Contacts of the helix formed by residues 120 - 143 (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 ALA 120 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B TYR* 3.7 35.3 - - + +
112B ILE 6.4 1.1 - - - -
119B VAL* 1.3 79.0 - - - +
121B ALA* 1.3 63.5 + - - +
123B LEU* 3.2 9.2 + - - +
124B PHE* 3.1 22.7 + - - +
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Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B TYR* 4.2 13.6 - - + +
119B VAL 3.6 0.4 - - - -
120B ALA* 1.3 79.6 - - - +
122B SER* 1.3 62.8 + - - +
124B PHE* 3.7 8.1 + - - +
125B LYS* 3.3 42.2 + - - +
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Residues in contact with SER 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B VAL* 3.3 12.0 + - - -
120B ALA 3.2 0.2 - - - -
121B ALA* 1.3 78.5 - - - +
123B LEU* 1.3 61.9 + - - +
125B LYS* 3.3 9.9 + - - +
126B LYS* 3.1 25.3 + - - +
170B GLU* 2.6 40.3 + - - -
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B VAL* 3.1 15.0 + - + +
120B ALA* 3.2 9.2 + - - +
122B SER* 1.3 74.6 - - - +
124B PHE* 1.3 56.6 + - - +
126B LYS* 3.1 23.4 + - + +
127B LEU* 2.7 54.3 + - + +
165B GLU* 3.6 30.3 - - + +
166B LEU* 5.5 5.4 - - + -
170B GLU* 3.6 28.0 - - + +
171B GLY* 4.1 9.9 - - - -
173B ALA* 6.4 0.2 - - + -
186B TYR* 5.5 6.7 - - + +
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Residues in contact with PHE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B PRO* 4.4 2.0 - - + -
106B VAL* 3.6 27.6 - - + +
107B VAL* 3.5 38.4 - - + -
110B TYR* 4.0 32.7 - + + +
120B ALA 3.1 15.5 + - - +
121B ALA* 3.8 8.1 - - - +
123B LEU* 1.3 75.6 - - - +
125B LYS* 1.3 67.7 + - + +
127B LEU* 3.6 4.2 - - - +
128B LEU* 2.8 63.1 + - + +
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Residues in contact with LYS 125 (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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121B ALA* 3.3 26.8 + - - +
122B SER* 3.6 9.4 - - - +
123B LEU 3.3 0.4 - - - -
124B PHE* 1.3 90.6 - - + +
126B LYS* 1.3 63.2 + - + +
128B LEU* 3.6 7.7 + - + +
129B ALA* 3.1 23.9 + - - +
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Residues in contact with LYS 126 (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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122B SER* 3.1 16.5 + - - +
123B LEU* 3.1 11.1 + - - +
125B LYS* 1.3 75.2 - - + +
127B LEU* 1.3 60.7 + - - +
129B ALA* 3.4 5.0 + - - +
130B GLY 3.0 23.7 + - - -
161B TYR* 3.2 32.9 - - + +
165B GLU* 2.4 53.5 + - + +
170B GLU* 3.2 47.2 - - - +
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Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B VAL* 3.5 25.4 - - + -
109B PHE* 4.3 29.6 - - + -
123B LEU* 2.7 40.0 + - + +
124B PHE* 4.5 1.8 - - - +
126B LYS* 1.3 70.9 - - - +
128B LEU* 1.3 54.4 + - - +
130B GLY* 3.3 1.9 + - - -
131B SER* 2.8 35.4 + - - -
162B MET* 3.6 53.4 - - + +
165B GLU* 5.0 6.3 - - + -
166B LEU* 3.8 17.7 - - + -
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Residues in contact with LEU 128 (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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103B PRO* 4.2 32.1 - - + -
106B VAL* 4.1 7.3 - - + +
124B PHE* 2.8 50.5 + - + +
125B LYS* 3.7 9.2 - - + +
127B LEU* 1.3 71.2 - - - +
129B ALA* 1.3 56.6 + - - +
131B SER* 2.5 27.1 + - - +
132B LEU* 2.8 44.9 + - + +
