Contacts of the helix formed by residues 154 - 175 (chain B) in PDB entry 1Q4L
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 PRO 154 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B TYR* 3.7 20.9 - - + +
152B THR 3.1 5.4 - - - +
153B LEU* 1.3 89.3 - - + +
155B VAL* 1.3 66.3 + - - +
156B ILE* 2.9 19.6 + - + +
157B TYR* 2.9 30.2 + - + +
158B VAL 3.4 5.7 + - - -
351B PRO* 5.9 1.3 - - + -
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Residues in contact with VAL 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LEU 3.2 5.5 + - - +
154B PRO* 1.3 70.7 - - - +
156B ILE* 1.3 64.6 + - - +
158B VAL* 3.2 9.8 + - + +
159B LYS* 3.0 49.5 + - + +
251B LEU* 4.3 19.5 - - + -
306B ARG* 6.2 1.8 - - - +
309B THR* 6.4 0.2 - - + -
310B PRO* 4.0 33.7 - - + -
339B PHE* 4.7 3.6 - - + -
342B GLU* 4.9 2.2 - - - +
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Residues in contact with ILE 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B PRO* 2.9 17.9 + - + -
155B VAL* 1.3 81.7 - - - +
157B TYR* 1.3 76.0 + - + +
159B LYS* 3.1 9.0 + - + +
160B LEU* 3.0 32.3 + - + +
342B GLU* 3.8 34.5 - - + +
343B LEU* 4.2 17.3 - - + -
348B VAL* 4.4 10.5 - - + -
349B LYS 5.0 8.5 - - - +
350B LEU* 5.8 0.2 - - + -
351B PRO* 4.1 26.9 - - + -
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Residues in contact with TYR 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B TYR* 5.0 6.7 - - - -
153B LEU* 4.0 19.3 - - + -
154B PRO* 2.9 36.1 + - + +
156B ILE* 1.3 81.5 - - + +
158B VAL* 1.3 65.8 + - - +
160B LEU* 4.4 12.6 - - + -
161B TYR* 2.8 61.0 + + + -
191B PRO 5.5 6.7 + - - -
194B ALA* 4.8 12.6 - - + -
350B LEU* 5.1 2.9 - - + +
351B PRO* 3.4 45.0 - - + +
352B ASN* 4.9 5.0 + - - +
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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
----------------------------------------------------------
153B LEU* 3.9 31.6 - - + +
154B PRO 3.4 10.7 + - - +
155B VAL* 3.2 13.1 + - + +
157B TYR* 1.3 77.0 - - - +
159B LYS* 1.3 58.5 + - - +
161B TYR* 4.1 0.4 - - - +
162B MET* 3.0 39.6 + - + +
247B LEU* 3.7 28.0 - - + -
250B LEU* 4.2 26.5 - - + +
251B LEU* 4.2 19.1 - - + -
339B PHE* 4.2 5.8 - - + -
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Residues in contact with LYS 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B VAL* 3.0 32.8 + - + +
156B ILE* 3.3 8.1 - - + +
158B VAL* 1.3 73.9 - - - +
160B LEU* 1.3 66.1 + - - +
163B TYR* 2.9 24.6 + - - +
310B PRO* 5.8 1.8 - - - -
338B SER 5.7 0.2 + - - -
339B PHE* 3.2 48.5 + - + +
340B PHE* 3.3 20.6 - - + -
342B GLU* 3.0 45.0 + - + +
343B LEU* 4.0 12.3 - - + -
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Residues in contact with LEU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ILE* 3.0 20.2 + - + +
157B TYR* 3.3 17.5 + - + +
159B LYS* 1.3 79.2 - - - +
161B TYR* 1.3 66.9 + - + +
163B TYR* 3.9 1.4 - - - +
164B GLN* 2.9 36.4 + - - +
194B ALA* 3.9 12.3 - - + +
343B LEU* 3.6 28.5 - - + +
350B LEU* 3.4 31.4 - - + -
356B THR* 4.4 6.7 - - + -
357B PRO* 4.2 15.9 - - + -
359B LEU* 4.1 22.2 - - + -
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Residues in contact with TYR 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B VAL* 4.5 9.9 - - + -
142B VAL* 4.8 9.2 - - + +
153B LEU* 4.3 18.4 - - + +
157B TYR* 2.8 59.6 + + + +
158B VAL* 4.1 2.5 - - - +
160B LEU* 1.3 75.1 - - + +
162B MET* 1.3 65.9 + - - +
164B GLN* 3.3 3.6 + - - +
165B LEU* 3.0 19.8 + - - +
189B LEU* 3.4 50.1 - - + +
190B ASP 5.5 1.2 + - - -
