Contacts of the helix formed by residues 146 - 166 (chain E) 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 GLN 146 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141E ILE* 3.6 32.1 + - + +
142E PRO 3.7 2.5 - - - +
143E PRO* 3.2 28.0 + - - +
144E GLU 3.4 0.6 - - - -
145E GLN* 1.3 77.1 - - - +
147E MET* 1.3 65.3 + - - +
148E ASN 3.4 0.2 - - - -
149E TYR* 3.6 8.2 + - + +
150E GLY* 3.5 14.9 + - - -
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Residues in contact with MET 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E PRO 4.5 2.4 + - - +
144E GLU 4.9 4.1 + - - +
146E GLN* 1.3 77.4 - - - +
148E ASN* 1.3 72.2 + - - +
150E GLY* 3.1 3.2 + - - -
151E ILE* 3.1 44.6 + - + +
220E ARG* 5.8 1.3 - - - -
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Residues in contact with ASN 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E GLU 5.0 3.2 + - - +
145E GLN* 3.0 36.6 + - - +
147E MET* 1.3 89.1 - - - +
149E TYR* 1.3 61.7 - - - +
151E ILE* 4.1 0.9 - - - +
152E LEU* 3.3 30.4 + - - +
220E ARG* 3.9 45.2 + - + +
223E GLU* 3.4 12.9 + - - -
224E LEU* 4.5 8.5 - - + -
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Residues in contact with TYR 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E LEU* 3.6 40.5 + - + +
137E VAL* 4.7 3.6 - - + -
139E GLN* 3.8 31.9 + - + -
141E ILE* 3.5 30.1 - - + -
145E GLN 3.9 9.2 + - - +
146E GLN* 3.6 13.1 + - + +
147E MET 3.2 0.8 - - - -
148E ASN* 1.3 76.8 - - - +
150E GLY* 1.3 66.9 + - - +
152E LEU* 4.1 1.3 - - - +
153E LYS* 3.2 60.2 + - + +
224E LEU* 3.7 13.4 - - + +
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Residues in contact with GLY 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E GLN 3.5 7.9 + - - -
147E MET 3.1 6.4 + - - -
149E TYR* 1.3 80.5 - - - +
151E ILE* 1.3 53.9 + - - +
153E LYS* 3.3 3.6 + - - +
154E GLN* 2.7 42.3 + - - +
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Residues in contact with ILE 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E MET* 3.1 38.9 + - + +
148E ASN 4.1 3.6 - - - +
149E TYR 3.5 0.4 - - - -
150E GLY* 1.3 74.8 - - - +
152E LEU* 1.3 63.3 + - - +
154E GLN* 3.4 11.9 + - - +
155E LYS* 3.1 50.2 + - - +
209E GLU* 4.0 18.6 - - + +
217E ASP* 4.9 0.7 - - - +
220E ARG* 3.5 40.2 - - - +
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Residues in contact with LEU 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E MET* 4.6 7.2 - - + -
134E LEU* 3.9 18.4 - - + -
148E ASN 3.3 18.0 + - - +
149E TYR 4.1 1.1 - - - +
150E GLY 3.3 0.6 - - - -
151E ILE* 1.3 76.0 - - - +
153E LYS* 1.3 62.5 + - - +
155E LYS* 3.2 14.9 + - - +
156E ILE* 3.3 19.1 + - + +
213E LEU* 4.9 4.4 - - + +
217E ASP* 3.5 43.7 - - + +
220E ARG* 3.9 13.0 - - + -
221E LEU* 3.7 42.8 - - + +
224E LEU* 4.3 11.7 - - + -
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Residues in contact with LYS 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E LEU* 3.9 14.8 - - + +
149E TYR* 3.2 54.1 + - + +
150E GLY* 3.9 4.0 - - - +
152E LEU* 1.3 79.5 - - - +
154E GLN* 1.3 60.7 + - - +
156E ILE* 4.1 6.8 - - + +
157E ALA* 3.4 21.5 + - - +
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Residues in contact with GLN 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E GLY 2.7 18.7 + - - +
151E ILE* 3.4 14.2 - - - +
152E LEU 3.1 0.2 - - - -
153E LYS* 1.3 76.3 - - - +
155E LYS* 1.3 65.9 + - + +
157E ALA* 3.6 6.7 + - - +
158E LEU* 3.3 20.1 + - + +
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Residues in contact with LYS 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E ILE* 3.1 24.9 - - - +
152E LEU* 3.2 6.8 + - - +
154E GLN* 1.3 78.4 - - + +
156E ILE* 1.3 60.2 + - - +
158E LEU* 3.0 8.8 + - - +
159E TYR* 2.9 36.8 + - + -
209E GLU* 2.7 20.9 + - - -
210E ASN 2.6 27.9 + - - +
211E PRO* 3.9 13.9 - - + +
212E ARG 2.7 25.7 + - - +
213E LEU* 4.0 12.8 - - + -
214E THR* 3.9 4.6 - - - +
217E ASP* 3.1 30.9 + - - +
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Residues in contact with ILE 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E MET* 3.7 22.2 - - + +
130E MET* 4.2 4.9 - - + +
131E LYS* 3.7 54.5 - - + +
