Contacts of the helix formed by residues 146 - 170 (chain B) in PDB entry 5SY1
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 ASN 146 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B LEU* 5.1 3.0 - - - +
62B GLN* 3.8 22.8 - - - +
144B LEU* 3.7 23.8 + - - +
145B HIS* 1.3 76.7 - - - +
147B LYS* 1.3 64.2 + - - +
148B VAL* 3.3 22.2 + - + +
149B GLY* 3.0 18.7 + - - -
150B TYR* 3.2 24.6 - - - -
204B LEU* 5.4 0.7 - - - -
212B GLU* 3.5 16.4 - - + +
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Residues in contact with LYS 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ASN* 1.3 74.0 - - - +
148B VAL* 1.3 72.7 + - + +
149B GLY 3.3 0.2 - - - -
150B TYR 4.5 0.2 - - - -
151B VAL* 3.3 34.4 + - + +
204B LEU* 4.6 13.0 - - + +
212B GLU* 3.1 19.5 + - - +
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Residues in contact with VAL 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B VAL* 5.1 2.9 - - + -
55B LEU* 5.7 2.2 - - + -
58B LEU* 3.8 30.7 - - + -
144B LEU* 5.9 0.7 - - + -
146B ASN* 3.2 19.4 - - - +
147B LYS* 1.3 90.7 - - + +
149B GLY* 1.3 63.5 + - - +
151B VAL* 4.3 1.4 - - - +
152B LEU* 3.3 41.8 + - + +
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Residues in contact with GLY 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 6.1 2.7 - - - -
141B CYS* 3.3 34.4 - - - -
144B LEU* 5.4 5.2 - - - -
146B ASN* 3.0 19.4 + - - -
148B VAL* 1.3 80.1 - - - +
150B TYR* 1.3 55.0 + - - +
152B LEU* 3.5 2.3 + - - +
153B GLY* 2.7 28.9 + - - -
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Residues in contact with TYR 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LEU* 6.1 0.4 - - + -
141B CYS* 5.0 9.9 - - + -
142B GLY* 4.7 5.3 + - - -
145B HIS* 2.5 60.4 + - + -
146B ASN 3.2 22.7 + - - -
148B VAL 3.5 0.2 - - - -
149B GLY* 1.3 76.2 - - - +
151B VAL* 1.3 62.0 + - - +
153B GLY* 4.0 2.7 - - - +
154B SER* 2.7 35.9 + - - -
200B TYR* 3.8 37.0 - + - +
203B LEU* 3.3 37.3 - - + +
204B LEU* 3.7 35.0 - - + -
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Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B LYS* 3.3 30.4 + - + +
148B VAL* 4.3 2.0 - - - +
149B GLY 3.4 0.4 - - - -
150B TYR* 1.3 79.5 - - - +
152B LEU* 1.3 66.0 + - + +
154B SER* 4.2 3.0 - - - -
155B LEU* 3.5 22.2 + - + +
204B LEU* 3.8 24.7 - - + -
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Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B VAL* 4.6 31.4 - - + -
54B VAL* 4.5 18.6 - - + -
55B LEU* 5.7 4.7 - - + -
141B CYS* 4.4 4.0 - - - -
148B VAL* 3.3 36.8 + - + +
149B GLY* 3.8 4.0 - - - +
151B VAL* 1.3 81.2 - - + +
153B GLY* 1.3 61.6 + - - +
154B SER 3.6 0.2 + - - -
155B LEU* 3.9 8.5 + - + +
156B LEU* 3.3 29.7 + - - +
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Residues in contact with GLY 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU* 4.3 1.4 - - - +
141B CYS* 3.6 16.2 - - - -
149B GLY 2.7 22.2 + - - -
150B TYR* 3.7 2.0 - - - -
151B VAL 3.2 0.4 - - - -
152B LEU* 1.3 73.6 - - - +
154B SER* 1.3 63.0 + - - +
156B LEU* 3.6 6.4 + - - +
157B SER 3.2 14.4 + - - -
200B TYR* 3.2 29.1 - - - -
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Residues in contact with SER 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B TYR 2.7 26.0 + - - -
151B VAL* 4.2 4.3 - - - -
152B LEU 3.4 0.2 - - - -
153B GLY* 1.3 72.8 - - - +
155B LEU* 1.3 52.5 + - - +
