3 75.3 - - - +
157A ALA* 1.3 52.5 + - - +
159A TYR* 3.3 7.2 + - - +
160A GLU* 2.8 56.4 + - - +
213A LEU* 4.9 15.9 - - + -
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Residues in contact with ALA 157 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A LYS 3.3 13.0 + - - +
154A GLN* 3.3 13.5 - - - +
156A ILE* 1.3 78.9 - - - +
158A LEU* 1.3 52.3 + - - +
160A GLU* 3.2 9.9 + - - +
161A ASP* 2.6 38.7 + - - +
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Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A GLN* 3.2 9.2 + - + +
155A LYS* 3.0 12.9 + - - +
157A ALA* 1.3 77.3 - - - +
159A TYR* 1.3 65.4 - - + +
161A ASP* 3.3 8.2 - - - +
162A LYS* 3.1 49.7 + - + +
196A ILE* 3.8 17.9 - - + +
211A PRO* 3.6 39.9 - - + +
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Residues in contact with TYR 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ASP* 2.9 47.2 + - + -
124A VAL* 5.7 0.7 - - + -
127A MET* 3.6 30.7 - - + -
155A LYS* 3.0 29.8 + - + -
156A ILE* 3.6 7.6 - - - +
158A LEU* 1.3 79.5 - - + +
160A GLU* 1.3 56.9 + - - +
162A LYS* 3.5 1.9 + - - +
163A LEU* 3.1 37.8 + - + +
193A LEU* 4.1 26.5 - - + +
196A ILE* 4.9 7.2 - - + -
211A PRO 4.0 13.0 - - - -
212A ARG* 3.1 30.6 - - + +
213A LEU* 3.3 27.8 + - + -
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Residues in contact with GLU 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A MET* 3.6 16.0 - - + +
131A LYS* 3.3 31.0 + - - +
156A ILE* 2.8 37.3 + - - +
157A ALA* 3.8 7.3 + - - +
159A TYR* 1.3 70.2 - - - +
161A ASP* 1.3 54.1 + - - +
163A LEU* 4.0 8.0 - - + +
164A SER* 2.6 35.5 + - - -
170A ILE 5.7 0.7 - - - +
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Residues in contact with ASP 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ALA 2.6 22.4 + - - +
158A LEU* 3.3 11.4 - - - +
160A GLU* 1.3 72.6 - - - +
162A LYS* 1.3 78.6 + - - +
164A SER* 2.4 24.3 + - - -
165A ARG* 3.0 47.8 + - - +
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Residues in contact with LYS 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A LEU* 3.1 39.9 + - + +
159A TYR 4.1 3.1 - - - +
161A ASP* 1.3 91.0 + - - +
163A LEU* 1.3 62.5 + - - +
165A ARG* 3.1 22.3 + - + +
166A ALA 3.3 5.5 + - - -
192A ALA* 3.2 43.6 + - + +
193A LEU* 4.2 12.8 - - + -
195A SER* 2.8 29.8 + - - -
196A ILE* 4.2 6.5 - - + +
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Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A VAL* 4.6 12.3 - - + -
127A MET* 4.5 22.0 - - + -
159A TYR* 3.1 27.4 + - + +
160A GLU* 4.2 7.2 - - + +
162A LYS* 1.3 76.8 - - - +
164A SER* 1.3 57.1 + - - +
166A ALA* 3.2 5.1 + - + +
167A GLY 3.1 8.0 + - - -
168A ILE* 3.1 52.4 + - + +
170A ILE* 4.5 20.4 - - + +
179A LEU* 6.1 0.9 - - + -
189A LEU* 3.6 31.6 - - + -
192A ALA* 5.3 3.1 - - + -
193A LEU* 4.9 8.7 - - + -
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Residues in contact with SER 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A GLU 2.6 17.7 + - - -
161A ASP* 2.4 29.5 + - - -
163A LEU* 1.3 72.0 - - - +
165A ARG* 1.3 74.1 + - - +
166A ALA 3.1 6.4 + - - -
167A GLY* 3.6 10.2 + - - +
168A ILE 4.8 2.0 - - - -
169A VAL* 6.2 3.6 - - - -
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Residues in contact with ARG 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ASP* 3.0 41.0 + - - +
162A LYS* 3.1 17.2 + - + +
164A SER* 1.3 89.7 + - - +
166A ALA* 1.3 57.6 + - - +
167A GLY 3.7 0.2 - - - -
192A ALA* 5.9 1.1 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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