Contacts of the helix formed by residues 154 - 175 (chain A) in PDB entry 1H8F
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A TYR* 3.7 15.3 - - + +
152A THR 3.6 7.2 - - - +
153A LEU* 1.3 96.1 - - + +
155A VAL* 1.3 55.6 + - - +
156A ILE* 3.8 11.4 - - + -
157A TYR* 2.8 49.8 + - + +
158A VAL 3.2 6.6 + - - -
351A PRO* 5.8 0.7 - - + -
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Residues in contact with VAL 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LEU 3.3 3.6 + - - +
154A PRO* 1.3 69.9 - - - +
156A ILE* 1.3 62.1 + - - +
158A VAL* 3.0 10.6 + - + +
159A LYS* 2.9 48.7 + - - +
251A LEU* 5.4 8.7 - - + -
310A PRO* 4.3 29.4 - - + -
339A PHE* 4.0 16.8 - - + -
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Residues in contact with ILE 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A PRO* 3.8 19.7 - - + -
155A VAL* 1.3 78.8 - - - +
157A TYR* 1.3 74.1 + - + +
159A LYS* 3.4 7.2 + - + +
160A LEU* 3.0 37.4 + - + +
342A GLU* 3.6 30.0 + - - +
343A LEU* 4.3 17.7 - - + -
348A VAL* 4.5 11.9 - - + -
349A LYS 4.6 13.7 - - - +
351A PRO* 4.1 21.3 - - + -
356A THR* 5.9 0.2 - - + -
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Residues in contact with TYR 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A TYR* 4.9 5.2 - - - -
153A LEU* 3.6 30.1 - - + -
154A PRO* 2.8 37.4 + - + +
156A ILE* 1.3 72.0 - - + +
158A VAL* 1.3 61.5 + - - +
160A LEU* 4.4 10.8 - - + -
161A TYR* 2.9 62.6 + + + -
191A PRO 5.6 4.9 + - - -
194A ALA* 4.9 11.0 - - + -
350A LEU* 5.3 1.8 - - + -
351A PRO* 3.0 49.2 - - + +
352A ASN* 4.6 4.5 + - - +
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Residues in contact with VAL 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LEU* 3.8 29.4 - - + +
154A PRO 3.2 12.2 + - - +
155A VAL* 3.0 13.4 + - - +
157A TYR* 1.3 77.2 - - - +
159A LYS* 1.3 56.9 + - - +
161A TYR* 4.1 2.4 - - - +
162A MET* 2.9 38.1 + - + +
247A LEU* 3.6 30.1 - - + -
250A LEU* 4.1 28.9 - - + +
251A LEU* 4.2 14.4 - - + -
339A PHE* 4.2 7.0 - - + -
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Residues in contact with LYS 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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155A VAL* 2.9 37.1 + - + +
156A ILE* 3.6 8.3 - - - +
158A VAL* 1.3 74.1 - - - +
160A LEU* 1.3 65.7 + - - +
163A TYR* 2.9 25.3 + - - +
310A PRO* 6.0 2.0 - - - +
339A PHE* 3.3 45.3 + - + +
340A PHE* 3.2 20.1 - - + -
342A GLU* 2.8 47.4 + - + +
343A LEU* 3.8 15.5 - - + -
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Residues in contact with LEU 160 (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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156A ILE* 3.0 29.0 + - + +
157A TYR* 3.9 11.7 - - + +
159A LYS* 1.3 77.6 - - - +
161A TYR* 1.3 68.0 + - + +
163A TYR* 3.9 1.0 - - - +
164A GLN* 2.9 41.4 + - - +
194A ALA* 4.1 11.9 - - + +
343A LEU* 3.9 23.8 - - + +
350A LEU* 3.2 32.1 - - + -
356A THR* 4.2 6.5 - - + -
357A PRO* 4.1 17.9 - - + -
359A LEU* 3.9 20.4 - - + -
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Residues in contact with TYR 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A VAL* 4.4 10.1 - - + -
142A VAL* 4.8 8.7 - - + +
153A LEU* 3.8 31.0 - - + +
157A TYR* 2.9 49.2 + + + +
158A VAL* 4.1 2.5 - - - +
160A LEU* 1.3 74.4 - - + +
162A MET* 1.3 69.2 + - - +
164A GLN* 3.4 2.2 + - - +
165A LEU* 3.0 18.7 + - - +
189A LEU* 3.3 51.6 - - + +
190A ASP 5.5 1.4 + - - -
191A PRO* 5.6 4.9 + - - +
194A ALA* 4.1 24.9 - - + -
196A LEU* 3.3 24.3 - - + +