157B SER* 2.6 25.2 + - - -
158B TRP* 2.7 40.6 + - - -
200B TYR* 3.4 7.8 + - - +
201B PRO* 3.4 32.1 - - - +
204B LEU* 5.1 3.8 - - - +
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B VAL 3.5 14.7 + - - +
152B LEU* 4.4 8.7 - - + +
153B GLY 3.4 0.4 - - - -
154B SER* 1.3 78.1 - - - +
156B LEU* 1.3 56.6 + - + +
158B TRP* 3.5 18.4 + - + +
159B THR* 2.5 43.4 + - - +
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Residues in contact with LEU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE* 6.6 0.4 - - + -
47B ILE* 3.7 31.0 - - + -
48B SER* 6.1 1.3 - - - -
51B VAL* 4.3 19.1 - - + -
137B PRO* 4.2 27.6 - - + +
138B LEU* 3.8 20.0 - - + -
141B CYS* 5.4 0.4 - - - -
152B LEU 3.3 18.8 + - - +
153B GLY* 3.6 4.7 + - - +
154B SER 3.2 0.8 - - - -
155B LEU* 1.3 83.5 - - + +
157B SER* 1.3 61.9 + - - +
159B THR* 3.1 7.3 + - + +
160B HIS* 3.0 43.7 + - + +
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Residues in contact with SER 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU* 4.2 8.9 - - - +
153B GLY 3.2 8.4 + - - -
154B SER* 2.6 26.9 + - - -
156B LEU* 1.3 74.7 - - - +
158B TRP* 1.3 65.4 + - - +
160B HIS* 4.8 3.3 - - - +
161B PHE* 3.3 23.2 + - - +
193B LEU* 4.7 5.6 - - - +
196B LEU* 3.6 44.9 + - - -
197B SER* 4.1 9.2 - - - -
200B TYR* 4.3 4.2 - - - -
201B PRO* 5.2 0.5 - - - +
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Residues in contact with TRP 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B SER* 2.7 48.2 + - - -
155B LEU* 3.6 20.4 - - + +
157B SER* 1.3 76.7 + - - +
159B THR* 1.3 53.1 + - - +
161B PHE* 3.5 15.3 + + - +
162B GLY* 2.8 31.9 + - - -
197B SER* 4.6 24.9 - - - -
198B PHE* 5.7 6.5 - + - -
201B PRO* 4.3 19.4 - - + +
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Residues in contact with THR 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE* 3.8 28.9 - - + -
47B ILE* 6.4 0.2 - - + -
155B LEU* 2.5 31.4 + - - +
156B LEU* 3.1 13.0 + - + +
158B TRP* 1.3 74.9 - - - +
160B HIS* 1.3 61.2 + - - +
162B GLY* 3.0 2.6 + - - -
163B ILE* 2.9 42.1 + - + +
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Residues in contact with HIS 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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44B ILE* 3.5 38.1 - - + +
134B LEU* 3.7 20.4 - - + +
135B TYR* 4.1 23.5 - + + +
138B LEU* 4.7 16.2 - - + +
156B LEU* 3.0 39.6 + - + +
157B SER* 4.9 1.3 - - - +
159B THR* 1.3 78.7 - - - +
161B PHE* 1.3 61.2 + - - +
163B ILE* 4.4 6.4 - - + +
164B LEU* 3.3 25.3 + - - +
193B LEU* 3.7 24.1 - - + +
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Residues in contact with PHE 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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157B SER 3.3 20.2 + - - +
158B TRP* 3.8 17.3 - + - +
159B THR 3.3 0.4 - - - -
160B HIS* 1.3 78.2 - - - +
162B GLY* 1.3 63.1 + - - +
164B LEU* 5.0 2.0 - - + -
165B VAL* 3.3 48.0 + - + +
190B ILE* 4.1 30.5 - - + -
193B LEU* 4.0 17.8 - - + +
194B ALA* 4.2 22.9 - - + -
197B SER* 5.2 8.5 - - - -
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Residues in contact with GLY 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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158B TRP 2.8 16.6 + - - -
159B THR* 3.0 5.5 + - - -
161B PHE* 1.3 78.3 - - - +
163B ILE* 1.3 63.5 + - - +
165B VAL* 4.4 1.8 - - - +
