Contacts of the helix formed by residues 119 - 143 (chain C) 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 VAL 119 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C THR* 3.2 20.1 - - + -
118C SER* 1.3 85.3 - - - +
120C ALA* 1.3 62.3 + - - +
121C ALA 3.4 2.9 - - - -
122C SER* 3.1 7.1 + - - -
123C LEU* 3.0 37.7 + - + +
170C GLU* 3.5 42.4 - - + +
171C GLY* 4.6 0.4 - - - -
173C ALA* 3.9 17.5 - - + -
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Residues in contact with ALA 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C TYR* 3.3 19.3 - - + +
113C LEU* 3.7 18.4 - - + +
114C ALA* 3.4 43.1 - - + +
117C THR* 4.0 3.9 + - - +
118C SER 3.4 3.4 + - - +
119C VAL* 1.3 76.7 - - - +
121C ALA* 1.3 56.2 + - - +
123C LEU* 3.6 5.5 + - - +
124C PHE* 3.1 22.5 + - - +
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Residues in contact with ALA 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C TYR* 3.8 20.2 - - + +
118C SER 5.3 0.4 + - - -
119C VAL 3.4 0.6 - - - -
120C ALA* 1.3 76.3 - - - +
122C SER* 1.3 63.7 + - - +
124C PHE* 3.8 4.6 - - - +
125C LYS* 3.3 28.8 + - - +
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Residues in contact with SER 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C VAL* 3.1 7.4 + - - -
121C ALA* 1.3 77.6 - - - +
123C LEU* 1.3 63.6 + - - +
125C LYS* 3.0 21.5 + - - +
126C LYS* 3.2 17.8 + - - +
170C GLU* 2.8 38.8 + - - -
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Residues in contact with LEU 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C LEU* 3.8 36.3 - - + -
117C THR* 5.2 2.5 - - + -
119C VAL* 3.0 37.6 + - + +
120C ALA* 3.7 5.6 - - - +
122C SER* 1.3 77.0 - - - +
124C PHE* 1.3 53.4 + - - +
126C LYS* 2.9 7.8 + - + +
127C LEU* 2.7 42.4 + - + +
165C GLU* 3.3 38.8 - - + +
166C LEU* 4.1 11.4 - - + -
170C GLU* 4.3 9.8 + - + +
171C GLY* 4.0 14.8 - - - +
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Residues in contact with PHE 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C PRO* 4.9 2.0 - - + -
106C VAL* 3.6 22.6 - - + +
107C VAL* 3.5 35.9 - - + -
110C TYR* 3.4 33.4 - + + +
113C LEU* 5.3 1.0 - - - +
120C ALA 3.1 19.5 + - - +
121C ALA* 3.8 9.0 - - - +
122C SER 3.2 0.4 - - - -
123C LEU* 1.3 73.2 - - - +
125C LYS* 1.3 71.7 + - + +
127C LEU* 4.1 7.2 - - - +
128C LEU* 3.0 49.6 + - + +
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Residues in contact with LYS 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ALA* 3.3 22.4 + - - +
122C SER* 3.0 14.1 + - - +
124C PHE* 1.3 88.6 - - + +
126C LYS* 1.3 58.7 + - + +
128C LEU* 3.6 5.7 + - - +
129C ALA* 3.1 26.2 + - - +
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Residues in contact with LYS 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C SER* 3.2 11.2 + - - +
123C LEU* 2.9 9.6 + - + +
125C LYS* 1.3 80.8 - - + +
127C LEU* 1.3 55.5 + - - +
129C ALA* 3.2 8.2 + - - +
130C GLY 2.7 32.1 + - - -
161C TYR* 3.4 36.7 - - + +
165C GLU* 3.5 34.1 + - + +
170C GLU* 2.9 33.8 + - + +
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Residues in contact with LEU 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C VAL* 4.0 15.5 - - + +
109C PHE* 4.2 28.9 - - + -
110C TYR 5.8 0.2 - - - +
113C LEU* 4.6 7.0 - - + -
123C LEU* 2.7 31.3 + - + +
124C PHE* 4.1 1.3 - - - +
