Contacts of the helix formed by residues 147 - 169 (chain A) in PDB entry 4NJP
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 SER 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A PHE* 4.0 10.6 - - - -
145A HIS 3.8 0.2 - - - -
146A PHE* 1.3 80.6 + - - +
148A LEU* 1.3 64.9 + - - +
149A MET* 3.6 11.2 + - - +
150A HIS* 3.3 24.1 + - - +
151A ILE* 3.1 24.4 + - - +
246A GLY 4.6 5.0 + - - -
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Residues in contact with LEU 148 (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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108A PHE* 3.8 27.4 - - + -
147A SER* 1.3 71.7 - - - +
149A MET* 1.3 66.6 + - + +
151A ILE* 3.5 8.2 - - + +
152A LEU* 2.9 30.9 + - + +
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Residues in contact with MET 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 SER* 3.6 11.4 + - - +
148A LEU* 1.3 78.6 - - + +
150A HIS* 1.3 64.1 + - - +
152A LEU* 4.5 9.9 - - + -
153A PHE* 3.0 60.0 + - + +
245A PHE* 4.2 26.6 - - + -
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Residues in contact with HIS 150 (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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145A HIS* 3.6 17.5 - + - -
146A PHE* 3.3 28.2 + + - +
147A SER* 3.3 21.3 + - - +
148A LEU 3.2 0.2 - - - -
149A MET* 1.3 80.8 - - - +
151A ILE* 1.3 62.7 + - - +
153A PHE* 4.1 0.3 - - - +
154A ASN* 3.0 50.4 + - - +
198A GLY 3.6 21.6 + - - -
199A GLY* 4.4 1.0 - - - -
201A SER* 4.9 2.0 + - - -
245A PHE* 4.5 7.2 - - - -
246A GLY 4.3 8.3 - - - +
247A MET* 3.3 39.1 + - + +
248A SER* 3.9 13.0 + - - -
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Residues in contact with ILE 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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104A CYS* 3.6 32.3 - - + +
105A VAL* 4.1 8.3 - - + +
108A PHE* 3.7 31.6 - - + -
145A HIS* 3.6 31.6 - - + +
147A SER 3.1 12.9 + - - +
148A LEU* 3.5 14.1 - - + +
150A HIS* 1.3 80.1 - - - +
152A LEU* 1.3 65.6 + - - +
155A LEU* 3.0 45.8 + - + +
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Residues in contact with LEU 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 LEU* 2.9 22.6 + - + +
149A MET* 3.8 11.0 - - + +
151A ILE* 1.3 78.1 - - + +
153A PHE* 1.3 88.7 + - + +
155A LEU* 4.0 2.9 - - - +
156A LEU* 3.1 38.9 + - + +
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Residues in contact with PHE 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 MET* 3.0 59.1 + - + +
150A HIS 4.4 0.7 - - - +
152A LEU* 1.3 89.1 - - + +
154A ASN* 1.3 67.9 + - - +
156A LEU* 3.3 23.6 + - + +
157A TRP* 3.2 34.7 + - + -
236A TRP* 3.9 26.7 - + + +
245A PHE* 4.5 12.3 - + + -
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Residues in contact with ASN 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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145A HIS* 3.1 33.6 + - + +
150A HIS* 3.0 32.6 + - - +
151A ILE 4.0 1.1 - - - +
153A PHE* 1.3 78.1 - - - +
155A LEU* 1.3 59.9 + - + +
157A TRP* 3.5 1.7 + - - -
158A TRP* 2.9 27.9 + - - +
200A LEU* 3.6 10.8 + - + -
201A SER* 3.6 25.4 + - - +
204A VAL* 3.6 12.2 - - + +
236A TRP* 3.6 28.7 - - - +
245A PHE* 5.9 0.4 - - - -
247A MET* 5.0 2.0 - - - +
