Contacts of the helix formed by residues 147 - 168 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A ALA* 1.4 87.9 - - + +
148A VAL* 1.3 65.8 + - - +
149A LEU 3.2 0.6 + - - +
150A PRO* 3.3 28.3 - - + +
151A ALA* 3.2 22.0 + - - +
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Residues in contact with VAL 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A GLY* 3.8 20.6 - - - +
146A ALA 4.3 1.6 - - - +
147A PRO* 1.3 72.5 - - - +
149A LEU* 1.3 67.0 + - + +
152A PHE* 3.4 12.3 + - - +
204A TYR* 2.9 28.3 + - - +
208A TYR* 4.1 32.3 - - + +
209A LEU* 3.8 21.0 - - + +
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Residues in contact with LEU 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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147A PRO* 4.6 0.4 - - - +
148A VAL* 1.3 82.5 - - + +
150A PRO* 1.4 70.2 - - + +
152A PHE* 3.2 10.7 - - + +
153A ILE* 2.7 48.7 + - + +
209A LEU* 4.4 22.7 - - + -
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Residues in contact with PRO 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ALA* 5.8 0.2 - - + -
147A PRO* 3.3 45.5 - - + +
149A LEU* 1.4 98.6 - - + +
151A ALA* 1.3 60.7 + - - +
153A ILE* 3.2 12.8 + - + +
154A ILE* 3.1 34.7 + - + +
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Residues in contact with ALA 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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137A ALA* 3.4 32.9 - - - +
140A ALA* 5.0 0.2 - - + -
141A GLY* 3.8 18.2 - - - +
146A ALA* 4.4 10.5 - - + +
147A PRO 3.2 19.8 + - - +
148A VAL 4.1 1.6 - - - +
150A PRO* 1.3 75.0 - - - +
152A PHE* 1.3 54.2 + - - +
154A ILE* 3.0 11.7 + - - +
155A GLY 2.7 32.6 + - - -
204A TYR* 4.2 1.3 - - - +
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Residues in contact with PHE 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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148A VAL 3.4 13.2 + - - +
149A LEU* 3.2 14.5 + - + +
151A ALA* 1.3 77.8 - - - +
153A ILE* 1.3 61.6 + - + +
155A GLY* 3.6 0.7 - - - -
156A MET* 2.7 65.4 + - + +
201A PRO* 3.7 36.6 - - + -
204A TYR* 3.4 31.4 + + + -
205A ALA* 4.7 4.7 - - + -
209A LEU* 3.9 20.9 - - + -
301A RET 4.1 13.6 - - + +
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Residues in contact with ILE 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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149A LEU* 2.7 57.2 + - + +
150A PRO* 3.2 11.4 + - + +
152A PHE* 1.3 82.5 - - + +
154A ILE* 1.3 59.4 + - + +
156A MET* 3.1 8.7 + - + +
157A ALA* 2.8 28.5 + - + +
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Residues in contact with ILE 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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133A VAL* 3.9 22.5 - - + +
137A ALA* 3.9 10.3 - - + -
150A PRO* 3.1 25.3 + - + +
151A ALA* 3.0 9.1 + - - +
153A ILE* 1.3 72.8 - - + +
155A GLY* 1.3 66.8 + - - +
157A ALA* 3.1 9.9 + - + +
158A GLY 3.0 20.1 + - - -
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Residues in contact with GLY 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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134A MET* 3.6 24.9 - - - +
137A ALA* 3.2 16.8 - - - +
151A ALA 2.7 16.4 + - - -
152A PHE 3.6 4.7 - - - -
154A ILE* 1.3 73.2 - - - +
156A MET* 1.3 55.1 + - - +
158A GLY 3.3 0.9 + - - -
159A TRP 3.0 22.5 + - - -
301A RET 3.8 16.4 - - - +
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Residues in contact with MET 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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152A PHE* 2.7 62.3 + - + +
153A ILE* 3.1 11.0 + - + +
155A GLY* 1.3 72.3 - - - +
157A ALA* 1.3 52.6 + - - +
159A TRP* 3.2 30.9 + - + +
160A LEU* 2.6 62.9 + - + +
201A PRO* 3.7 22.0 - - - -
301A RET 4.1 5.6 - - + +
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Residues in contact with ALA 157 (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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133A VAL* 5.9 0.4 - - + -
153A ILE* 2.8 17.9 + - + +
154A ILE* 3.1 14.8 + - + +
156A MET* 1.3 70.0 - - - +
158A GLY* 1.3 56.4 + - - +
160A LEU* 3.5 7.2 - - - +
161A TYR* 2.6 39.4 + - - +
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Residues in contact with GLY 158 (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 GLY* 3.6 26.5 - - - -
133A VAL* 4.1 13.1 - - - +
134A MET 4.3 0.9 - - - -
154A ILE 3.0 12.9 + - - -
155A GLY 3.7 3.4 - - - -
157A ALA* 1.3 74.7 - - - +
159A TRP* 1.3 63.8 + - - +
161A TYR* 3.3 5.8 + - - +
