Contacts of the helix formed by residues 143 - 166 (chain M) in PDB entry 5PRC
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 HIS 143 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192L GLY* 3.5 20.4 - - - +
195L LEU* 3.5 42.1 - - + +
196L SER* 3.3 16.0 - - - -
199L ASN 3.6 18.2 - - - -
141M GLY* 3.4 8.7 + - - -
142M THR* 1.3 76.5 - - - +
144M ILE* 1.3 63.0 + - - +
146M TRP* 3.2 5.1 + - - -
147M ASN 3.0 11.8 + - - -
265M ARG* 5.0 0.9 - - - -
268M TRP* 2.9 38.4 + + - +
802M SO4 3.0 34.8 + - - -
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Residues in contact with ILE 144 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188L GLY 5.6 0.7 - - - -
189L LEU* 3.7 31.0 - - + +
192L GLY* 3.6 21.3 - - - +
193L LEU* 3.9 13.2 - - + +
196L SER* 5.2 3.8 - - - +
215L TYR* 3.7 33.7 - - + +
216L PHE* 3.8 12.1 - - + -
131M VAL* 3.9 9.6 - - + +
142M THR 3.2 1.0 - - - -
143M HIS* 1.3 71.7 - - - +
145M ALA* 1.3 66.6 + - - +
147M ASN* 2.9 19.2 + - - +
148M PHE* 2.9 11.3 + - - +
401M BPB 3.5 26.9 - - + +
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Residues in contact with ALA 145 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128M TRP* 2.8 33.9 + - + +
131M VAL* 3.9 11.7 + - + +
132M TYR* 3.6 47.3 - - + +
142M THR* 3.0 12.6 + - - +
144M ILE* 1.3 77.5 - - - +
146M TRP* 1.3 59.0 + - + +
148M PHE* 3.2 2.2 + - - +
149M ALA 3.0 14.7 + - - -
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Residues in contact with TRP 146 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128M TRP* 4.0 28.3 - + - -
132M TYR* 4.4 8.3 - + - -
142M THR* 3.0 44.4 + - - -
143M HIS* 3.6 8.3 - - - +
144M ILE 3.0 0.4 - - - -
145M ALA* 1.3 77.2 - - - +
147M ASN* 1.3 62.8 + - - +
149M ALA* 3.2 39.0 + - + +
150M ALA* 3.5 3.5 + - - +
268M TRP* 3.9 17.5 - - + -
272M LEU* 4.2 6.7 - - - +
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Residues in contact with ASN 147 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188L GLY* 3.9 7.6 - - - +
143M HIS 3.0 4.6 + - - +
144M ILE* 2.9 9.1 + - - +
146M TRP* 1.3 73.7 - - - +
148M PHE* 1.3 61.6 + - - +
150M ALA* 3.4 14.0 + - - +
151M ALA* 3.5 9.0 + - - +
268M TRP* 3.4 43.1 + - + +
271M SER* 3.3 27.8 + - - -
272M LEU* 3.5 18.9 + - - +
275M MET* 5.4 1.1 - - - +
401M BPB 3.3 34.5 - - + +
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Residues in contact with PHE 148 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124M LEU* 4.8 1.6 - - + -
127M TRP* 3.5 21.3 - + + -
128M TRP* 3.7 27.1 - + - -
131M VAL* 4.1 6.1 - - + -
144M ILE 2.9 10.9 + - - +
145M ALA* 3.4 10.3 - - - +
147M ASN* 1.3 75.6 - - - +
149M ALA* 1.3 59.5 + - - +
151M ALA* 3.1 5.8 + - + -
152M ILE* 2.8 44.1 + - + +
401M BPB 3.4 80.3 - + + +
806M BCB 3.5 24.7 - - + -
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Residues in contact with ALA 149 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128M TRP* 3.9 14.8 - - + +
145M ALA 3.0 12.3 + - - +
146M TRP* 3.3 34.1 - - + +
148M PHE* 1.3 75.9 - - - +
150M ALA* 1.3 52.7 + - - +
152M ILE* 3.2 6.9 + - - +
153M PHE* 2.7 35.3 + - - +
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Residues in contact with ALA 150 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146M TRP 3.5 2.5 + - - +
147M ASN 3.4 11.1 + - - +
148M PHE 3.1 0.4 - - - -
149M ALA* 1.3 77.9 - - - +
151M ALA* 1.3 63.7 + - - +
153M PHE* 3.1 8.4 + - - +
154M PHE* 3.0 23.0 + - - +
272M LEU* 3.7 24.2 - - + -