191B PRO* 5.5 5.4 + - - +
194B ALA* 4.2 24.5 - - + -
196B LEU* 3.4 23.6 - - + +
250B LEU* 4.8 11.7 - - + -
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Residues in contact with MET 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B VAL* 3.0 26.9 + - + +
161B TYR* 1.3 74.0 - - - +
163B TYR* 1.3 65.9 + - - +
165B LEU* 3.3 20.9 + - + +
166B PHE* 3.0 52.8 + - + -
187B LEU* 5.9 0.4 - - - -
243B ALA 3.4 24.9 - - - +
246B VAL* 3.9 22.4 - - - -
247B LEU* 3.5 36.6 - - + -
250B LEU* 4.4 7.4 - - + -
340B PHE* 3.9 16.2 - - + -
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Residues in contact with TYR 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B LYS 2.9 18.2 + - - +
160B LEU 3.9 1.8 - - - +
162B MET* 1.3 76.0 - - - +
164B GLN* 1.3 69.7 + - + +
166B PHE* 3.0 8.7 + - - +
167B ARG* 3.0 32.4 + - + -
335B CYS* 3.6 33.2 - - + -
340B PHE* 3.4 29.7 - + + -
343B LEU* 3.6 16.6 - - + -
344B ARG* 4.2 9.8 + - - -
359B LEU* 2.8 56.2 + - + -
360B PHE* 4.1 10.0 - + - -
362B PHE* 3.3 21.2 - + - -
377B LEU* 4.4 3.2 + - + +
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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
----------------------------------------------------------
108B ASN* 3.2 36.1 + - - +
160B LEU* 2.9 32.2 + - - +
161B TYR* 3.8 3.1 - - - +
162B MET 3.3 0.4 - - - -
163B TYR* 1.3 79.6 - - + +
165B LEU* 1.3 67.4 + - - +
167B ARG* 3.3 1.1 + - - +
168B SER* 3.0 21.3 + - - -
194B ALA 2.9 24.6 + - - -
195B VAL* 3.6 8.8 - - - +
196B LEU* 3.1 35.4 + - + +
357B PRO* 4.4 7.6 - - - +
358B ALA 5.0 1.4 - - - +
359B LEU* 4.1 23.4 - - + +
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Residues in contact with LEU 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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161B TYR 3.0 14.6 + - - +
162B MET* 3.6 25.1 - - + +
163B TYR 3.2 0.2 - - - -
164B GLN* 1.3 75.7 - - - +
166B PHE* 1.3 59.3 + - + +
168B SER* 2.7 30.9 + - - +
169B LEU* 3.0 24.0 + - + +
182B ILE* 4.3 19.3 - - + -
187B LEU* 3.9 37.9 - - + -
196B LEU* 4.3 12.9 - - + +
198B LEU* 4.7 2.7 - - + -
243B ALA* 4.0 28.3 - - + -
246B VAL* 4.9 2.0 - - + -
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Residues in contact with PHE 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 MET* 3.0 40.9 + - + -
163B TYR 3.0 6.8 + - - +
165B LEU* 1.3 73.7 - - - +
167B ARG* 1.3 65.0 + - - +
169B LEU* 3.1 13.2 + - + +
170B ALA* 2.8 21.0 + - - +
240B VAL* 5.0 6.1 - - + -
243B ALA* 3.7 26.9 - - + -
316B LEU* 4.5 3.8 - - + -
320B LEU* 3.8 38.6 - - + -
331B PRO* 3.5 22.2 - - + +
334B ALA* 3.8 25.6 - - + -
335B CYS* 3.5 16.8 - - - -
340B PHE* 4.1 19.7 - + - -
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Residues in contact with ARG 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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106B HIS* 4.0 14.5 + - + -
107B CYS* 3.9 11.1 - - - -
108B ASN* 3.5 18.6 - - - +
163B TYR* 3.0 31.3 + - + +
164B GLN 3.3 1.5 + - - +
166B PHE* 1.3 75.4 - - - +
168B SER* 1.3 65.6 + - - +
170B ALA* 3.0 16.9 + - - +
171B TYR* 3.0 13.9 + - - +
335B CYS* 3.7 13.0 - - - -
358B ALA 3.7 5.9 + - - -
359B LEU* 3.5 23.6 + - - +
361B ASN* 2.8 51.3 + - - +
362B PHE* 3.7 28.0 - - + +
366B GLU* 2.8 30.4 + - - +
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Residues in contact with SER 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B HIS* 4.2 7.7 - - - -
108B ASN* 3.5 30.3 - - - -
109B ILE* 4.0 10.4 - - - +
164B GLN 3.0 12.3 + - - -