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Residues in contact with LEU 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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101A MET* 4.0 44.0 - - + +
104A CYS* 4.2 14.6 - - + -
105A VAL* 4.3 9.0 - - + -
145A HIS* 5.2 1.8 - - + -
151A ILE* 3.0 43.2 + - + +
152A LEU* 4.0 3.8 - - - +
154A ASN* 1.3 77.9 - - + +
156A LEU* 1.3 58.6 + - - +
158A TRP* 3.8 4.4 - - + +
159A TRP* 2.8 30.8 + - - +
200A LEU* 4.1 24.2 - - + -
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Residues in contact with LEU 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 LEU* 3.1 36.4 + - + +
153A PHE* 3.3 34.3 + - + +
155A LEU* 1.3 75.1 - - - +
157A TRP* 1.3 62.2 + - + +
159A TRP* 3.5 26.0 - - + +
160A TYR* 3.0 30.4 + - - +
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Residues in contact with TRP 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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153A PHE* 3.2 24.5 + - + +
154A ASN* 3.6 4.7 - - - +
156A LEU* 1.3 79.7 - - + +
158A TRP* 1.3 58.7 - - - +
160A TYR* 4.5 12.3 - + + +
161A LEU* 2.8 65.2 + - + +
204A VAL* 3.6 20.4 - - + -
208A MET* 3.3 18.8 - - + -
225A LEU* 4.9 2.5 - - + -
229A LEU* 4.0 25.1 - - + -
232A PHE* 3.9 10.3 - - + -
233A ALA* 3.5 41.7 - - + -
236A TRP* 3.5 37.2 - + + +
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Residues in contact with TRP 158 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A VAL* 3.7 16.2 - - + -
97A THR* 2.9 31.7 + - + +
100A MET* 3.4 39.6 - - + +
101A MET* 3.5 25.4 - - + +
154A ASN 2.9 20.9 + - - +
155A LEU* 3.8 7.6 - - + +
157A TRP* 1.3 72.2 - - - +
159A TRP* 1.3 63.0 + - - +
162A GLY* 2.7 33.6 + - - +
163A GLY 3.2 1.6 + - - -
174A LEU* 3.9 26.9 - - + -
178A THR* 3.5 26.5 - - + -
200A LEU* 4.2 16.6 - - + -
203A VAL* 3.8 17.7 - - + -
204A VAL* 4.3 3.7 - - + +
207A LEU* 3.7 21.8 - - + -
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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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92A ARG 5.6 1.0 - - - -
93A ALA* 4.0 29.2 - - + +
97A THR* 4.3 4.7 - - + -
101A MET* 4.0 17.4 - - + +
155A LEU 2.8 20.1 + - - +
156A LEU* 3.5 27.1 - - + +
158A TRP* 1.3 83.7 - - - +
160A TYR* 1.3 64.9 + - + +
163A GLY* 3.1 18.8 + - - -
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Residues in contact with TYR 160 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A LEU 3.0 18.1 + - - +
157A TRP* 4.0 11.2 - + + +
158A TRP 3.2 0.2 - - - -
159A TRP* 1.3 78.9 - - + +
161A LEU* 1.3 80.8 + - + +
163A GLY 4.0 0.2 - - - -
164A ALA* 3.1 27.4 + - + +
168A ARG* 5.8 4.2 + - - -
224A TYR 5.3 5.8 + - - -
225A LEU* 4.9 3.1 - - + -
226A GLN* 4.9 10.7 + - - +
229A LEU* 3.1 36.8 - - + +
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Residues in contact with LEU 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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157A TRP* 2.8 49.4 + - + +
160A TYR* 1.3 92.5 - - + +
162A GLY* 1.3 63.9 + - - +
163A GLY 3.2 1.1 - - - -
164A ALA* 3.3 5.1 + - + +
165A VAL* 3.1 30.6 + - - +
204A VAL* 4.4 1.8 - - + +
207A LEU* 4.0 16.6 - - + -
208A MET* 3.8 35.9 - - + +
211A VAL* 4.3 27.0 - - + +
225A LEU* 4.6 12.6 - - + -
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Residues in contact with GLY 162 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A THR* 3.7 6.3 - - - -
158A TRP* 2.7 19.8 + - - -
161A LEU* 1.3 76.1 - - - +