275M MET* 3.8 18.4 - - + +
276M VAL* 4.3 13.5 - - + +
279M SER* 4.5 2.6 + - - -
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Residues in contact with ALA 151 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147M ASN 3.5 6.8 + - - +
148M PHE* 3.1 14.5 + - + +
150M ALA* 1.3 75.5 - - - +
152M ILE* 1.3 64.7 + - - +
154M PHE* 3.0 14.2 + - - +
155M VAL* 3.3 13.2 + - - +
275M MET* 3.6 19.8 - - + +
401M BPB 4.0 29.4 - - + -
806M BCB 4.0 18.3 - - + +
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Residues in contact with ILE 152 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121M THR* 6.0 0.4 - - + +
124M LEU* 3.8 35.9 - - + +
125M GLY* 5.4 1.3 - - - +
128M TRP* 3.9 22.7 - - + -
148M PHE* 2.8 53.2 + - + +
149M ALA* 3.6 7.6 - - - +
151M ALA* 1.3 70.1 - - - +
153M PHE* 1.3 64.2 + - - +
155M VAL* 3.2 7.1 + - - +
156M LEU* 3.0 35.6 + - + +
806M BCB 4.0 11.0 - - + -
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Residues in contact with PHE 153 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149M ALA 2.7 20.1 + - - +
150M ALA* 3.1 9.4 + - - +
152M ILE* 1.3 75.7 - - - +
154M PHE* 1.3 56.9 - - - +
156M LEU* 3.2 12.8 + - + +
157M CYS* 2.9 47.1 + - - -
161M ILE* 3.6 25.6 - - + -
279M SER* 3.8 20.9 - - - -
283M LEU* 4.4 16.2 - - + -
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Residues in contact with PHE 154 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150M ALA 3.0 11.6 + - - +
151M ALA 3.0 9.2 + - - +
153M PHE* 1.3 75.8 - - - +
155M VAL* 1.3 55.0 + - - +
157M CYS* 2.7 25.1 + - + +
158M ILE* 3.0 42.6 + - + +
275M MET* 3.6 28.7 - - + +
278M ALA* 3.9 13.0 - - + -
279M SER* 3.7 29.3 + - - +
282M ILE* 3.9 11.4 - - + -
805M BCB 3.9 5.2 - - + -
806M BCB 3.5 68.0 - + + -
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Residues in contact with VAL 155 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120M MET* 4.6 6.7 - - - -
124M LEU* 4.3 17.7 - - + -
151M ALA 3.7 4.7 - - - +
152M ILE 3.4 7.4 - - - +
154M PHE* 1.3 76.8 - - - +
156M LEU* 1.3 60.8 + - + +
158M ILE* 3.6 10.3 - - - +
159M GLY* 2.8 29.5 + - - -
600M NS5 4.3 31.9 - - + +
805M BCB 3.6 26.9 - - + +
806M BCB 3.6 32.3 - - + -
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Residues in contact with LEU 156 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121M THR* 4.4 28.7 - - + +
124M LEU* 5.4 2.7 - - + -
152M ILE* 3.0 31.8 + - + +
153M PHE* 3.2 19.1 - - + +
155M VAL* 1.3 83.8 - - + +
157M CYS* 1.3 57.5 + - - +
160M CYS* 2.8 40.1 + - + +
161M ILE* 2.9 32.8 + - + +
600M NS5 5.3 5.6 - - + -
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Residues in contact with CYS 157 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153M PHE* 2.9 54.5 + - - -
154M PHE* 2.7 18.2 + - + +
156M LEU* 1.3 71.6 - - - +
158M ILE* 1.3 60.1 + - - +
161M ILE* 3.4 10.8 + - - -
162M HIS* 2.8 31.8 + - - +
279M SER* 3.7 21.3 - - - -
282M ILE* 4.0 20.4 - - + -
283M LEU* 4.3 9.6 - - + -
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Residues in contact with ILE 158 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154M PHE* 3.0 48.1 + - + +
155M VAL* 3.6 13.9 - - - +
157M CYS* 1.3 79.5 - - - +
159M GLY* 1.3 62.8 + - - +
162M HIS* 4.9 3.6 - - - +
163M PRO* 4.1 5.9 - - - +
171M GLU 4.6 2.3 - - - +
172M GLY* 4.0 10.6 - - - -
173M VAL* 3.7 20.8 - - + +
183M TRP* 4.0 17.0 - - + -
282M ILE* 3.6 24.5 - - + -
600M NS5 4.4 9.6 - - + -
805M BCB 3.8 31.6 - - + -