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Residues in contact with ALA 129 (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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125B LYS 3.1 14.9 + - - +
126B LYS* 3.6 6.3 - - - +
127B LEU 3.4 0.2 - - - -
128B LEU* 1.3 76.7 - - - +
130B GLY* 1.3 64.1 + - - +
132B LEU* 3.2 9.0 + - - +
133B VAL* 2.9 33.7 + - + +
161B TYR* 5.1 4.5 - - + -
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Residues in contact with GLY 130 (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 3.0 13.5 + - - -
127B LEU 3.6 3.6 - - - -
129B ALA* 1.3 76.0 - - - +
131B SER* 1.3 51.1 + - - +
133B VAL* 3.2 4.3 + - - +
134B MET* 2.8 35.3 + - - +
158B GLY* 3.8 20.4 - - - -
161B TYR* 4.0 12.5 - - - -
162B MET* 3.8 12.3 - - - -
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Residues in contact with SER 131 (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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102B VAL* 3.6 29.2 - - - +
103B PRO* 5.4 0.3 - - - +
106B VAL* 4.4 3.5 - - - +
127B LEU 2.8 15.4 + - - -
128B LEU* 2.5 37.8 + - - +
130B GLY* 1.3 72.4 - - - +
132B LEU* 1.3 57.2 + - - +
134B MET* 3.4 8.4 + - - +
135B LEU* 2.9 36.0 + - - +
162B MET* 3.5 18.1 - - - -
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Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 4.2 24.5 - - + -
103B PRO* 6.1 2.9 - - + -
128B LEU* 2.8 51.9 + - + +
129B ALA* 3.8 6.1 - - - +
131B SER* 1.3 73.8 + - - +
133B VAL* 1.3 60.5 + - + +
135B LEU* 4.3 4.4 - - + +
136B GLY* 2.9 28.9 + - - -
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Residues in contact with VAL 133 (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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129B ALA* 2.9 24.8 + - + +
130B GLY* 3.6 5.2 - - - +
132B LEU* 1.3 73.9 - - + +
134B MET* 1.3 65.2 + - - +
136B GLY* 5.1 0.9 - - - -
137B ALA* 3.1 24.6 + - - +
154B ILE* 4.0 30.7 - - + +
157B ALA* 5.9 0.4 - - + -
158B GLY* 4.2 10.5 - - - +
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Residues in contact with MET 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B VAL* 6.2 1.6 - - - -
130B GLY 2.8 14.7 + - - +
131B SER* 3.4 10.1 - - - +
133B VAL* 1.3 75.3 - - - +
135B LEU* 1.3 66.7 + - - +
137B ALA* 3.8 2.1 - - - +
138B GLY* 3.1 19.2 + - - -
155B GLY* 3.5 29.8 - - - +
158B GLY* 4.3 0.8 - - - -
159B TRP* 3.4 22.7 - - + +
162B MET* 3.3 34.1 - - - -
197B TRP* 3.8 9.6 - - + -
301B RET 3.0 57.3 - - + +
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Residues in contact with LEU 135 (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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95B TYR* 3.4 15.4 - - + +
98B TRP* 3.7 61.5 - - + +
99B LEU* 4.1 15.3 - - + +
102B VAL* 3.8 19.1 - - + -
103B PRO* 5.7 0.4 - - + -
131B SER 2.9 22.6 + - - +
132B LEU* 4.3 4.3 - - - +
134B MET* 1.3 75.5 - - + +
136B GLY* 1.3 53.4 + - - +
138B GLY 3.3 1.0 + - - -
139B PHE* 2.8 34.0 + - - +
301B RET 4.2 27.1 - - + -
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Residues in contact with GLY 136 (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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132B LEU 2.9 22.6 + - - -
133B VAL* 4.0 0.7 - - - -
135B LEU* 1.3 72.8 - - - +
137B ALA* 1.3 56.0 + - - +