250A LEU* 4.9 10.5 - - + -
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Residues in contact with MET 162 (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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158A VAL* 2.9 25.9 + - + +
161A TYR* 1.3 78.1 - - - +
163A TYR* 1.3 64.1 + - - +
165A LEU* 3.0 24.1 + - + +
166A PHE* 2.9 47.2 + - + -
187A LEU* 5.9 0.4 - - - -
243A ALA 3.3 26.2 - - - +
246A VAL* 4.2 13.7 - - - -
247A LEU* 3.6 42.4 - - + +
250A LEU* 4.2 8.7 - - + -
340A PHE* 3.7 17.5 - - + -
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Residues in contact with TYR 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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159A LYS 2.9 19.9 + - - +
160A LEU 3.9 2.0 - - - +
162A MET* 1.3 76.0 - - - +
164A GLN* 1.3 66.4 + - + +
166A PHE* 3.3 5.8 + - - +
167A ARG* 3.1 32.6 + - - +
335A CYS* 3.5 43.0 - - + -
340A PHE* 3.5 24.5 - + + -
343A LEU* 3.6 14.4 - - + -
344A ARG* 4.2 8.1 - - - -
359A LEU* 2.6 61.5 + - + -
360A PHE* 3.9 10.1 - + - -
362A PHE* 3.3 20.4 - + - -
377A LEU* 4.3 3.0 + - + +
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Residues in contact with GLN 164 (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 ASN* 3.0 33.4 - - - +
160A LEU* 2.9 35.7 + - - +
161A TYR* 3.9 3.5 - - - +
163A TYR* 1.3 76.2 - - + +
165A LEU* 1.3 66.9 + - - +
167A ARG* 3.2 3.5 + - - +
168A SER* 3.0 23.2 + - - -
194A ALA 3.0 23.2 + - - -
195A VAL* 3.3 9.4 - - - +
196A LEU* 2.9 36.5 + - + +
357A PRO* 4.4 6.3 - - - +
359A LEU* 4.0 23.8 - - + -
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Residues in contact with LEU 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 TYR 3.0 14.4 + - - +
162A MET* 3.0 25.1 + - + +
164A GLN* 1.3 76.8 - - - +
166A PHE* 1.3 57.4 + - + +
168A SER* 2.7 25.6 + - - +
169A LEU* 2.9 38.4 + - + +
182A ILE* 4.2 15.5 - - + -
187A LEU* 3.9 37.9 - - + -
196A LEU* 4.1 12.5 - - + +
198A LEU* 4.6 2.5 - - + -
243A ALA* 3.9 23.3 - - + -
246A VAL* 4.9 2.2 - - + -
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Residues in contact with PHE 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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162A MET* 2.9 40.9 + - + +
163A TYR* 3.8 0.4 - - - +
165A LEU* 1.3 74.3 - - - +
167A ARG* 1.3 53.9 + - - +
169A LEU* 4.1 12.1 - - + -
170A ALA* 2.7 32.6 + - - +
240A VAL* 4.9 7.4 - - + -
243A ALA* 3.6 27.6 - - + -
316A LEU* 4.3 4.0 - - + -
320A LEU* 3.5 34.3 - - + -
331A PRO* 3.3 30.3 - - + +
334A ALA* 3.6 27.8 - - + -
335A CYS* 3.5 12.6 - - - -
340A PHE* 4.0 21.5 - + - -
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Residues in contact with ARG 167 (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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106A HIS* 4.0 15.0 + - - +
107A CYS* 6.3 0.4 - - - +
108A ASN* 3.9 18.3 - - - +
163A TYR* 3.1 33.3 + - + +
164A GLN* 3.6 8.1 - - - +
166A PHE* 1.3 73.5 - - - +
168A SER* 1.3 69.4 + - - +
170A ALA* 3.0 7.0 + - - +
171A TYR* 2.8 24.8 + - - +
335A CYS* 4.0 9.2 - - - -
358A ALA 3.2 19.0 + - - -
359A LEU* 3.6 12.5 - - - +
361A ASN* 2.8 42.0 + - - -
362A PHE* 3.9 25.0 - - + +
366A GLU* 3.2 34.6 + - - +
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Residues in contact with SER 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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106A HIS* 4.3 5.7 + - - -
108A ASN* 3.4 26.9 - - - -
109A ILE* 3.7 13.2 - - - -
164A GLN 3.0 8.1 + - - -
165A LEU* 2.7 27.2 + - - +
