Contacts of the helix formed by residues 119 - 143 (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 VAL 119 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A THR* 3.3 21.3 - - - +
118A SER* 1.3 80.9 - - - +
120A ALA* 1.3 62.1 + - - +
121A ALA 3.1 2.8 + - - -
122A SER* 2.9 25.0 + - - -
123A LEU* 3.2 19.5 + - + -
170A GLU* 3.3 50.7 - - + +
171A GLY* 5.0 0.2 - - - -
173A ALA* 3.8 11.4 - - + -
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Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A TYR* 3.2 26.0 - - + +
113A LEU* 3.8 8.2 - - + +
114A ALA* 3.8 26.7 - - + +
117A THR* 3.7 21.1 + - - +
118A SER 3.2 3.0 + - - +
119A VAL* 1.3 75.8 - - - +
121A ALA* 1.3 61.0 + - - +
123A LEU* 3.6 9.6 + - - +
124A PHE 3.2 17.0 + - - -
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Residues in contact with ALA 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A TYR* 3.9 15.8 - - + +
118A SER 4.7 2.5 + - - +
119A VAL 3.1 1.4 + - - -
120A ALA* 1.3 75.1 - - - +
122A SER* 1.3 64.8 + - - +
124A PHE* 3.4 5.9 + - - +
125A LYS* 3.3 36.3 + - - +
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Residues in contact with SER 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A VAL* 2.9 14.4 + - - -
121A ALA* 1.3 74.8 - - - +
123A LEU* 1.3 58.9 + - - +
125A LYS* 3.3 14.2 + - - +
126A LYS* 2.8 35.1 + - - +
170A GLU* 2.9 35.2 + - - -
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Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 3.7 37.7 - - + -
117A THR* 4.2 3.1 - - + +
119A VAL* 3.2 37.1 + - + +
120A ALA* 3.6 9.4 - - - +
121A ALA 3.3 0.2 - - - -
122A SER* 1.3 77.9 + - - +
124A PHE* 1.3 51.7 + - - +
126A LYS* 3.2 7.4 + - + +
127A LEU* 2.8 44.5 + - + +
165A GLU* 3.8 33.4 - - + +
166A LEU* 4.1 15.3 - - + -
170A GLU* 4.4 10.3 + - + -
171A GLY* 4.1 12.3 - - - +
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Residues in contact with PHE 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A PRO* 4.5 2.0 - - + -
106A VAL* 3.7 17.5 - - + -
107A VAL* 3.7 39.5 - - + -
110A TYR* 3.7 34.1 - + + +
113A LEU* 5.8 0.6 - - - +
120A ALA 3.2 11.0 + - - +
121A ALA* 3.6 10.8 - - - +
123A LEU* 1.3 78.8 - - - +
125A LYS* 1.3 67.6 + - + +
127A LEU* 3.4 8.1 + - - +
128A LEU* 2.9 53.9 + - + +
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Residues in contact with LYS 125 (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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121A ALA* 3.3 30.5 + - - +
122A SER* 3.7 11.3 - - - +
123A LEU 3.3 0.2 - - - -
124A PHE* 1.3 89.2 - - + +
126A LYS* 1.3 56.7 + - - +
128A LEU* 3.3 6.5 + - + +
129A ALA* 3.0 30.4 + - - +
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Residues in contact with LYS 126 (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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122A SER* 2.8 22.8 + - - +
123A LEU* 3.5 8.3 - - + +
125A LYS* 1.3 73.8 - - - +
127A LEU* 1.3 56.3 + - - +
129A ALA* 3.3 7.4 + - - +
130A GLY* 2.9 24.6 + - - -
161A TYR* 3.1 35.9 - - + +
162A MET* 6.1 0.4 - - - -
165A GLU* 3.4 38.8 + - + +
170A GLU* 2.7 34.1 + - + +
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A VAL* 3.7 22.2 - - + +
109A PHE* 4.9 11.9 - - + -
110A TYR* 5.9 0.9 - - - +
113A LEU* 4.4 11.9 - - + -
123A LEU* 2.8 32.6 + - + +
124A PHE* 3.8 3.4 - - - +
126A LYS* 1.3 69.8 - - + +
128A LEU* 1.3 60.6 + - - +
130A GLY 3.5 0.2 + - - -
131A SER* 3.0 24.9 + - - -
162A MET* 3.4 61.4 - - + +
165A GLU* 5.6 2.0 - - + -
