Contacts of the helix formed by residues 165 - 184 (chain B) in PDB entry 1F5Q
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 GLU 165 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B PRO* 3.9 19.4 - - + +
164B ARG* 1.3 80.7 + - - +
166B ASP* 1.3 75.7 + - - +
168B LEU* 4.3 8.6 + - - +
169B ASN* 4.7 5.4 + - - +
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Residues in contact with ASP 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 ALA* 4.9 0.7 - - + -
163B PRO* 2.9 24.1 + - + +
165B GLU* 1.3 87.3 - - - +
167B TYR* 1.3 71.5 + - + +
168B LEU 2.9 2.1 + - - -
169B ASN* 3.2 15.3 + - - +
170B ILE* 3.2 19.4 + - + +
208B TYR* 3.7 16.5 - - + -
210B TYR* 2.5 44.3 + - - +
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Residues in contact with TYR 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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9B PHE* 4.0 22.6 - + + -
154B CYS* 3.8 34.3 - - - -
157B LEU* 3.7 37.5 + - + +
158B HIS* 3.3 33.4 + - - +
162B ALA* 3.9 18.9 + - + -
163B PRO 3.4 20.0 - - - -
164B ARG* 3.3 22.0 + - - +
166B ASP* 1.3 74.1 - - - +
168B LEU* 1.3 53.3 + - - +
170B ILE* 3.2 1.3 + - - +
171B TYR* 2.7 37.7 + - - +
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Residues in contact with LEU 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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164B ARG 4.5 2.0 + - - +
165B GLU 4.3 7.5 + - - +
166B ASP 2.9 4.4 + - - -
167B TYR* 1.3 77.9 - - - +
169B ASN* 1.3 66.5 + - + +
171B TYR* 3.2 5.3 + - + +
172B ASN* 3.0 51.0 + - - +
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Residues in contact with ASN 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 GLU 4.7 3.7 + - - +
166B ASP* 3.2 9.3 + - - +
168B LEU* 1.3 84.4 - - + +
170B ILE* 1.3 62.9 + - - +
172B ASN* 3.5 7.5 + - - +
173B LEU* 3.2 39.6 + - - +
208B TYR* 4.1 15.6 + - - +
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Residues in contact with ILE 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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153B ILE* 4.2 7.9 - - + -
157B LEU* 3.9 27.8 - - + -
166B ASP* 3.2 20.8 + - + +
167B TYR 3.2 6.7 + - - +
168B LEU 3.1 0.4 - - - -
169B ASN* 1.3 73.6 - - - +
171B TYR* 1.3 68.6 + - - +
173B LEU* 3.0 17.2 + - + +
174B CYS* 3.0 28.3 + - - -
203B THR* 4.7 3.8 - - - +
204B MET* 4.1 25.1 - - + -
208B TYR* 3.9 25.4 - - + +
210B TYR* 3.6 23.3 - - - +
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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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8B GLY* 5.5 7.2 - - - -
67B ASN* 5.0 5.8 + - + +
68B ASN* 3.4 28.5 + - - -
150B THR* 3.7 33.5 - - + +
151B ASP* 5.6 0.7 - - - -
153B ILE* 4.5 13.8 - - + +
154B CYS* 3.9 25.6 - - - -
157B LEU* 6.3 0.2 - - + -
167B TYR* 2.7 22.5 + - + +
168B LEU* 3.6 5.6 - - + +
170B ILE* 1.3 75.1 - - - +
172B ASN* 1.3 71.9 + - - +
174B CYS* 3.2 2.1 + - - +
175B ARG* 2.9 51.2 + - + +
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Residues in contact with ASN 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 LEU* 3.0 48.3 + - - +
169B ASN* 3.8 9.1 - - - +
171B TYR* 1.3 87.6 - - - +
173B LEU* 1.3 59.1 + - + +
175B ARG* 2.9 33.4 + - - +
176B PRO* 3.2 19.5 - - - +
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Residues in contact with LEU 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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169B ASN* 3.2 37.1 + - - +
170B ILE* 3.0 8.5 + - + +
172B ASN* 1.3 81.0 - - + +
174B CYS* 1.3 61.2 + - - +
176B PRO* 3.1 20.6 - - + +
177B LYS* 4.0 14.3 - - - +
203B THR* 3.9 31.4 - - + +
208B TYR* 5.4 4.7 - - - +
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Residues in contact with CYS 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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153B ILE* 3.3 24.7 - - + -
170B ILE* 3.0 24.1 + - - +
171B TYR 3.8 0.4 - - - +
173B LEU* 1.3 78.2 - - - +
175B ARG* 1.3 67.3 + - - +
177B LYS* 3.1 7.3 + - - +
178B ILE* 3.0 23.8 + - + +
199B CYS* 3.9 28.5 - - + -
200B MET* 3.9 17.0 - - - -
203B THR* 3.7 21.5 - - - -
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Residues in contact with ARG 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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67B ASN* 3.3 40.3 + - + +
150B THR* 4.7 6.3 - - + -
153B ILE* 4.7 0.8 - - - +
171B TYR* 2.9 35.0 + - + +
172B ASN* 2.9 36.0 + - - +
174B CYS* 1.3 74.1 - - - +
176B PRO* 1.3 88.5 - - + +
178B ILE* 3.0 20.5 + - - +