167A ARG* 1.3 78.5 - - - +
169A LEU* 1.3 58.5 + - - +
171A TYR* 3.3 7.6 + - - +
172A ILE* 3.0 34.4 + - - +
196A LEU* 5.3 0.6 - - - +
198A LEU* 3.9 17.8 + - - +
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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 LEU* 2.9 34.5 + - + +
166A PHE* 3.5 14.6 - - + +
167A ARG 3.0 0.2 - - - -
168A SER* 1.3 75.8 + - - +
170A ALA* 1.3 64.6 + - - +
172A ILE* 4.0 11.2 - - + -
173A HIS* 2.9 44.5 + - + +
182A ILE* 3.7 28.5 - - + -
198A LEU* 4.1 11.0 - - + -
239A ASP* 4.2 18.2 - - + +
240A VAL* 4.8 2.7 - - - +
243A ALA* 4.0 22.2 - - + -
331A PRO* 3.6 13.2 - - + -
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Residues in contact with ALA 170 (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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166A PHE 2.7 19.7 + - - +
167A ARG* 3.0 8.0 + - - +
169A LEU* 1.3 72.2 - - - +
171A TYR* 1.3 61.0 + - - +
173A HIS* 4.0 1.6 - - - +
174A SER* 3.2 23.6 + - - -
331A PRO* 3.4 18.1 - - + +
332A LEU* 4.0 32.5 - - + +
362A PHE* 6.0 0.2 - - + -
366A GLU* 4.4 13.5 - - + +
369A SER* 5.9 0.8 - - - +
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Residues in contact with TYR 171 (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 LYS 4.0 1.2 + - - -
104A LEU* 3.5 25.2 - - + -
105A ASP* 2.9 37.4 + - - +
106A HIS* 3.6 35.2 - - + +
109A ILE* 3.6 19.5 - - + -
167A ARG 2.8 15.1 + - - +
168A SER* 3.5 4.0 - - - +
170A ALA* 1.3 74.2 - - - +
172A ILE* 1.3 68.3 + - + +
174A SER* 2.7 25.8 + - - -
175A PHE* 3.2 34.9 - + - -
363A THR* 5.2 2.2 - - + -
365A GLN* 4.4 11.4 - - + -
366A GLU* 3.9 20.6 - - + +
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Residues in contact with ILE 172 (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 LEU* 4.0 22.4 - - + -
109A ILE* 3.4 29.6 - - + -
168A SER 3.0 13.1 + - - +
169A LEU* 3.5 18.4 - - + +
171A TYR* 1.3 78.5 - - - +
173A HIS* 1.3 70.6 + - + +
175A PHE* 3.1 12.2 + - - +
177A ILE* 3.1 45.2 + - + +
179A HIS* 3.9 31.0 - - + +
198A LEU* 4.4 6.5 - - + -
201A PHE* 4.1 10.5 - - + -
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Residues in contact with HIS 173 (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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169A LEU* 2.9 29.3 + - + +
170A ALA 4.0 3.4 - - - +
172A ILE* 1.3 84.4 - - + +
174A SER* 1.3 55.1 + - - +
176A GLY* 2.7 24.7 + - - -
177A ILE 3.2 20.6 - - - +
178A CYS* 4.4 0.2 - - - -
236A SER* 3.3 43.6 + - - -
239A ASP* 3.1 30.4 + - + +
240A VAL* 4.6 3.1 - - + -
331A PRO* 3.5 30.9 - - + +
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Residues in contact with SER 174 (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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170A ALA 3.2 13.1 + - - -
171A TYR* 2.7 21.3 + - - -
173A HIS* 1.3 76.2 - - - +
175A PHE* 1.3 58.8 + - - +
176A GLY 3.2 1.2 + - - -
365A GLN* 2.8 52.8 + - - +
366A GLU* 5.1 1.1 - - - -
368A SER* 3.6 11.0 + - - -
369A SER* 5.7 5.6 - - - -
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Residues in contact with PHE 175 (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 LYS* 3.5 40.4 - - + -
104A LEU* 4.6 4.0 - - + -
171A TYR* 3.2 62.8 - + - -
172A ILE* 3.1 11.7 + - - +
173A HIS 3.0 1.0 - - - -
174A SER* 1.3 78.3 + - - +
176A GLY* 1.3 51.7 + - - +
177A ILE* 3.2 16.8 - - + -
206A GLN* 2.5 30.7 + - - +
365A GLN* 3.7 24.5 - - + -
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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