Contacts of the helix formed by residues 147 - 165 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146B ALA* 1.3 87.6 - - + +
148B VAL* 1.3 64.3 + - - +
149B LEU* 3.4 1.1 - - + -
150B PRO* 3.2 36.4 - - + +
151B ALA* 3.3 12.0 + - - +
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Residues in contact with VAL 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B GLY 3.8 17.7 - - - +
146B ALA 4.3 1.6 - - - +
147B PRO* 1.3 73.7 - - - +
149B LEU* 1.3 61.7 + - + +
151B ALA* 4.1 1.1 - - - -
152B PHE* 2.9 27.7 + - - +
204B TYR* 3.1 27.3 + - - +
208B TYR* 3.9 30.7 - - + +
209B LEU* 3.4 25.4 - - + -
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Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B VAL* 1.3 80.7 - - + +
150B PRO* 1.4 73.2 - - + +
152B PHE* 3.0 9.2 + - + +
153B ILE* 3.0 43.5 + - + +
209B LEU* 4.6 22.7 - - + -
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Residues in contact with PRO 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ALA* 5.9 1.6 - - + -
147B PRO* 3.2 39.5 - - + +
149B LEU* 1.4 94.4 - - + +
151B ALA* 1.3 54.4 + - - +
153B ILE* 3.2 9.3 + - + +
154B ILE* 3.0 44.6 + - + +
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Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ALA* 3.4 34.5 - - - +
138B GLY* 4.5 1.2 + - - -
140B ALA* 4.8 0.7 - - + -
141B GLY* 3.7 18.4 - - - +
146B ALA* 4.4 9.1 - - + +
147B PRO 3.3 19.0 + - - +
148B VAL 3.4 5.2 - - - +
150B PRO* 1.3 78.8 - - - +
152B PHE* 1.3 55.9 + - - +
154B ILE* 4.6 4.3 - - - -
155B GLY* 2.9 25.1 + - - -
204B TYR* 3.8 3.8 - - - +
301B RET 5.3 0.2 - - - +
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Residues in contact with PHE 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B VAL 2.9 16.2 + - - +
149B LEU* 3.0 13.4 + - + +
151B ALA* 1.3 72.1 - - - +
153B ILE* 1.3 73.7 + - + +
155B GLY 3.7 0.3 - - - -
156B MET* 2.8 66.0 + - + +
201B PRO* 3.6 32.1 - - + -
204B TYR* 3.5 24.0 + + + -
205B ALA* 4.6 6.7 - - + -
209B LEU* 3.6 24.9 - - + -
301B RET 3.9 9.4 - - + -
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Residues in contact with ILE 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LEU* 3.0 34.2 + - + +
150B PRO* 3.2 9.2 + - + +
152B PHE* 1.3 83.3 - - + +
154B ILE* 1.3 57.5 + - + +
156B MET* 3.3 7.3 + - + +
157B ALA* 2.7 35.2 + - + +
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Residues in contact with ILE 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B VAL* 4.0 21.4 - - + +
137B ALA* 4.0 13.5 - - + -
150B PRO* 3.0 28.1 + - + +
151B ALA* 4.5 3.6 - - - +
153B ILE* 1.3 77.3 - - + +
155B GLY* 1.3 57.7 + - - +
157B ALA* 3.2 10.1 + - + +
158B GLY* 2.9 25.5 + - - -
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Residues in contact with GLY 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B MET* 3.5 22.8 - - - +
137B ALA* 3.5 13.4 - - - +
138B GLY 4.8 0.2 - - - -
151B ALA 2.9 18.1 + - - -
152B PHE 3.7 1.1 - - - -
154B ILE* 1.3 76.0 - - - +
156B MET* 1.3 56.4 + - - +
158B GLY* 3.3 2.4 + - - -
159B TRP* 3.0 24.9 + - - +
301B RET 3.8 15.0 - - - -
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Residues in contact with MET 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B PHE* 2.8 68.7 + - + +
153B ILE* 3.5 9.0 - - + +
155B GLY* 1.3 68.4 - - - +
157B ALA* 1.3 56.4 + - - +
159B TRP* 3.4 32.7 + - - +
160B LEU* 2.7 59.4 + - + +
201B PRO* 3.6 12.3 - - + -
301B RET 3.8 7.9 - - + -
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Residues in contact with ALA 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B VAL* 5.9 0.4 - - + -
153B ILE* 2.7 20.0 + - + +