806M BCB 3.9 7.6 - - + +
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Residues in contact with GLY 159 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113M TRP* 3.5 24.3 - - - -
155M VAL 2.8 18.5 + - - -
158M ILE* 1.3 80.4 - - - +
160M CYS* 1.3 56.6 + - - +
163M PRO* 3.8 8.6 - - - +
169M TRP* 4.2 2.4 - - - -
173M VAL* 4.9 2.5 - - - -
600M NS5 3.6 34.4 - - - +
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Residues in contact with CYS 160 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156M LEU* 2.8 26.3 + - + +
159M GLY* 1.3 74.3 - - - +
161M ILE* 1.3 72.1 + - + +
163M PRO* 3.0 9.0 - - - +
164M THR* 2.9 29.6 + - - +
169M TRP* 4.3 7.4 - - + -
600M NS5 2.9 67.3 - - - -
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Residues in contact with ILE 161 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153M PHE* 3.6 33.0 - - + -
156M LEU* 2.9 39.6 + - + +
157M CYS* 4.0 7.6 - - - +
160M CYS* 1.3 77.7 - - + +
162M HIS* 1.3 60.4 + - - +
164M THR* 3.0 9.5 + - + -
165M LEU* 2.8 37.8 + - + +
283M LEU* 4.1 20.4 - - + -
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Residues in contact with HIS 162 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157M CYS* 2.8 24.2 + - - +
158M ILE* 4.9 4.7 - - - -
161M ILE* 1.3 73.0 - - - +
163M PRO* 1.3 68.5 - - + +
165M LEU* 3.4 10.3 + - - +
166M VAL* 3.1 36.9 + - + +
171M GLU* 2.8 31.3 + - + +
187M PHE* 3.4 25.6 - + - -
191M TYR* 3.5 19.1 - + - -
282M ILE* 3.5 25.9 + - + +
283M LEU* 5.4 1.3 - - - +
285M THR 3.2 27.0 + - - -
287M THR* 5.1 1.8 + - - -
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Residues in contact with PRO 163 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102M MET* 3.8 2.9 - - - +
157M CYS 3.9 3.8 - - - +
158M ILE 4.1 3.8 - - - +
159M GLY 3.8 13.2 - - - +
160M CYS 3.0 19.3 - - - +
162M HIS* 1.3 97.2 - - + +
164M THR* 1.3 51.6 + - - +
166M VAL* 3.5 4.0 - - + +
167M GLY* 2.7 29.3 + - - -
168M SER 2.8 34.0 + - - +
169M TRP* 4.1 15.5 - - + -
171M GLU* 4.2 5.2 - - + -
172M GLY* 4.0 22.2 - - - +
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Residues in contact with THR 164 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102M MET* 3.4 31.6 - - + +
160M CYS* 2.9 17.3 + - - +
161M ILE* 3.3 11.3 - - - -
163M PRO* 1.3 77.9 - - - +
165M LEU* 1.3 65.3 + - + +
167M GLY* 3.1 12.6 + - - -
169M TRP* 4.2 6.6 - - - -
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Residues in contact with LEU 165 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C ARG* 3.7 17.1 + - - -
161M ILE* 2.8 32.1 + - + +
162M HIS* 3.7 8.1 - - - +
163M PRO 3.3 0.2 - - - -
164M THR* 1.3 78.2 - - + +
166M VAL* 1.3 60.4 + - + +
167M GLY* 4.5 0.2 - - - -
282M ILE 5.6 0.2 - - - +
283M LEU* 3.7 36.8 - - + +
287M THR* 3.9 33.2 - - + +
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Residues in contact with VAL 166 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C ARG* 3.3 18.9 - - - +
217C GLY 2.9 21.5 + - - -
220C ARG* 3.4 26.0 - - - +
162M HIS* 3.1 44.9 - - + +
163M PRO* 3.5 10.1 - - + +
165M LEU* 1.3 77.0 - - - +
167M GLY* 1.3 59.7 + - - +
168M SER 3.5 5.6 - - - +
171M GLU* 4.1 12.6 - - + -
286M GLY* 3.7 29.6 - - - +
287M THR* 3.9 3.4 - - - +
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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
------------------------------------------------------------
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