Contacts of the helix formed by residues 147 - 168 (chain E) in PDB entry 4KNF
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 147 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146E ALA* 1.3 88.9 - - + +
148E VAL* 1.3 65.2 + - - +
149E LEU 3.1 2.1 + - - +
150E PRO* 3.4 24.4 - - + +
151E ALA* 3.3 18.9 + - - +
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Residues in contact with VAL 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141E GLY* 4.1 15.0 - - - +
146E ALA 3.3 2.1 + - - -
147E PRO* 1.3 73.0 - - - +
149E LEU* 1.3 61.2 + - + +
151E ALA* 4.6 0.7 - - - -
152E PHE* 3.3 14.1 + - - +
204E TYR* 2.8 36.6 + - + +
208E TYR* 3.3 40.8 - - + +
209E LEU* 3.3 25.1 - - + +
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Residues in contact with LEU 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E PRO* 4.6 0.2 - - - +
148E VAL* 1.3 82.5 - - + +
150E PRO* 1.4 76.1 - - + +
151E ALA 3.2 1.3 - - - -
152E PHE* 3.0 23.0 + - + +
153E ILE* 3.0 33.1 + - + +
209E LEU* 4.7 15.0 - - + -
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Residues in contact with PRO 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146E ALA* 6.0 0.2 - - + -
147E PRO* 3.4 37.7 - - + +
149E LEU* 1.4 95.7 - - + +
151E ALA* 1.3 60.7 + - - +
153E ILE* 3.2 9.4 + - + +
154E ILE* 3.0 32.0 + - + +
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Residues in contact with ALA 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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137E ALA* 3.4 32.4 - - - +
138E GLY 4.5 0.4 + - - -
140E ALA* 4.9 0.9 - - + -
141E GLY* 3.7 20.9 - - - +
146E ALA* 4.5 11.5 - - + +
147E PRO 3.3 18.7 + - - +
150E PRO* 1.3 79.7 - - - +
152E PHE* 1.3 57.7 + - - +
154E ILE* 4.7 3.8 - - - -
155E GLY* 3.0 24.9 + - - -
204E TYR* 3.8 4.5 - - - +
301E RET 5.0 0.2 - - - +
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Residues in contact with PHE 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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138E GLY* 6.1 0.2 - - - -
148E VAL 3.3 13.6 + - - +
149E LEU* 3.0 13.5 + - + +
151E ALA* 1.3 78.0 - - - +
153E ILE* 1.3 76.9 + - + +
155E GLY 3.4 0.9 + - - -
156E MET* 2.9 59.5 + - + +
201E PRO* 3.8 36.3 - - + -
204E TYR* 3.4 29.8 + + + -
205E ALA* 4.7 5.2 - - + -
209E LEU* 3.7 23.1 - - + -
301E RET 4.2 11.7 - - + +
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Residues in contact with ILE 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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149E LEU* 3.0 28.4 + - + +
150E PRO* 3.2 9.8 + - + +
152E PHE* 1.3 96.5 - - + +
154E ILE* 1.3 63.3 + - + +
156E MET* 3.4 8.0 + - + +
157E ALA* 3.0 26.6 + - + +
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Residues in contact with ILE 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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133E VAL* 4.1 18.1 - - + +
137E ALA* 3.8 14.1 - - + -
150E PRO* 3.0 23.1 + - + +
151E ALA* 3.8 5.2 - - - +
153E ILE* 1.3 77.0 - - + +
155E GLY* 1.3 61.1 + - - +
156E MET 3.0 1.3 - - - -
157E ALA* 2.8 25.7 + - + +
158E GLY 3.2 9.7 + - - -
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Residues in contact with GLY 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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134E MET* 3.5 29.8 - - - +
137E ALA* 3.2 20.6 - - - +
151E ALA 3.0 11.5 + - - -
154E ILE* 1.3 76.2 - - - +
156E MET* 1.3 60.4 + - - +
159E TRP 3.3 15.9 + - - -
301E RET 3.8 16.7 - - - +
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Residues in contact with MET 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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152E PHE* 2.9 48.8 + - + +
153E ILE* 3.4 10.5 - - + +
155E GLY* 1.3 79.9 - - - +
157E ALA* 1.3 56.7 + - - +
159E TRP* 3.4 28.3 + - + +
160E LEU* 3.0 47.9 + - + +
201E PRO* 3.9 19.7 - - + -
301E RET 3.8 6.5 - - - +
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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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133E VAL* 5.7 0.9 - - + -
153E ILE* 3.0 12.7 + - + +
154E ILE* 2.8 17.6 + - + +
156E MET* 1.3 74.7 - - - +
158E GLY* 1.3 54.8 + - - +
160E LEU* 3.2 7.2 + - - +
161E TYR* 2.7 37.8 + - - +
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Residues in contact with GLY 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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130E GLY* 3.5 28.3 - - - +
133E VAL* 4.2 8.7 - - - +
134E MET* 4.2 5.8 - - - -
154E ILE 3.2 7.3 + - - -
155E GLY 3.5 4.0 + - - -
157E ALA* 1.3 74.9 - - - +
159E TRP* 1.3 67.5 + - - +
161E TYR* 3.5 5.7 + - - +