126C LYS* 1.3 73.4 - - - +
128C LEU* 1.3 60.1 + - - +
130C GLY 3.4 0.7 + - - -
131C SER* 3.0 20.3 + - - -
162C MET* 3.4 56.0 - - + +
165C GLU* 4.8 4.0 - - + -
166C LEU* 3.8 36.3 - - + -
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Residues in contact with LEU 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C PRO* 3.9 37.2 - - + +
106C VAL* 4.2 11.1 - - + +
124C PHE* 3.0 39.9 + - + +
125C LYS* 3.6 6.5 - - - +
127C LEU* 1.3 75.0 - - - +
129C ALA* 1.3 63.9 + - - +
131C SER* 2.4 30.2 + - - +
132C LEU* 3.0 25.9 + - + +
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Residues in contact with ALA 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C LYS 3.1 12.2 + - - +
126C LYS* 3.3 12.1 - - - +
128C LEU* 1.3 77.7 - - - +
130C GLY* 1.3 65.0 + - - +
132C LEU* 3.4 6.6 + - - +
133C VAL* 3.3 26.0 + - + +
161C TYR* 5.1 4.5 - - + -
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Residues in contact with GLY 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C LYS 2.7 18.7 + - - -
127C LEU 3.7 1.8 - - - -
129C ALA* 1.3 76.0 - - - +
131C SER* 1.3 51.2 + - - +
133C VAL* 3.2 4.1 + - - +
134C MET* 2.8 33.7 + - - +
158C GLY* 3.8 17.1 - - - -
161C TYR* 4.0 12.0 - - - -
162C MET* 3.9 14.1 - - - -
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Residues in contact with SER 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C VAL* 3.6 29.8 - - - +
103C PRO* 5.8 0.2 - - - +
106C VAL* 4.5 1.7 - - - +
127C LEU 3.0 12.2 + - - -
128C LEU* 2.4 35.3 + - - +
130C GLY* 1.3 74.2 - - - +
132C LEU* 1.3 62.2 + - - +
134C MET* 3.5 8.6 - - - +
135C LEU* 2.9 35.6 + - - +
162C MET* 3.7 16.6 - - - -
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Residues in contact with LEU 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C LEU* 4.2 24.2 - - + -
103C PRO* 5.3 7.2 - - + -
128C LEU* 3.0 27.4 + - + +
129C ALA* 4.0 6.1 - - - +
131C SER* 1.3 86.0 + - - +
133C VAL* 1.3 56.6 + - + +
135C LEU* 3.1 9.8 + - + +
136C GLY* 2.7 34.1 + - - -
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Residues in contact with VAL 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C ALA 3.3 11.1 + - - +
130C GLY* 3.2 7.9 + - - +
132C LEU* 1.3 76.2 - - + +
134C MET* 1.3 67.0 + - - +
135C LEU 3.1 0.2 + - - -
136C GLY* 4.5 1.1 - - - +
137C ALA* 2.9 27.6 + - - +
154C ILE* 4.0 31.2 - - + +
157C ALA* 5.8 0.9 - - + -
158C GLY* 4.3 8.1 - - - +
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Residues in contact with MET 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C VAL* 4.7 3.6 - - + -
130C GLY 2.8 19.8 + - - +
131C SER* 3.5 18.2 - - - +
133C VAL* 1.3 74.3 - - - +
135C LEU* 1.3 66.4 + - + +
138C GLY* 3.1 24.9 + - - -
155C GLY* 3.6 32.5 - - - +
158C GLY* 4.0 0.8 - - - -
159C TRP* 3.5 29.6 - - - +
162C MET* 4.7 2.2 - - - +
197C TRP* 4.0 17.0 - - + -
301C RET 3.3 62.0 - - + +
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Residues in contact with LEU 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C TYR* 3.3 18.9 - - + +
98C TRP* 3.6 63.9 - - + +
99C LEU* 4.0 14.8 - - + +
102C VAL* 3.9 15.5 - - + -
103C PRO* 5.6 0.4 - - + -
131C SER* 2.9 23.7 + - - +
132C LEU* 3.7 7.9 - - + +
134C MET* 1.3 85.8 - - + +
136C GLY* 1.3 59.9 + - - +
138C GLY 4.5 0.2 - - - +
139C PHE* 2.9 28.7 + - - +