163A GLY* 1.3 57.0 + - - +
165A VAL* 3.5 1.3 + - - +
166A GLU* 3.0 23.7 + - - +
174A LEU* 3.4 34.8 - - - +
207A LEU* 3.9 11.0 - - - +
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Residues in contact with GLY 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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92A ARG 5.5 2.9 - - - +
93A ALA* 5.5 6.1 - - - -
94A GLY 5.7 0.2 - - - -
97A THR* 3.4 19.8 + - - -
158A TRP 3.2 2.6 + - - -
159A TRP* 3.1 22.0 + - - -
160A TYR 4.0 0.2 - - - -
162A GLY* 1.3 74.4 - - - +
164A ALA* 1.3 62.2 + - - +
166A GLU* 3.4 1.6 + - - +
167A LYS* 3.0 25.1 + - - +
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Residues in contact with ALA 164 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A TYR* 3.1 25.5 + - + +
161A LEU* 3.6 7.9 - - + +
162A GLY 3.3 0.4 - - - -
163A GLY* 1.3 73.3 - - - +
165A VAL* 1.3 66.7 + - + +
167A LYS* 3.3 4.7 + - - +
168A ARG* 3.0 47.1 + - - +
211A VAL* 5.6 4.3 - - + -
223A ILE* 4.0 16.8 - - + -
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Residues in contact with VAL 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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161A LEU 3.1 16.4 + - - +
162A GLY* 3.8 6.5 - - - +
164A ALA* 1.3 76.4 - - - +
166A GLU* 1.3 56.9 + - - +
169A LEU* 2.9 36.5 + - + +
170A GLY 3.1 6.1 + - - -
173A LYS* 3.8 28.7 - - + -
174A LEU* 4.3 12.8 - - + +
177A ILE* 4.1 10.5 - - + -
207A LEU* 4.2 11.0 - - + -
210A TYR* 4.4 11.2 - - + -
211A VAL* 3.8 23.1 - - + -
223A ILE* 4.4 9.2 - - + -
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Residues in contact with GLU 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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94A GLY* 3.3 19.0 - - - +
95A PRO* 3.2 5.4 - - + +
96A VAL* 2.9 29.4 + - - +
97A THR* 2.5 42.3 + - - +
162A GLY 3.0 16.3 + - - +
163A GLY* 3.8 3.4 - - - +
164A ALA 3.2 0.4 - - - -
165A VAL* 1.3 78.5 - - - +
167A LYS* 1.3 62.5 + - - +
170A GLY* 3.4 24.9 + - - +
171A SER* 2.8 31.6 + - - +
174A LEU* 4.0 5.6 - - + -
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Residues in contact with LYS 167 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A GLU* 3.6 47.2 + - + +
92A ARG 5.4 8.5 - - - +
163A GLY 3.0 17.5 + - - +
164A ALA* 4.1 4.0 - - - +
166A GLU* 1.3 79.4 - - - +
168A ARG* 1.3 88.3 + - + +
169A LEU 3.7 0.2 + - - -
170A GLY* 5.0 0.5 + - - -
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Residues in contact with ARG 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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160A TYR* 5.8 4.2 + - - -
164A ALA* 3.0 27.1 + - - +
167A LYS* 1.3 103.5 - - + +
169A LEU* 1.3 67.4 + - + +
221A SER 4.5 6.8 - - - +
222A GLY* 2.4 43.2 + - - -
223A ILE* 3.9 22.3 - - + +
224A TYR* 4.5 15.9 + - - -
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Residues in contact with LEU 169 (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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165A VAL* 2.9 22.5 + - + +
167A LYS 3.5 0.6 - - - -
168A ARG* 1.3 89.8 - - - +
170A GLY* 1.3 56.4 + - - +
173A LYS* 4.1 23.1 - - - +
210A TYR* 3.5 38.6 - - + +
214A ARG* 3.8 22.2 - - - +
221A SER* 4.2 17.0 - - - +
223A ILE* 3.8 22.0 - - + -
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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