134E LEU* 3.6 31.2 - - + -
152E LEU* 3.3 12.7 + - + +
153E LYS* 4.1 7.2 - - + +
154E GLN 3.4 0.2 - - - -
155E LYS* 1.3 75.2 - - + +
157E ALA* 1.3 58.2 + - - +
159E TYR* 3.2 8.3 + - - +
160E GLU* 2.8 34.2 + - - +
213E LEU* 5.1 10.1 - - + -
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Residues in contact with ALA 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E LYS 3.4 11.7 + - - +
154E GLN* 3.7 10.1 - - - +
155E LYS 3.2 0.2 - - - -
156E ILE* 1.3 77.8 - - - +
158E LEU* 1.3 53.4 + - - +
160E GLU* 3.6 9.3 - - - +
161E ASP* 2.6 37.7 + - - +
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Residues in contact with LEU 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154E GLN* 3.3 11.0 + - + +
155E LYS* 3.0 11.6 + - - +
157E ALA* 1.3 78.5 - - - +
159E TYR* 1.3 64.3 + - + +
161E ASP* 3.7 10.2 - - - +
162E LYS* 3.2 39.6 + - + +
196E ILE* 3.6 35.7 - - + -
211E PRO* 4.0 23.3 - - + +
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Residues in contact with TYR 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E ASP* 2.9 51.9 + - + -
124E VAL* 5.4 0.2 - - - -
127E MET* 3.6 34.8 - - + -
155E LYS* 2.9 27.8 + - + -
156E ILE* 3.4 9.0 - - - +
158E LEU* 1.3 82.4 - - + +
160E GLU* 1.3 57.8 + - - +
162E LYS* 3.2 7.6 + - - +
163E LEU* 3.0 33.3 + - + +
193E LEU* 4.4 16.6 - - + +
196E ILE* 4.5 8.7 - - + -
211E PRO 3.7 20.0 - - - -
212E ARG* 3.2 15.5 - - + +
213E LEU* 3.1 31.9 + - + +
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Residues in contact with GLU 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E MET* 3.6 17.7 - - + +
131E LYS* 3.2 38.3 - - - +
156E ILE* 2.8 26.7 + - - +
157E ALA* 3.8 7.8 - - - +
159E TYR* 1.3 71.4 - - - +
161E ASP* 1.3 60.0 + - - +
163E LEU* 3.7 10.2 - - + +
164E SER* 2.8 33.3 + - - -
170E ILE 4.7 7.5 - - - +
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Residues in contact with ASP 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157E ALA 2.6 23.0 + - - +
158E LEU* 3.7 12.7 - - - +
159E TYR 3.2 0.2 - - - -
160E GLU* 1.3 72.7 - - - +
162E LYS* 1.3 70.0 + - - +
164E SER* 3.0 18.9 + - - -
165E ARG* 2.3 53.8 + - - -
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Residues in contact with LYS 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158E LEU* 3.2 36.1 + - + +
159E TYR 3.2 9.0 + - - +
161E ASP* 1.3 88.1 + - - +
163E LEU* 1.3 61.9 + - - +
165E ARG* 3.4 19.4 - - - +
166E ALA 3.5 3.3 + - - -
192E ALA* 3.2 39.7 - - + +
193E LEU* 3.9 17.3 - - + -
195E SER* 2.8 32.8 + - - -
196E ILE* 4.2 13.5 - - + +
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Residues in contact with LEU 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E VAL* 4.7 7.9 - - + -
127E MET* 3.9 28.0 - - + -
159E TYR* 3.0 17.9 + - + +
160E GLU* 3.7 9.2 - - + +
162E LYS* 1.3 76.1 - - - +
164E SER* 1.3 58.6 + - - +
166E ALA* 3.2 3.0 + - - -
167E GLY 3.1 3.8 + - - -
168E ILE* 2.7 59.5 + - + +
170E ILE* 4.1 26.9 - - + +
189E LEU* 3.8 28.7 - - + -
192E ALA* 4.9 2.7 - - + -
193E LEU* 4.6 11.7 - - + -
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Residues in contact with SER 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E GLU 2.8 18.7 + - - -
161E ASP* 3.0 17.7 + - - -
163E LEU* 1.3 71.3 - - - +
165E ARG* 1.3 71.1 + - - +
167E GLY* 3.0 14.4 + - - +
168E ILE 3.7 6.2 + - - +
169E VAL* 5.7 5.2 - - - -
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Residues in contact with ARG 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E ASP* 2.3 52.1 + - - +
162E LYS* 3.4 13.0 - - - +
164E SER* 1.3 86.4 + - - +
166E ALA* 1.3 57.8 + - + +
167E GLY 3.2 1.8 + - - -
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Residues in contact with ALA 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E LYS 3.5 8.4 + - - +
163E LEU 3.2 6.7 + - - +
164E SER 3.2 0.4 - - - -
165E ARG* 1.3 77.0 - - + +
167E GLY* 1.3 63.0 + - - +
168E ILE* 3.3 8.4 + - + +
188E LYS* 3.2 59.0 - - + +
191E LYS* 6.2 0.7 - - + -
192E ALA* 4.4 4.3 - - + -
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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