Contacts of the helix formed by residues 164 - 187 (chain B) in PDB entry 5A6C
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 164 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B PHE* 6.0 1.3 - - + -
163B PHE* 1.4 96.0 - - - +
165B GLU* 1.3 67.8 + - - +
166B GLU* 3.1 19.8 + - + +
167B VAL* 3.3 23.0 + - + -
168B ARG* 3.1 15.6 + - - +
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Residues in contact with GLU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B PHE 4.6 0.2 - - - -
164B PRO* 1.3 72.8 - - - +
166B GLU* 1.3 65.7 + - - +
168B ARG* 3.3 23.2 - - - +
169B ASP* 2.9 52.9 + - - +
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Residues in contact with GLU 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B PHE* 3.6 28.5 - - + -
164B PRO* 3.2 21.3 - - - +
165B GLU* 1.3 83.1 + - - +
167B VAL* 1.3 60.6 + - + +
168B ARG 3.1 0.9 - - - -
169B ASP* 3.2 7.2 + - - +
170B ALA* 2.9 31.9 + - - +
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Residues in contact with VAL 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B GLY 3.7 17.0 - - - +
152B PHE* 3.7 38.8 - - + +
163B PHE* 4.6 9.4 - - + -
164B PRO* 3.3 30.1 + - + +
166B GLU* 1.3 75.0 - - + +
168B ARG* 1.3 58.2 + - - +
170B ALA* 4.1 2.9 - - - -
171B LEU* 2.9 49.1 + - + +
208B LEU* 5.6 0.4 - - + -
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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
----------------------------------------------------------
163B PHE* 4.6 24.3 - - + +
164B PRO 3.1 13.4 + - - +
165B GLU* 3.3 29.4 - - - +
167B VAL* 1.3 77.6 - - - +
169B ASP* 1.3 60.8 + - - +
171B LEU* 3.9 0.7 - - - +
172B GLN* 2.9 49.3 + - + +
208B LEU* 3.3 41.2 + - - +
210B ASN* 4.6 7.7 + - - +
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Residues in contact with ASP 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B GLU* 2.9 47.2 + - - +
166B GLU* 3.2 7.0 + - - +
168B ARG* 1.3 78.0 - - - +
170B ALA* 1.3 57.8 + - - +
172B GLN* 3.8 4.0 - - - +
173B ALA* 2.9 31.8 + - - +
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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
----------------------------------------------------------
145B TYR* 3.4 24.4 - - + +
148B LYS* 4.1 22.7 - - + -
149B GLY* 4.0 22.9 - - - +
152B PHE* 5.4 2.0 - - + -
166B GLU 2.9 16.0 + - - +
167B VAL 4.2 0.2 - - - +
169B ASP* 1.3 77.7 - - - +
171B LEU* 1.3 57.5 + - - +
173B ALA* 3.7 0.2 - - - +
174B ALA* 3.0 25.5 + - - +
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Residues in contact with LEU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B HIS* 3.6 36.1 - - + +
149B GLY* 4.3 20.0 - - - -
167B VAL* 2.9 37.6 + - + +
170B ALA* 1.3 75.2 - - - +
172B GLN* 1.3 60.8 + - - +
174B ALA* 3.2 4.0 - - - +
175B VAL* 2.9 30.8 + - - +
204B THR* 3.3 11.6 - - + +
207B LEU* 3.7 39.7 - - + +
208B LEU* 3.8 20.6 - - + -
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Residues in contact with GLN 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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168B ARG* 2.9 33.6 + - + +
169B ASP* 3.8 4.7 - - - +
171B LEU* 1.3 74.2 - - - +
173B ALA* 1.3 65.1 + - - +
175B VAL* 2.9 27.6 + - - +
176B ASP* 3.0 33.2 + - - +
208B LEU* 3.9 18.5 - - + +
210B ASN* 5.2 2.3 - - - +