179B PHE* 3.1 41.7 + - + -
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Residues in contact with PRO 176 (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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172B ASN 3.2 18.6 - - - +
173B LEU* 3.1 18.2 - - + +
175B ARG* 1.3 107.4 - - + +
177B LYS* 1.3 62.2 + - + +
179B PHE* 3.6 8.3 + - + +
180B CYS* 3.3 28.6 + - - -
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Residues in contact with LYS 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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173B LEU* 4.0 14.1 - - - +
174B CYS 3.1 7.0 + - - +
176B PRO* 1.3 80.1 - - + +
178B ILE* 1.3 58.4 + - - +
180B CYS* 3.3 4.2 + - - +
181B ALA* 3.0 27.2 + - - +
199B CYS* 3.6 19.7 - - + -
202B LEU* 3.8 25.6 - - + +
203B THR* 3.7 22.0 - - + -
236B VAL* 4.0 6.6 - - + +
237B ASP* 4.8 0.4 + - - -
240B ILE* 3.6 33.9 - - + +
73C GLU* 2.9 34.4 + - - -
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Residues in contact with ILE 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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71B PRO* 6.0 0.2 - - + -
149B SER* 3.8 26.2 - - - +
150B THR* 4.0 27.8 - - + +
153B ILE* 3.3 35.2 - - + -
174B CYS* 3.1 15.7 - - + +
175B ARG 3.0 6.0 + - - +
177B LYS* 1.3 75.0 - - - +
179B PHE* 1.3 61.1 + - + +
181B ALA* 3.2 7.1 + - - +
182B LEU* 3.0 42.6 + - + +
195B ILE* 4.4 7.0 - - + -
196B THR* 5.3 1.6 - - - -
199B CYS* 3.6 18.4 - - + -
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Residues in contact with PHE 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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57B PHE* 3.9 23.8 - + + -
67B ASN* 3.0 44.9 - - - -
70B PHE* 3.6 32.3 - + + -
71B PRO* 3.3 26.7 - - + -
150B THR* 4.0 8.3 - - + -
175B ARG* 3.1 34.6 + - + +
176B PRO* 3.8 8.1 - - + +
178B ILE* 1.3 81.7 - - + +
180B CYS* 1.3 63.0 + - - +
182B LEU* 3.3 10.1 + - + +
183B CYS* 3.3 22.5 + - - -
243B PHE* 5.5 1.6 - - + -
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Residues in contact with CYS 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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176B PRO* 3.3 15.6 + - - -
177B LYS 3.6 7.9 - - - +
178B ILE 3.2 0.2 - - - -
179B PHE* 1.3 77.3 - - - +
181B ALA* 1.3 65.7 + - - +
183B CYS* 3.2 12.3 + - - +
184B ASP* 3.3 8.7 + - - +
239B ALA* 3.4 24.5 - - - +
240B ILE* 3.9 26.0 - - + -
243B PHE* 3.9 40.7 - - + -
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Residues in contact with ALA 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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177B LYS 3.0 14.4 + - - +
178B ILE* 3.2 13.2 + - - +
180B CYS* 1.3 78.2 - - - +
182B LEU* 1.3 57.3 + - + +
184B ASP 2.8 16.1 + - - +
187B SER* 2.7 37.0 + - - +
188B ALA* 3.3 7.1 + - - -
195B ILE* 4.3 19.1 - - + -
199B CYS* 5.6 0.2 - - - -
236B VAL* 4.6 10.1 - - + -
239B ALA* 3.7 6.3 - - + +
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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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49B ARG* 3.0 30.8 + - - -
53B THR* 4.3 1.2 - - - +
70B PHE* 4.3 11.0 - - + -
71B PRO* 3.9 36.1 - - + +
74B VAL* 4.1 23.8 - - + +
75B ALA* 5.8 1.3 - - + +
149B SER* 5.8 3.1 - - - +
178B ILE* 3.0 34.6 + - + +
179B PHE* 3.5 12.8 - - + +
180B CYS 3.2 0.4 - - - -
181B ALA* 1.3 78.5 - - + +
183B CYS* 1.3 58.3 + - - +
188B ALA* 3.3 16.9 - - + +
195B ILE* 5.5 7.9 - - + -
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Residues in contact with CYS 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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49B ARG* 4.0 4.5 + - - -
50B LYS* 4.7 14.9 - - - +
53B THR* 3.6 33.5 + - - +
54B THR* 4.6 6.6 - - + +
57B PHE* 5.0 0.7 - - - -
70B PHE* 3.7 20.9 - - - -
179B PHE 3.3 15.9 - - - -
180B CYS 3.2 8.5 + - - +
182B LEU* 1.3 77.4 - - - +
184B ASP* 1.3 57.3 + - - +
185B GLY 3.8 2.5 + - - -
243B PHE* 3.5 32.8 - - + -
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Residues in contact with ASP 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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180B CYS 3.3 2.7 + - - +
181B ALA 2.8 7.8 + - - +
183B CYS* 1.3 79.3 - - - +
185B GLY* 1.3 55.1 + - - +
186B ARG* 3.3 34.8 + - - +
187B SER* 3.1 17.7 + - - +
188B ALA* 2.7 35.0 + - - +
235B LEU* 4.9 1.6 - - - +
238B ILE* 4.6 9.1 - - - +
239B ALA* 3.6 24.1 + - + +
242B SER* 3.5 20.1 + - - -
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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