166B TRP* 3.2 25.8 + - - +
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Residues in contact with ILE 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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37B GLU* 4.4 5.4 - - - +
40B PHE* 4.0 38.4 - - + -
44B ILE* 3.8 33.7 - - + -
159B THR* 2.9 26.0 + - + +
160B HIS* 4.4 7.0 - - + +
162B GLY* 1.3 76.4 - - - +
164B LEU* 1.3 59.4 + - - +
166B TRP* 3.5 8.3 + - + +
167B GLN* 3.0 54.9 + - + +
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Residues in contact with LEU 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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160B HIS 3.3 15.1 + - - +
161B PHE* 4.5 3.1 - - + +
163B ILE* 1.3 80.5 - - - +
165B VAL* 1.3 64.0 + - + +
167B GLN* 3.2 20.9 + - - +
168B LYS* 3.3 30.3 + - + +
186B SER* 4.7 12.8 - - - +
189B GLN* 3.9 39.9 - - + +
190B ILE* 3.7 30.7 - - + +
193B LEU* 4.3 9.6 - - + -
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Residues in contact with VAL 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 PHE* 3.3 51.6 + - + +
162B GLY* 4.4 2.0 - - - +
164B LEU* 1.3 78.4 - - + +
166B TRP* 1.3 63.6 + - - +
168B LYS* 3.1 6.8 + - - +
169B VAL* 3.1 34.2 + - + +
190B ILE* 4.5 17.5 - - + -
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Residues in contact with TRP 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ASP* 4.7 6.5 - - + -
33B PRO* 3.6 45.5 - - + -
36B ASP* 5.6 2.2 - - - -
40B PHE* 4.2 24.2 - + - -
162B GLY 3.2 20.2 + - - +
163B ILE* 4.0 7.9 - - - +
165B VAL* 1.3 77.7 - - - +
167B GLN* 1.3 59.8 + - + +
168B LYS 3.4 0.2 + - - -
169B VAL* 3.8 13.4 + - + +
170B ASP* 2.9 25.0 + - - +
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Residues in contact with GLN 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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33B PRO* 3.8 27.1 + - + +
34B THR* 5.7 0.9 - - - +
37B GLU* 2.4 39.5 + - - +
40B PHE* 4.9 1.6 - - - -
163B ILE* 3.0 35.3 + - + +
164B LEU* 3.6 15.9 - - - +
165B VAL 3.2 0.4 - - - -
166B TRP* 1.3 79.3 - - + +
168B LYS* 1.3 73.9 + - - +
170B ASP* 2.9 19.7 - - - +
171B CYS* 3.5 12.0 - - - -
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Residues in contact with LYS 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B LEU* 3.4 28.0 - - + +
165B VAL* 3.1 7.6 + - - +
167B GLN* 1.3 98.2 - - - +
169B VAL* 1.3 64.1 + - - +
170B ASP 3.2 7.3 - - - +
171B CYS* 4.7 11.6 + - - +
172B PRO* 3.9 18.4 + - + +
174B THR* 5.1 2.6 + - - -
182B ALA* 3.5 43.6 + - - +
183B LEU* 4.6 22.5 - - + +
186B SER* 4.7 8.1 + - - +
190B ILE* 4.8 13.9 - - + -
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Residues in contact with VAL 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B VAL* 3.1 29.0 + - + +
166B TRP* 4.3 12.6 - - + +
167B GLN 3.6 0.6 - - - -
168B LYS* 1.3 79.7 - - - +
170B ASP* 1.3 61.6 + - + +
172B PRO* 4.0 10.9 - - - +
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Residues in contact with ASP 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B CYS* 5.7 0.3 - - - -
33B PRO* 3.6 25.7 - - - +
166B TRP* 2.9 28.5 - - - +
167B GLN* 2.9 27.2 - - - +
168B LYS 3.2 4.5 - - - -
169B VAL* 1.3 81.9 - - - +
171B CYS* 1.3 72.3 + - + +
172B PRO* 4.4 0.4 - - - -
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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