Contacts of the helix formed by residues 151 - 172 (chain B) in PDB entry 1LCP
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 GLN 151 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B LEU* 3.4 26.3 - - + +
148B SER* 3.3 19.2 + - - +
149B GLU 3.4 2.0 + - - -
150B ASP* 1.3 75.9 - - - +
152B GLU* 1.3 57.4 + - - +
154B TRP* 3.3 11.8 + - - -
155B GLN* 2.9 65.7 + - - +
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Residues in contact with GLU 152 (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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149B GLU 5.3 0.4 + - - -
150B ASP 3.3 1.0 + - - -
151B GLN* 1.3 77.3 - - - +
153B ALA* 1.3 64.1 + - - +
155B GLN* 3.4 12.1 + - - +
156B ARG* 3.1 22.2 + - + +
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Residues in contact with ALA 153 (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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116B ALA* 3.8 14.6 - - + +
117B GLN* 3.4 20.8 - - + +
150B ASP* 3.2 13.2 + - + +
152B GLU* 1.3 77.0 - - - +
154B TRP* 1.3 65.7 + - - +
156B ARG* 3.1 11.2 + - - +
157B GLY 3.0 18.2 + - - -
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Residues in contact with TRP 154 (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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110B VAL* 3.7 45.1 - - + -
116B ALA* 3.7 19.4 - - + +
119B ALA* 4.0 4.9 - - + -
120B ALA* 3.3 46.0 - - + +
123B ALA* 4.2 7.9 - - + -
124B VAL* 5.5 2.7 - - + -
143B ALA* 4.2 10.7 + - + -
144B LYS* 3.8 23.4 - - - +
145B LEU* 3.7 34.4 - - + +
150B ASP 3.0 13.4 + - - +
151B GLN* 3.6 30.3 - - - +
153B ALA* 1.3 75.6 - - - +
155B GLN* 1.3 65.7 + - + +
157B GLY 3.0 3.1 + - - -
158B VAL* 3.0 36.6 + - + +
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Residues in contact with GLN 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B GLN* 2.9 54.6 + - - +
152B GLU* 3.7 9.9 - - - +
154B TRP* 1.3 76.0 - - + +
156B ARG* 1.3 57.4 + - - +
158B VAL* 3.3 11.2 + - + +
159B LEU* 3.0 28.1 + - - +
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Residues in contact with ARG 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B GLN* 3.3 25.7 - - - +
152B GLU* 3.1 13.7 + - + +
153B ALA* 3.1 13.4 + - - +
155B GLN* 1.3 76.2 - - - +
157B GLY* 1.3 59.4 + - - +
159B LEU* 3.1 8.6 + - - +
160B PHE* 3.0 62.8 + - + -
290B LEU* 3.8 22.8 - - + +
477B GLU* 4.9 1.6 + - - -
480B PHE* 3.4 53.1 - - - +
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Residues in contact with GLY 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B GLN* 3.5 32.4 - - - +
120B ALA* 3.9 6.3 - - - -
121B GLU* 3.7 8.9 - - - +
153B ALA 3.0 11.3 + - - -
154B TRP 3.0 3.8 + - - -
156B ARG* 1.3 74.0 - - - +
158B VAL* 1.3 64.4 + - - +
160B PHE 3.3 0.2 + - - -
161B ALA* 2.9 27.5 + - - +
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Residues in contact with VAL 158 (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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120B ALA* 3.7 7.5 - - + +
124B VAL* 4.2 24.6 - - + +
154B TRP* 3.0 46.0 + - + +
155B GLN* 3.3 10.5 + - - +
157B GLY* 1.3 74.2 - - - +
159B LEU* 1.3 58.2 + - - +
161B ALA* 3.8 0.9 - - - +
162B SER* 2.8 44.5 + - - +
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Residues in contact with LEU 159 (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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155B GLN 3.0 14.3 + - - +
156B ARG* 3.1 11.0 + - - +