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Residues in contact with ALA 173 (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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145B TYR* 3.9 26.5 - - + -
169B ASP 2.9 19.2 + - - +
170B ALA* 3.7 5.4 - - - +
172B GLN* 1.3 75.2 - - - +
174B ALA* 1.3 62.6 + - - +
175B VAL 3.3 0.2 + - - -
176B ASP* 3.3 11.5 + - - +
177B PHE* 3.0 35.3 + - + -
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Residues in contact with ALA 174 (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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142B GLY* 3.8 15.5 - - - +
145B TYR* 3.7 23.0 - - + +
146B HIS* 4.0 3.4 - - - +
170B ALA 3.0 16.4 + - - +
171B LEU* 3.2 13.2 - - - +
172B GLN 3.2 0.2 - - - -
173B ALA* 1.3 75.5 - - - +
175B VAL* 1.3 57.1 + - - +
177B PHE* 3.3 2.8 + - - +
178B TYR* 3.0 38.0 + - + -
204B THR* 3.8 13.2 - - + -
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Residues in contact with VAL 175 (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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171B LEU 2.9 19.6 + - - +
172B GLN* 2.9 22.6 + - - +
174B ALA* 1.3 72.6 - - - +
176B ASP* 1.3 69.1 + - - +
178B TYR* 3.0 6.6 + - - +
179B GLU* 2.9 42.0 + - - +
201B LEU* 3.8 19.8 - - + +
204B THR* 3.6 13.5 - - + +
205B HIS* 4.2 15.5 - - + +
208B LEU* 3.5 22.9 - - + -
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Residues in contact with ASP 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B GLN* 3.0 34.5 + - - +
173B ALA* 3.3 13.1 + - - +
175B VAL* 1.3 74.9 - - - +
177B PHE* 1.3 61.4 + - + +
179B GLU* 2.8 34.8 + - - +
180B GLU* 2.9 24.9 + - + +
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Residues in contact with PHE 177 (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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119B GLN* 5.4 6.5 - - - -
122B LEU* 5.0 3.1 - - + -
138B LEU* 3.9 26.2 - - + +
141B LEU* 3.4 40.6 - - + -
142B GLY* 3.9 16.2 - - - +
145B TYR* 3.4 38.1 - + - -
173B ALA* 3.0 29.6 + - + -
174B ALA 3.7 6.7 - - - +
176B ASP* 1.3 76.9 - - + +
178B TYR* 1.3 61.6 + - - +
180B GLU* 3.9 17.1 - - - +
181B ASN* 3.0 25.1 + - - +
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Residues in contact with TYR 178 (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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139B TYR* 3.8 29.4 - + - -
142B GLY* 3.4 25.9 + - - -
143B ASN* 2.7 27.8 + - - -
146B HIS* 4.2 7.9 - - + +
174B ALA* 3.0 26.9 + - + -
175B VAL 3.0 8.9 + - - +
177B PHE* 1.3 77.1 - - - +
179B GLU* 1.3 55.8 + - - +
181B ASN* 3.8 3.9 - - + +
182B LEU* 2.9 28.7 + - - +
197B ALA* 4.3 18.1 - - + +
200B ASN* 3.1 31.3 + - + +
201B LEU* 3.5 26.8 - - + +
204B THR* 3.5 24.2 - - - -
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Residues in contact with GLU 179 (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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175B VAL* 2.9 28.0 + - - +
176B ASP* 2.8 25.1 + - - +
178B TYR* 1.3 76.5 - - - +
180B GLU* 1.3 59.4 + - - +
182B LEU* 3.7 9.3 - - + +
183B SER* 2.9 30.7 + - - -
201B LEU* 4.2 17.6 - - + +
205B HIS* 4.7 6.8 + - - -
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Residues in contact with GLU 180 (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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126B ARG* 3.5 24.3 + - - -
138B LEU* 3.8 24.0 - - + +
176B ASP* 2.9 24.5 + - + +
177B PHE* 3.9 23.5 + - - +