165B LEU* 2.7 25.7 + - - +
167B ARG* 1.3 77.5 - - - +
169B LEU* 1.3 59.4 + - - +
171B TYR* 3.5 4.4 + - - +
172B ILE* 3.2 27.9 + - - +
196B LEU* 6.0 0.2 - - - -
198B LEU* 3.6 19.3 - - - +
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Residues in contact with LEU 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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165B LEU* 3.0 21.0 + - + +
166B PHE* 3.6 15.9 - - + +
167B ARG 3.1 0.2 - - - -
168B SER* 1.3 79.3 + - - +
170B ALA* 1.3 66.9 + - - +
171B TYR 3.1 1.8 - - - -
172B ILE* 4.0 21.3 - - + -
173B HIS* 2.9 34.2 + - + +
182B ILE* 4.0 22.7 - - + -
198B LEU* 4.3 6.5 - - + -
239B ASP* 3.9 40.4 - - + +
240B VAL* 4.6 2.7 - - - +
243B ALA* 4.3 15.0 - - + -
331B PRO* 3.8 13.9 - - + -
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Residues in contact with ALA 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 PHE 2.8 16.4 + - - +
167B ARG* 3.5 10.1 - - - +
169B LEU* 1.3 72.8 - - - +
171B TYR* 1.3 57.9 + - - +
173B HIS* 4.1 2.2 - - - +
174B SER* 3.0 29.3 + - - -
331B PRO* 3.3 19.6 - - + +
332B LEU* 3.8 32.5 - - + +
366B GLU* 4.4 12.2 - - + +
369B SER* 5.7 5.0 - - - -
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Residues in contact with TYR 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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103B LYS 4.2 1.2 + - - -
104B LEU* 3.7 21.0 - - + -
105B ASP* 2.9 41.5 + - - +
106B HIS* 3.4 37.9 - + + +
109B ILE* 3.7 19.1 - - + -
167B ARG 3.0 7.6 + - - +
168B SER 3.5 7.0 - - - +
170B ALA* 1.3 75.4 - - - +
172B ILE* 1.3 68.5 + - + +
174B SER* 2.7 25.5 + - - -
175B PHE* 3.3 34.2 - + - -
363B THR* 5.2 3.1 - - - -
365B GLN* 4.2 16.2 - - + -
366B GLU* 4.1 16.3 - - + +
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Residues in contact with ILE 172 (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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104B LEU* 4.2 11.7 - - + -
109B ILE* 3.4 30.7 - - + -
168B SER 3.2 10.0 + - - +
169B LEU* 3.6 25.6 - - + +
171B TYR* 1.3 80.6 - - + +
173B HIS* 1.3 68.3 + - + +
175B PHE* 3.0 18.6 + - - +
177B ILE* 3.2 39.2 + - + +
179B HIS* 4.0 26.2 - - + +
198B LEU* 4.5 6.7 - - + -
201B PHE* 4.2 18.2 - - + -
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Residues in contact with HIS 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B LEU* 2.9 24.0 + - + +
170B ALA* 4.1 3.6 - - - +
172B ILE* 1.3 83.0 - - + +
174B SER* 1.3 55.4 + - - +
176B GLY* 2.6 25.4 + - - +
177B ILE 3.0 29.8 - - - +
236B SER* 3.2 42.2 - - - +
239B ASP* 2.8 33.4 + - + +
240B VAL* 4.8 3.6 - - + -
331B PRO* 3.6 29.4 - - + +
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Residues in contact with SER 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ALA 3.0 16.7 + - - -
171B TYR* 2.7 18.0 + - - -
173B HIS* 1.3 75.8 - - - +
175B PHE* 1.3 58.6 + - - +
176B GLY 3.3 0.8 + - - -
365B GLN* 2.9 46.5 + - - +
366B GLU 5.1 2.2 - - - -
368B SER* 3.8 11.0 + - - -
369B SER* 5.5 5.4 - - - -
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Residues in contact with PHE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LYS* 3.9 40.4 - - + +
104B LEU* 4.9 2.7 - - + -
171B TYR* 3.3 59.7 - + - -
172B ILE* 3.0 10.9 + - - +
173B HIS 2.9 0.6 - - - -
174B SER* 1.3 79.6 + - - +
176B GLY* 1.3 61.2 + - - +
177B ILE* 3.5 15.5 + - + +
206B GLN* 3.4 19.8 + - - +
365B GLN* 3.0 30.3 - - + -
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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