158B VAL* 1.3 74.7 - - - +
160B PHE* 1.3 71.3 + - + +
162B SER* 3.3 2.9 + - - -
163B GLY* 3.1 18.5 + - - -
286B SER* 4.0 11.4 + - - +
289B LYS* 3.1 59.0 + - + +
290B LEU* 3.8 39.3 - - + -
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Residues in contact with PHE 160 (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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117B GLN* 4.0 13.2 - - - -
121B GLU* 3.7 19.1 - - - +
156B ARG* 3.0 61.5 + - + +
157B GLY 3.9 0.7 - - - +
159B LEU* 1.3 83.4 - - + +
161B ALA* 1.3 62.7 + - - +
163B GLY* 3.2 10.7 + - - -
164B GLN 3.3 9.2 + - - -
290B LEU* 4.1 11.0 - - + -
393B THR* 5.3 2.9 - - + -
473B ARG* 3.7 34.9 - - + +
476B ILE* 3.7 39.7 - - + +
477B GLU* 3.6 33.2 - - + -
480B PHE* 5.1 0.9 - - + -
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Residues in contact with ALA 161 (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 GLU* 4.1 9.2 - - + -
124B VAL* 3.6 31.0 - - + -
125B LEU* 3.6 28.1 - - + +
157B GLY 2.9 17.5 + - - +
158B VAL 3.8 0.7 - - - +
160B PHE* 1.3 74.7 - - - +
162B SER* 1.3 59.4 + - - +
164B GLN* 3.2 2.2 + - - -
165B ASN* 2.9 31.5 + - - -
473B ARG* 4.6 2.9 - - - +
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Residues in contact with SER 162 (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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124B VAL* 4.3 7.2 - - - +
158B VAL* 2.8 33.2 + - - +
159B LEU* 3.3 5.6 + - - -
161B ALA* 1.3 76.5 - - - +
163B GLY* 1.3 61.9 + - - +
165B ASN* 3.8 9.7 - - - +
166B LEU* 3.0 23.9 + - - +
289B LYS* 4.3 8.3 - - - -
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Residues in contact with GLY 163 (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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159B LEU 3.1 10.5 + - - -
160B PHE 3.2 4.0 + - - -
161B ALA 3.2 0.6 - - - -
162B SER* 1.3 76.1 - - - +
164B GLN* 1.3 60.5 + - - +
166B LEU* 3.3 7.2 + - - +
167B ALA 3.3 15.1 + - - -
282B SER* 3.5 15.9 - - - -
286B SER* 3.4 24.2 - - - -
289B LYS* 3.9 2.9 - - - +
472B THR* 4.0 9.4 - - - -
476B ILE* 4.7 0.2 - - - -
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Residues in contact with GLN 164 (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 LEU* 3.7 17.6 - - + +
160B PHE 3.3 10.1 + - - +
161B ALA 3.2 8.6 + - - +
163B GLY* 1.3 76.9 - - - +
165B ASN* 1.3 56.4 + - - +
167B ALA* 3.1 5.2 + - - +
168B ARG* 2.9 27.6 + - - +
395B ASP* 4.5 5.6 + - - +
462B TYR* 5.7 0.8 - - - -
463B LEU* 3.9 22.2 - - - +
468B ALA 3.0 23.6 + - - +
469B GLY 3.5 15.7 - - - +
470B ARG* 4.0 11.1 - - - +
472B THR* 4.0 17.0 - - - +
473B ARG* 2.9 37.2 + - + +
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Residues in contact with ASN 165 (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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124B VAL* 3.1 42.8 + - - +
125B LEU* 3.5 6.8 - - - +
128B TYR* 3.7 28.6 - - + +
161B ALA 2.9 12.8 + - - +
162B SER* 3.8 6.9 - - - +
163B GLY 3.3 0.2 - - - -
164B GLN* 1.3 73.8 - - - +
166B LEU* 1.3 61.2 + - - +
168B ARG* 2.9 35.1 + - - +
169B ARG* 2.9 29.8 + - - +
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Residues in contact with LEU 166 (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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162B SER 3.0 13.3 + - - +
163B GLY* 3.5 11.0 - - - +
164B GLN 3.2 0.2 - - - -
165B ASN* 1.3 74.7 - - - +
167B ALA* 1.3 63.9 + - - +
169B ARG* 3.2 18.5 + - - +
170B LEU* 3.0 44.9 + - + +