154B ILE* 3.2 16.4 + - + +
156B MET* 1.3 73.1 - - - +
158B GLY* 1.3 52.9 + - - +
160B LEU* 3.2 10.9 + - - +
161B TYR* 2.8 36.7 + - - +
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Residues in contact with GLY 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLY* 3.8 22.5 - - - -
133B VAL* 4.2 14.5 - - - +
134B MET* 4.3 1.8 - - - -
154B ILE 2.9 13.6 + - - -
155B GLY 3.3 2.7 + - - -
157B ALA* 1.3 72.5 - - - +
159B TRP* 1.3 66.6 + - - +
161B TYR* 3.2 16.5 + - - +
162B MET* 3.3 15.2 + - - +
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Residues in contact with TRP 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B MET* 3.4 21.5 - - + +
155B GLY 3.0 12.9 + - - +
156B MET* 3.5 31.0 - - + +
158B GLY* 1.3 73.8 - - - +
160B LEU* 1.3 64.9 + - + +
162B MET* 2.9 26.8 + - + +
163B ILE* 3.4 21.7 + - + +
193B ILE* 2.9 24.1 + - + +
194B VAL* 3.3 21.8 - - + -
197B TRP* 3.7 29.6 - + + -
198B ALA* 3.5 32.5 - - + -
201B PRO* 3.8 16.4 - - + -
301B RET 3.8 16.6 - - + -
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Residues in contact with LEU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B MET* 2.7 52.4 + - + +
157B ALA* 3.6 8.1 - - - +
159B TRP* 1.3 80.2 - - + +
161B TYR* 1.3 56.2 + - - +
163B ILE* 3.3 19.9 + - + +
164B TYR* 3.0 28.9 + - - +
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Residues in contact with TYR 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B LYS* 3.2 52.9 - - - +
129B ALA* 5.1 4.3 - - + -
130B GLY* 4.0 20.6 - - - -
157B ALA 2.8 20.6 + - - +
158B GLY* 3.4 6.1 - - - +
159B TRP 3.2 0.2 - - - -
160B LEU* 1.3 72.2 - - - +
162B MET* 1.3 61.8 + - - +
164B TYR* 3.7 14.0 - + - +
165B GLU* 3.0 52.4 + - + +
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Residues in contact with MET 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B VAL* 4.2 10.3 - - + -
109B PHE* 6.5 1.1 - - + -
127B LEU* 3.6 44.1 - - + +
130B GLY* 3.8 13.2 - - - -
131B SER* 3.5 13.2 - - - -
134B MET* 3.3 30.1 - - - -
158B GLY 3.3 12.5 + - - +
159B TRP* 2.9 8.3 + - + +
161B TYR* 1.3 76.5 - - + +
163B ILE* 1.3 58.3 + - - +
165B GLU* 3.5 8.0 + - - +
166B LEU* 2.7 29.8 + - - +
193B ILE* 4.7 12.3 - - + -
197B TRP* 3.7 26.0 - - + -
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Residues in contact with ILE 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B TRP* 3.4 50.5 + - + +
160B LEU* 3.3 19.6 + - + +
162B MET* 1.3 73.0 - - - +
164B TYR* 1.3 65.6 + - - +
166B LEU* 3.0 19.2 + - - +
167B TYR* 3.1 36.8 - - + -
193B ILE* 4.2 13.9 - - + +
194B VAL* 4.3 27.6 - - + -
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Residues in contact with TYR 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B LEU 3.0 16.3 + - - +
161B TYR* 3.7 15.7 - + - +
162B MET 3.4 0.2 - - - -
163B ILE* 1.3 77.5 - - - +
165B GLU* 1.3 84.0 + - + +
167B TYR* 2.9 26.6 + - + +
168B MET* 3.1 44.2 + - + +
169B GLY* 4.9 2.6 - - - -
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Residues in contact with GLU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B LEU* 3.6 14.4 - - + +
126B LYS* 2.4 44.8 + - + +
127B LEU* 5.0 5.6 - - + -
161B TYR* 3.0 50.8 + - + +
162B MET* 3.9 6.3 - - - +
163B ILE 3.3 0.8 - - - -
164B TYR* 1.3 93.0 - - - +
166B LEU* 1.3 58.2 + - - +
167B TYR 3.3 2.5 - - - -
168B MET 5.0 0.4 - - - -
169B GLY* 3.7 5.4 - - - -
170B GLU 3.5 13.0 + - - -
171B GLY* 3.1 25.6 + - - -
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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
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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