166A LEU* 4.3 29.8 - - + -
193A ILE* 4.7 5.2 - - + -
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Residues in contact with LEU 128 (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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103A PRO* 3.8 40.2 - - + +
106A VAL* 4.2 10.0 - - + +
124A PHE* 2.9 40.8 + - + +
125A LYS* 3.8 7.0 - - + +
127A LEU* 1.3 75.0 - - - +
129A ALA* 1.3 62.8 + - - +
131A SER* 3.1 21.5 + - - +
132A LEU* 3.2 35.5 + - + +
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Residues in contact with ALA 129 (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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125A LYS 3.0 13.0 + - - +
126A LYS* 3.5 11.9 - - - +
127A LEU 3.3 0.2 - - - -
128A LEU* 1.3 74.6 - - - +
130A GLY* 1.3 65.0 + - - +
132A LEU* 3.9 6.0 - - - +
133A VAL* 3.1 29.6 + - + +
161A TYR* 5.1 4.3 - - + -
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Residues in contact with GLY 130 (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 2.9 15.6 + - - -
127A LEU 3.8 2.0 - - - -
128A LEU 3.4 0.2 - - - -
129A ALA* 1.3 76.9 - - - +
131A SER* 1.3 56.5 + - - +
133A VAL* 3.3 5.7 + - - +
134A MET* 2.9 27.4 + - - +
158A GLY* 3.6 17.8 - - - -
161A TYR* 4.1 13.0 - - - -
162A MET* 3.9 13.5 - - - -
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Residues in contact with SER 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A VAL* 3.8 28.9 - - - +
103A PRO* 5.5 0.7 - - - +
106A VAL* 4.6 1.2 - - - +
127A LEU 3.0 15.1 + - - -
128A LEU* 3.1 21.1 + - - +
129A ALA 3.3 0.2 - - - -
130A GLY* 1.3 75.9 - - - +
132A LEU* 1.3 58.8 + - - +
134A MET* 3.2 9.8 - - - +
135A LEU* 2.8 38.8 + - - +
162A MET* 3.7 19.8 - - - -
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU* 3.8 29.4 - - + -
103A PRO* 5.3 5.6 - - + -
128A LEU* 3.2 38.4 + - + +
129A ALA* 3.9 5.6 - - - +
130A GLY 3.3 0.2 - - - -
131A SER* 1.3 82.8 + - - +
133A VAL* 1.3 59.0 + - - +
135A LEU* 4.1 8.2 - - + +
136A GLY* 2.8 28.6 + - - -
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Residues in contact with VAL 133 (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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129A ALA* 3.1 16.7 + - + +
130A GLY* 3.5 7.9 - - - +
132A LEU* 1.3 74.7 - - - +
134A MET* 1.3 65.1 + - - +
136A GLY* 5.1 0.2 - - - -
137A ALA* 2.9 25.3 + - - +
154A ILE* 3.9 34.1 - - + +
157A ALA* 5.9 0.2 - - + -
158A GLY* 4.1 9.9 - - - +
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Residues in contact with MET 134 (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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102A VAL* 6.1 0.9 - - - -
130A GLY 2.9 13.7 + - - +
131A SER* 3.2 17.0 - - - +
133A VAL* 1.3 77.2 - - - +
135A LEU* 1.3 64.6 + - - +
137A ALA 3.6 0.2 + - - -
138A GLY* 3.1 19.9 + - - -
155A GLY* 3.6 30.1 - - - +
158A GLY* 4.5 0.2 - - - -
159A TRP* 3.4 32.8 - - + +
162A MET* 4.5 0.7 - - - +
197A TRP* 4.0 11.0 - - + -
201A PRO* 5.3 0.4 - - + -
301A RET 2.5 76.4 - - + +
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Residues in contact with LEU 135 (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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95A TYR* 3.4 15.0 - - + +
98A TRP* 3.6 64.4 - - + +
99A LEU* 3.7 17.3 - - + +
102A VAL* 4.1 13.5 - - + -
103A PRO* 5.5 0.7 - - + -
131A SER* 2.8 23.1 + - - +
132A LEU* 4.1 7.6 - - + +
134A MET* 1.3 73.9 - - + +
136A GLY* 1.3 59.3 + - - +
139A PHE* 2.9 31.5 + - - +
301A RET 4.3 23.8 - - + -