162E MET* 3.1 24.6 + - - +
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Residues in contact with TRP 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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134E MET* 3.8 6.7 - - - +
155E GLY 3.3 6.3 + - - -
156E MET* 3.5 31.6 - - + +
157E ALA 3.3 0.6 - - - -
158E GLY* 1.3 74.1 - - - +
160E LEU* 1.3 74.3 + - + +
162E MET* 2.8 37.8 + - + +
163E ILE* 3.0 26.2 + - + +
193E ILE* 3.0 28.7 + - + -
194E VAL* 3.6 14.1 - - + -
197E TRP* 3.5 32.3 - + + +
198E ALA* 3.6 33.4 - - + -
201E PRO* 4.2 7.2 - - + -
301E RET 3.6 32.3 - - + -
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Residues in contact with LEU 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156E MET* 3.0 31.8 + - + +
157E ALA* 3.7 5.6 - - - +
159E TRP* 1.3 102.4 - - + +
161E TYR* 1.3 51.7 + - - +
163E ILE* 3.2 18.2 + - + +
164E TYR* 2.6 36.0 + - - +
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Residues in contact with TYR 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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126E LYS* 3.3 40.6 - - - +
129E ALA* 5.5 1.8 - - + -
130E GLY* 4.1 17.7 - - - -
157E ALA 2.7 21.6 + - - +
158E GLY* 3.7 5.2 - - - +
160E LEU* 1.3 73.0 - - - +
162E MET* 1.3 59.4 + - - +
164E TYR* 3.5 19.8 - + - +
165E GLU* 2.9 66.0 + - + +
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Residues in contact with MET 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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106E VAL* 5.2 2.0 - - - -
127E LEU* 3.4 59.9 - - + +
130E GLY* 4.0 7.2 - - - -
131E SER* 3.7 14.6 - - - -
134E MET* 3.4 26.9 - - + -
158E GLY 3.1 12.1 + - - +
159E TRP* 2.8 34.0 + - + +
161E TYR* 1.3 72.8 - - - +
163E ILE* 1.3 60.1 + - - +
165E GLU 3.5 0.2 + - - -
166E LEU* 3.2 22.7 + - - +
193E ILE* 4.0 10.1 - - + -
197E TRP* 3.3 34.5 - - + -
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Residues in contact with ILE 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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159E TRP* 3.0 40.2 + - + +
160E LEU* 3.7 21.1 - - + +
162E MET* 1.3 74.4 - - - +
164E TYR* 1.3 67.9 + - - +
166E LEU* 3.4 3.5 + - - -
167E TYR* 3.1 46.4 + - + +
193E ILE* 3.5 35.7 - - + +
194E VAL* 4.1 16.4 - - + -
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Residues in contact with TYR 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 LEU 2.6 20.7 + - - +
161E TYR* 3.3 28.2 + + - +
163E ILE* 1.3 73.4 - - - +
165E GLU* 1.3 83.6 + - - +
167E TYR* 5.4 0.4 - - - -
168E MET* 2.8 49.2 + - + +
169E GLY* 3.0 27.6 + - - -
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Residues in contact with GLU 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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123E LEU* 3.5 16.8 - - + +
126E LYS* 3.4 26.0 + - + +
127E LEU* 4.6 6.5 - - + -
161E TYR* 2.9 62.4 + - + +
162E MET* 3.9 4.0 - - - +
163E ILE 3.4 0.2 - - - -
164E TYR* 1.3 86.3 - - + +
166E LEU* 1.3 54.0 + - - +
169E GLY* 3.5 6.6 - - - +
170E GLU* 3.2 28.1 + - - +
171E GLY* 2.7 32.4 + - - -
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Residues in contact with LEU 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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109E PHE* 5.3 1.1 - - + -
113E LEU* 4.0 37.2 - - + -
123E LEU* 4.9 5.4 - - + -
127E LEU* 4.1 19.1 - - + -
162E MET 3.2 21.0 + - - +
163E ILE 4.0 2.9 - - - +
164E TYR 3.3 0.2 - - - -
165E GLU* 1.3 77.9 - - - +
167E TYR* 1.3 64.2 + - + +
171E GLY* 3.3 22.2 - - - +
186E TYR* 4.3 3.6 + - + -
189E MET* 4.1 11.9 - - + -
190E MET* 3.6 36.0 - - + +
193E ILE* 3.9 37.2 - - + -
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Residues in contact with TYR 167 (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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163E ILE* 3.1 31.1 + - + +
164E TYR* 5.4 0.2 - - - -
166E LEU* 1.3 82.4 - - + +
168E MET* 1.3 85.7 + - + +
169E GLY 3.8 0.2 - - - -
171E GLY 4.7 0.2 - - - -
172E LYS* 3.9 14.1 + - - +
190E MET* 2.7 57.2 + - + +
191E MET* 4.7 0.9 - - - -
193E ILE* 4.9 2.7 - - + -
194E VAL* 3.3 27.3 - - + +
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Residues in contact with MET 168 (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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164E TYR* 2.8 31.1 + - + +
167E TYR* 1.3 103.7 - - + +
169E GLY* 1.3 67.7 + - - +
172E LYS* 3.8 36.6 + - + +
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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) + - + + + + + -
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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