179B GLU* 1.3 71.6 - - + +
181B ASN* 1.3 68.4 + - - +
183B SER* 3.2 8.4 + - - -
184B LEU* 3.0 24.8 + - - +
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Residues in contact with ASN 181 (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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135B ALA* 2.8 41.8 + - - +
138B LEU* 3.6 15.8 - - + +
139B TYR* 3.6 21.1 - - - +
177B PHE 3.0 18.0 + - - +
178B TYR* 3.8 7.2 - - + +
180B GLU* 1.3 78.2 - - - +
182B LEU* 1.3 57.7 + - - +
184B LEU* 3.2 3.1 + - - +
185B VAL* 3.0 44.2 + - - +
193B ALA* 4.7 2.4 - - - +
197B ALA* 3.6 21.4 - - + +
380B GLU* 5.7 0.4 + - - -
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Residues in contact with LEU 182 (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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178B TYR 2.9 21.6 + - - +
179B GLU* 3.7 10.3 - - + +
180B GLU 3.2 0.6 - - - -
181B ASN* 1.3 77.5 - - - +
183B SER* 1.3 58.9 + - - +
185B VAL* 3.3 6.5 + - - +
186B THR* 2.9 37.9 + - - +
194B GLN* 3.8 26.2 - - + +
197B ALA* 4.4 6.5 - - + -
198B PHE* 3.6 50.3 - - + -
201B LEU* 4.9 11.7 - - + -
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Residues in contact with SER 183 (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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179B GLU 2.9 15.5 + - - -
180B GLU* 3.2 11.3 + - - -
182B LEU* 1.3 78.1 - - - +
184B LEU* 1.3 62.2 + - - +
186B THR* 3.1 12.6 - - - +
187B ALA* 3.1 26.3 + - - +
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Residues in contact with LEU 184 (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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131B LYS* 4.3 11.0 - - + +
134B GLU* 3.3 45.1 - - + +
135B ALA* 4.1 15.0 - - + +
138B LEU* 4.1 11.4 - - + -
180B GLU 3.0 14.8 + - - +
181B ASN 3.8 2.9 - - - +
182B LEU 3.2 0.2 - - - -
183B SER* 1.3 80.8 + - - +
185B VAL* 1.3 58.1 + - + +
186B THR 3.1 4.2 + - - -
187B ALA* 3.7 8.3 + - + +
188B LEU* 3.2 35.0 + - + +
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Residues in contact with VAL 185 (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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135B ALA* 3.5 30.7 - - + -
181B ASN* 3.0 33.2 + - - +
182B LEU* 3.4 11.2 - - - +
184B LEU* 1.3 76.8 - - - +
186B THR* 1.3 56.7 + - - +
188B LEU* 3.8 10.3 - - + -
189B GLY 3.6 0.2 + - - -
190B ASP* 3.1 25.1 + - + +
193B ALA* 4.2 19.3 - - + -
194B GLN* 2.8 44.3 - - + +
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Residues in contact with THR 186 (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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182B LEU* 2.9 26.0 + - - +
183B SER* 3.1 13.6 - - - +
185B VAL* 1.3 80.0 - - - +
187B ALA* 1.3 59.5 + - + +
188B LEU 3.2 4.5 + - - -
189B GLY* 3.6 8.8 + - - -
194B GLN* 3.1 22.6 + - - +
198B PHE* 5.9 0.7 - - - -
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Residues in contact with ALA 187 (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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216A ILE* 3.7 11.1 - - - +
183B SER 3.1 13.9 + - - +
184B LEU* 3.7 9.8 + - + +
185B VAL 3.5 0.2 - - - -
186B THR* 1.3 77.6 - - + +
188B LEU* 1.3 68.5 + - + +
189B GLY 3.6 0.9 - - - -
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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