301C RET 4.6 8.7 - - + -
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Residues in contact with GLY 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LEU 2.7 19.4 + - - -
133C VAL* 3.8 1.8 - - - -
135C LEU* 1.3 70.4 - - - +
137C ALA* 1.3 58.6 + - - +
139C PHE* 3.8 7.2 - - - +
140C ALA* 3.0 29.3 + - - +
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Residues in contact with ALA 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C VAL 2.9 16.1 + - - +
136C GLY* 1.3 72.4 - - - +
138C GLY* 1.3 68.9 + - - +
140C ALA* 3.1 15.9 + - - +
141C GLY 3.1 9.2 + - - -
151C ALA* 3.4 18.5 - - - +
154C ILE* 3.7 18.6 - - + -
155C GLY* 3.4 29.2 - - - +
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Residues in contact with GLY 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C TYR* 3.3 9.9 - - - -
134C MET 3.1 11.9 + - - -
135C LEU 3.8 2.7 - - - -
137C ALA* 1.3 78.1 - - - +
139C PHE* 1.3 62.1 + - - +
141C GLY* 3.1 10.0 + - - -
142C GLU* 3.2 15.9 + - - +
151C ALA 5.1 0.4 - - - -
204C TYR* 3.8 5.4 - - - -
301C RET 3.3 33.0 - - - +
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Residues in contact with PHE 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ILE* 3.6 41.3 - - + -
91C THR* 4.0 13.5 - - + -
92C VAL* 3.8 25.8 - - + -
95C TYR* 3.2 38.9 - + + -
135C LEU 2.9 20.6 + - - +
136C GLY* 3.8 7.0 - - - +
138C GLY* 1.3 71.6 - - - +
140C ALA* 1.3 54.8 + - - +
142C GLU* 3.4 0.8 + - - +
143C ALA* 2.7 59.8 + - + +
145C LEU* 4.6 11.2 - - + -
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Residues in contact with ALA 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C GLY 3.0 14.7 + - - +
137C ALA* 3.1 11.6 + - - +
139C PHE* 1.3 75.2 - - - +
141C GLY* 1.3 64.5 + - - +
143C ALA* 3.4 1.3 + - - -
144C GLY 3.1 2.9 + - - -
145C LEU* 2.9 44.8 + - + +
146C ALA* 3.5 22.4 + - + -
151C ALA* 4.7 1.3 - - + -
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Residues in contact with GLY 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C ALA 3.1 4.4 + - - -
138C GLY 3.1 5.7 + - - -
140C ALA* 1.3 82.2 - - - +
142C GLU* 1.3 59.8 + - - +
144C GLY* 3.2 10.7 + - - -
146C ALA 3.9 10.0 - - - +
148C VAL* 4.2 14.9 - - - +
151C ALA* 3.6 12.3 - - - +
204C TYR* 3.4 24.0 - - - -
208C TYR* 4.8 1.0 - - - -
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Residues in contact with GLU 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C THR* 5.0 0.3 + - - -
91C THR* 3.6 25.8 + - + +
95C TYR* 2.6 27.8 + - + +
138C GLY 3.2 15.1 + - - +
139C PHE 4.2 0.9 - - - +
141C GLY* 1.3 74.8 - - - +
143C ALA* 1.3 60.6 + - - +
144C GLY 3.1 1.5 + - - -
204C TYR* 3.7 9.9 - - + -
208C TYR* 2.7 53.3 + - + +
220C LEU* 3.7 9.5 - - - +
224C TYR* 2.4 32.9 + - - -
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Residues in contact with ALA 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ILE* 5.8 4.3 - - + -
91C THR* 4.7 2.2 - - - +
139C PHE* 2.7 49.4 + - + +
140C ALA 4.0 0.2 - - - +
142C GLU* 1.3 72.2 - - - +
144C GLY* 1.3 60.7 + - - +
145C LEU* 3.5 24.3 + - + +
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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
------------------------------------------------------------
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