162A MET* 3.1 25.5 + - - +
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Residues in contact with TRP 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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134A MET* 3.4 35.8 - - + +
155A GLY 3.0 6.7 + - - -
156A MET* 3.5 38.8 - - + +
158A GLY* 1.3 76.2 - - - +
160A LEU* 1.3 68.4 + - + +
162A MET* 3.2 11.9 + - - +
163A ILE* 3.2 31.9 + - + +
193A ILE* 3.0 32.7 + - + +
194A VAL* 3.6 13.0 - - + -
197A TRP* 3.9 17.3 - + + -
198A ALA* 3.5 30.3 - - + -
201A PRO* 3.6 22.0 - - + -
301A RET 3.6 7.9 - - + -
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Residues in contact with LEU 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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156A MET* 2.6 47.6 + - + +
157A ALA* 3.1 6.3 + - - +
159A TRP* 1.3 75.8 - - + +
161A TYR* 1.3 56.2 + - - +
163A ILE* 3.3 24.5 + - + +
164A TYR* 2.8 35.8 + - - +
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Residues in contact with TYR 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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126A LYS* 3.1 52.5 - - + +
129A ALA* 5.1 3.8 - - + -
130A GLY* 4.1 17.9 - - - -
157A ALA 2.6 22.1 + - - +
158A GLY* 3.7 4.3 - - - +
160A LEU* 1.3 69.8 - - - +
162A MET* 1.3 66.9 + - - +
164A TYR* 3.5 13.3 + + - +
165A GLU* 3.0 46.0 + - + +
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Residues in contact with MET 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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106A VAL* 4.3 7.0 - - + -
109A PHE* 5.6 0.4 - - + -
127A LEU* 3.4 51.3 - - + +
130A GLY* 3.9 14.8 - - - -
131A SER* 3.7 23.1 - - - -
134A MET* 4.5 5.8 - - - +
158A GLY 3.1 14.5 + - - +
159A TRP* 3.3 8.3 - - - +
161A TYR* 1.3 76.6 - - - +
163A ILE* 1.3 66.5 + - + +
165A GLU* 3.1 15.5 + - - +
166A LEU* 3.1 17.1 + - - +
193A ILE* 5.0 9.6 - - + -
197A TRP* 3.7 39.3 - - + -
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Residues in contact with ILE 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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159A TRP* 3.2 46.7 + - + +
160A LEU* 3.6 22.2 - - + +
162A MET* 1.3 78.8 - - - +
164A TYR* 1.3 64.0 + - - +
166A LEU* 3.2 6.6 + - - +
167A TYR* 3.0 50.9 + - + -
168A MET* 5.8 3.4 - - + -
193A ILE* 3.7 25.3 - - + +
194A VAL* 4.2 16.8 - - + -
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Residues in contact with TYR 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 LEU 2.8 19.7 + - - +
161A TYR* 3.6 15.0 - + - +
163A ILE* 1.3 73.8 - - - +
165A GLU* 1.3 84.4 + - + +
168A MET* 2.7 72.8 + - + -
169A GLY* 3.0 24.5 + - - -
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Residues in contact with GLU 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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123A LEU* 3.8 11.4 - - + +
126A LYS* 3.4 38.5 + - + +
127A LEU* 5.6 3.1 - - + -
161A TYR* 3.0 48.9 + - + +
162A MET* 3.1 5.6 + - - +
164A TYR* 1.3 95.7 - - + +
166A LEU* 1.3 55.6 + - - +
169A GLY* 3.6 3.2 - - - +
170A GLU* 2.9 31.8 + - - +
171A GLY* 2.7 32.6 + - - -
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Residues in contact with LEU 166 (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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113A LEU* 3.8 36.3 - - + -
123A LEU* 4.1 12.6 - - + -
127A LEU* 4.3 14.4 - - + -
162A MET 3.1 12.9 + - - +
163A ILE* 3.6 9.2 - - - +
165A GLU* 1.3 76.8 - - - +
167A TYR* 1.3 60.9 + - + +
171A GLY* 3.4 24.1 - - - +
172A LYS* 4.7 0.2 - - - -
186A TYR* 4.4 1.8 + - + -
189A MET* 4.5 9.4 - - + -
190A MET* 3.7 37.7 - - + +
193A ILE* 3.4 35.7 - - + -
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Residues in contact with TYR 167 (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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163A ILE* 3.0 36.3 + - + +
164A TYR 4.1 1.1 - - - +
166A LEU* 1.3 81.4 - - + +
168A MET* 1.3 78.8 + - + +
172A LYS* 4.2 12.4 - - - +
190A MET* 3.0 55.1 + - + +
191A MET* 4.5 10.3 - - + +
193A ILE* 6.1 1.1 - - + -
194A VAL* 3.9 23.9 - - + +
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Residues in contact with MET 168 (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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163A ILE* 5.4 3.6 - - + -
164A TYR* 2.7 58.8 + - + +
166A LEU 3.7 0.2 - - - -
167A TYR* 1.3 89.0 - - + +
169A GLY* 1.3 65.6 + - - +
172A LYS* 3.2 25.3 + - - +
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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