186B ILE* 4.3 8.5 - - + -
187B VAL* 6.0 4.0 - - + -
190B ASN* 3.9 43.1 - - + +
282B SER* 3.6 18.8 - - - +
285B VAL* 4.5 16.4 - - + -
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Residues in contact with ALA 167 (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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163B GLY 3.3 3.8 + - - +
164B GLN 3.1 9.8 + - - +
166B LEU* 1.3 81.2 - - - +
168B ARG* 1.3 62.4 + - - +
170B LEU* 3.4 2.0 + - - +
171B MET* 3.0 30.5 + - - +
278B ALA* 4.0 19.9 - - + +
279B THR* 4.4 1.8 - - + -
282B SER* 3.4 15.0 + - - +
469B GLY* 3.9 10.8 - - - -
472B THR* 3.5 23.6 - - - +
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Residues in contact with ARG 168 (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 LEU* 3.1 22.8 + - - +
128B TYR* 3.6 35.4 + - + +
164B GLN* 2.9 20.7 + - - +
165B ASN* 2.9 33.4 + - - +
167B ALA* 1.3 74.3 - - - +
169B ARG* 1.3 58.8 + - - +
171B MET* 3.3 4.1 + - - +
172B GLU* 2.8 34.9 + - + +
463B LEU* 3.5 22.9 - - - +
464B ARG* 3.7 30.9 + - - +
467B MET* 3.4 20.1 + - - +
468B ALA* 3.3 33.1 + - - +
469B GLY* 4.5 2.7 - - - +
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Residues in contact with ARG 169 (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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128B TYR* 3.4 23.9 + - + +
130B TYR* 4.6 10.6 - - + -
132B ASP* 5.3 6.5 + - - +
165B ASN 2.9 14.3 + - - +
166B LEU* 3.5 23.8 - - - +
168B ARG* 1.3 71.9 - - - +
170B LEU* 1.3 65.5 + - - +
172B GLU* 4.0 2.4 - - - +
173B THR* 2.7 42.5 + - - +
178B MET* 5.3 4.8 - - - +
182B LYS* 5.6 1.4 - - - +
186B ILE* 3.5 47.3 - - - +
189B GLU* 4.7 3.8 + - - -
190B ASN* 4.7 4.2 - - - +
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Residues in contact with LEU 170 (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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166B LEU* 3.0 38.7 + - + +
167B ALA 3.7 3.6 - - - +
169B ARG* 1.3 79.2 - - - +
171B MET* 1.3 58.8 + - - +
173B THR 3.9 1.4 + - - -
178B MET* 3.6 36.4 - - + +
183B PHE* 3.9 23.8 - - + +
186B ILE* 3.9 26.5 - - + -
187B VAL* 4.5 11.2 - - + -
274B MET* 3.3 19.8 - - + +
278B ALA* 4.1 8.1 - - + +
281B CYS* 5.8 0.4 - - + -
282B SER* 4.2 10.1 - - - +
490B ZN 2.8 21.3 - - - -
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Residues in contact with MET 171 (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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167B ALA 3.0 18.1 + - - +
168B ARG 3.7 0.4 - - - +
170B LEU* 1.3 76.7 - - - +
172B GLU* 1.3 57.9 + - - +
271B ARG* 3.7 13.3 - - - +
272B ALA* 3.9 11.2 - - + +
274B MET* 3.8 8.3 - - - -
275B GLY* 3.8 34.3 - - - +
278B ALA* 4.0 8.7 - - + -
279B THR* 4.8 3.4 - - - -
359B THR* 5.2 1.1 - - + -
450B ILE* 5.5 3.8 - - + -
453B VAL 5.4 0.2 - - - +
454B MET* 3.6 48.2 - - + +
467B MET* 3.7 14.5 - - + +
469B GLY* 3.8 30.5 - - - +
470B ARG 5.6 1.3 - - - +
490B ZN 2.8 16.5 - - - -
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Residues in contact with GLU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B TYR* 6.0 1.3 - - + -
130B TYR* 3.7 37.0 - - + +
168B ARG 2.8 21.0 + - - +
169B ARG 4.0 2.2 - - - +
171B MET* 1.3 73.6 - - - +
173B THR* 1.3 62.1 + - - +
174B PRO* 3.4 2.9 - - - +
271B ARG* 2.9 52.8 + - - +
465B LYS 4.9 0.3 - - - +
466B GLY* 3.5 10.1 - - - -
467B MET* 2.9 39.2 + - + +
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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