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Residues in contact with GLY 136 (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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132A LEU 2.8 22.1 + - - -
133A VAL 3.7 0.7 - - - -
135A LEU* 1.3 70.8 - - - +
137A ALA* 1.3 58.1 + - - +
139A PHE* 3.2 8.6 + - - +
140A ALA* 2.9 30.3 + - - +
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Residues in contact with ALA 137 (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 2.9 15.1 + - - +
136A GLY* 1.3 73.5 - - - +
138A GLY* 1.3 64.8 + - - +
140A ALA* 3.0 9.8 + - - +
141A GLY 3.0 19.2 + - - -
151A ALA* 3.4 19.7 - - - +
154A ILE* 3.9 15.3 - - + -
155A GLY* 3.2 31.0 - - - +
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Residues in contact with GLY 138 (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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95A TYR* 3.2 16.2 - - - -
134A MET 3.1 9.6 + - - -
135A LEU 3.9 2.5 - - - -
137A ALA* 1.3 77.3 - - - +
139A PHE* 1.3 62.3 + - - +
141A GLY* 3.4 2.1 + - - -
142A GLU* 3.1 26.3 + - - +
151A ALA* 5.3 0.7 - - - -
204A TYR* 3.6 5.8 - - - -
301A RET 3.6 26.1 - - - +
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Residues in contact with PHE 139 (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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91A THR* 4.2 13.0 - - + -
92A VAL* 4.2 19.3 - - + -
95A TYR* 3.4 41.7 - + + -
135A LEU 2.9 18.8 + - - +
136A GLY* 3.2 7.2 + - - +
138A GLY* 1.3 73.9 - - - +
140A ALA* 1.3 58.7 + - - +
142A GLU 3.1 1.4 + - - -
143A ALA* 2.8 56.4 + - + +
145A LEU* 4.5 11.9 - - + -
25E ILE* 3.7 41.5 - - + -
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Residues in contact with ALA 140 (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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136A GLY 2.9 16.5 + - - +
137A ALA* 3.0 11.0 + - - +
139A PHE* 1.3 77.2 - - + +
141A GLY* 1.3 62.2 + - - +
144A GLY 3.1 3.3 + - - -
145A LEU* 2.8 45.0 + - + -
146A ALA* 3.4 22.0 + - + -
151A ALA* 5.0 0.4 - - + -
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Residues in contact with GLY 141 (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 3.0 10.3 + - - -
138A GLY 3.6 1.3 - - - -
140A ALA* 1.3 79.3 - - - +
142A GLU* 1.3 62.5 + - - +
144A GLY* 3.2 10.2 + - - -
146A ALA 3.8 10.0 - - - +
148A VAL* 3.8 18.9 - - - +
151A ALA* 3.8 12.6 - - - +
204A TYR* 3.6 21.3 - - - -
208A TYR* 5.3 0.2 - - - -
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Residues in contact with GLU 142 (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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89A THR* 5.0 0.7 + - - -
91A THR* 3.7 25.9 + - + +
95A TYR* 2.5 33.5 + - + +
138A GLY 3.1 14.9 + - - +
139A PHE 3.1 2.0 + - - +
141A GLY* 1.3 74.6 - - - +
143A ALA* 1.3 59.0 + - - +
144A GLY* 3.2 1.1 + - - -
204A TYR* 3.5 8.6 - - + -
208A TYR* 2.6 59.1 + - + +
220A LEU* 3.8 10.0 - - - +
224A TYR* 2.8 24.1 + - - -
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Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A THR* 4.9 4.3 - - + -
92A VAL* 6.1 1.1 - - + -
139A PHE* 2.8 50.5 + - + +
142A GLU* 1.3 73.1 - - - +
144A GLY* 1.3 61.7 + - - +
145A LEU* 3.6 18.1 + - + +
25E ILE* 5.5 5.8 - - + -
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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
------------------------------------------------------------
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