139B PHE* 3.4 6.0 + - - +
140B ALA* 2.9 28.7 + - - +
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Residues in contact with ALA 137 (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 3.1 18.2 + - - +
136B GLY* 1.3 71.9 - - - +
138B GLY* 1.3 67.1 + - - +
140B ALA* 3.2 10.2 - - - +
141B GLY 3.1 19.1 + - - -
151B ALA* 3.4 31.0 - - - +
154B ILE* 4.0 15.3 - - + -
155B GLY* 3.5 15.7 - - - +
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Residues in contact with GLY 138 (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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95B TYR* 3.3 9.6 - - - -
134B MET 3.1 11.6 + - - -
135B LEU 3.6 3.1 - - - -
137B ALA* 1.3 77.3 - - - +
139B PHE* 1.3 61.7 + - - +
141B GLY* 3.3 1.6 + - - -
142B GLU* 3.1 26.5 + - - +
151B ALA 4.5 1.3 + - - -
155B GLY* 4.8 0.4 - - - -
204B TYR* 3.8 5.3 - - - -
301B RET 3.6 32.0 - - - +
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Residues in contact with PHE 139 (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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25A ILE* 3.8 38.6 - - + -
91B THR* 4.0 15.3 - - + -
92B VAL* 4.1 23.3 - - + -
95B TYR* 3.3 38.7 - + + -
135B LEU 2.8 19.3 + - - +
136B GLY* 3.7 6.3 - - - +
138B GLY* 1.3 72.6 - - - +
140B ALA* 1.3 59.7 + - - +
142B GLU* 3.0 2.1 + - - -
143B ALA* 2.7 60.1 + - + +
145B LEU* 4.5 13.7 - - + -
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Residues in contact with ALA 140 (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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136B GLY 2.9 15.1 + - - +
137B ALA* 3.2 15.3 - - - +
139B PHE* 1.3 75.9 - - - +
141B GLY* 1.3 59.6 + - - +
143B ALA 3.7 0.2 + - - -
144B GLY 3.2 1.7 + - - -
145B LEU* 2.8 47.5 + - + +
146B ALA* 3.4 21.0 + - + +
151B ALA* 4.8 0.9 - - + -
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Residues in contact with GLY 141 (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 3.1 7.9 + - - -
138B GLY 3.7 1.1 - - - -
140B ALA* 1.3 78.6 - - - +
142B GLU* 1.3 61.1 + - - +
144B GLY* 3.2 12.8 + - - -
146B ALA 3.7 13.7 - - - +
148B VAL* 3.8 15.0 - - - +
151B ALA* 3.7 8.8 - - - +
204B TYR* 3.4 23.3 - - - -
208B TYR* 4.9 0.7 - - - -
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Residues in contact with GLU 142 (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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89B THR* 5.0 0.9 - - - +
91B THR* 3.8 27.1 + - + +
95B TYR* 2.5 32.3 + - + +
138B GLY 3.1 15.1 + - - +
139B PHE 3.0 2.5 + - - +
141B GLY* 1.3 75.4 - - - +
143B ALA* 1.3 60.5 + - - +
144B GLY 3.2 1.3 + - - -
204B TYR* 3.7 5.8 + - + -
208B TYR* 2.5 54.7 + - + +
220B LEU* 3.8 11.6 - - - +
224B TYR* 2.6 25.6 + - - -
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Residues in contact with ALA 143 (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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25A ILE* 5.8 4.5 - - + -
91B THR* 4.6 3.8 - - + +
92B VAL* 6.3 0.2 - - + -
139B PHE* 2.7 53.0 + - + +
142B GLU* 1.3 72.0 - - - +
144B GLY* 1.3 61.0 + - - +
145B LEU* 3.7 18.4 + - + +
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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
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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