Contacts of the helix formed by residues 177 - 191 (chain B) in PDB entry 5F2R
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 177 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B GLY 5.0 2.2 + - - -
101B ARG* 6.1 1.8 - - - +
175B TYR 3.1 3.8 + - - +
176B PHE* 1.3 75.6 - - - +
178B ASP* 1.3 66.5 + - - +
179B ALA* 3.0 10.9 + - - +
180B GLN* 2.9 42.4 + - - +
181B ARG* 3.0 24.5 + - - +
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Residues in contact with ASP 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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177B ASN* 1.3 78.2 - - - +
179B ALA* 1.3 58.6 + - - +
181B ARG* 3.4 10.7 + - - +
182B GLN* 2.9 30.3 + - - +
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Residues in contact with ALA 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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100B GLY* 3.3 22.0 - - - +
177B ASN* 3.0 8.4 + - - +
178B ASP* 1.3 78.2 - - - +
180B GLN* 1.3 59.3 + - - +
182B GLN* 3.4 6.3 + - - +
183B ALA* 2.9 32.1 + - - +
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Residues in contact with GLN 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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96B LYS 5.3 1.0 - - - +
99B ILE* 3.3 20.2 - - - +
100B GLY* 3.8 14.1 - - - +
101B ARG* 3.3 37.1 + - - +
175B TYR* 4.1 6.3 + - - -
176B PHE* 3.4 43.6 - - + +
177B ASN* 2.9 43.2 + - - +
179B ALA* 1.3 76.4 - - - +
181B ARG* 1.3 60.2 + - - +
183B ALA* 3.4 2.1 + - - +
184B THR* 2.9 29.1 + - - -
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Residues in contact with ARG 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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172B VAL* 3.7 15.1 - - + +
173B PRO 3.7 5.5 + - - -
174B ALA 3.1 16.0 + - - -
176B PHE* 2.9 35.1 + - + -
177B ASN 3.0 18.2 + - - +
178B ASP* 3.7 10.8 - - - +
180B GLN* 1.3 75.7 - - - +
182B GLN* 1.3 62.9 + - - +
184B THR* 3.3 8.7 + - - -
185B LYS* 3.2 26.9 + - - +
198B ILE* 4.1 29.7 + - + +
200B ASN* 2.9 34.5 + - - +
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Residues in contact with GLN 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 ASP 2.9 18.1 + - - +
179B ALA* 3.9 6.3 - - - +
180B GLN 3.4 0.2 - - - -
181B ARG* 1.3 75.8 - - - +
183B ALA* 1.3 57.9 + - - +
185B LYS* 3.3 25.8 + - - +
186B ASP* 2.9 61.8 + - - +
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Residues in contact with ALA 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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99B ILE* 3.8 11.6 - - + +
100B GLY* 3.7 26.0 - - - +
143B GLU* 3.4 22.5 - - + +
179B ALA 2.9 19.5 + - - +
180B GLN 3.9 1.8 - - - +
181B ARG 3.2 0.2 - - - -
182B GLN* 1.3 75.0 - - - +
184B THR* 1.3 59.3 + - - +
186B ASP* 3.4 10.2 + - - +
187B ALA* 2.9 23.4 + - - +
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Residues in contact with THR 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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35B LEU* 4.2 16.5 - - + +
99B ILE* 4.2 12.8 - - - +
150B LEU* 4.5 1.7 - - - +
170B VAL* 3.8 28.2 - - + +
171B THR 4.7 0.7 - - - +
172B VAL* 3.8 17.0 - - + +
176B PHE* 3.7 17.3 - - - -
180B GLN 2.9 14.8 + - - -
181B ARG 3.3 8.5 + - - -
183B ALA* 1.3 75.4 - - - +
185B LYS* 1.3 64.7 + - - +
187B ALA* 3.3 6.0 + - - +
188B GLY* 3.2 16.8 + - - -
195B VAL* 4.7 2.4 - - - +
198B ILE* 4.1 4.9 - - + -
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Residues in contact with LYS 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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181B ARG* 3.2 17.4 + - - +
182B GLN* 3.4 32.5 - - - +
184B THR* 1.3 77.8 - - - +
186B ASP* 1.3 58.1 + - - +
188B GLY* 3.1 3.8 + - - -
189B THR* 3.0 29.0 + - - +
195B VAL* 3.9 36.5 + - + +
196B MET 5.0 6.7 + - - -
197B ARG* 5.5 0.2 - - - +
198B ILE* 3.8 28.9 - - + +
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Residues in contact with ASP 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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143B GLU* 4.6 12.4 - - + +
182B GLN* 2.9 47.6 + - - +
183B ALA* 3.6 12.2 - - - +
184B THR 3.2 0.2 - - - -
185B LYS* 1.3 74.2 - - - +
187B ALA* 1.3 65.9 + - - +
189B THR* 3.1 10.5 + - - -
190B ILE* 2.9 33.8 + - + +
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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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35B LEU* 5.1 0.9 - - + -
99B ILE* 4.6 0.7 - - + -
143B GLU* 3.4 29.2 - - + +
146B SER* 3.9 12.1 - - - -
147B ALA* 3.2 18.1 - - - +
150B LEU* 3.7 15.0 - - + -
183B ALA 2.9 14.3 + - - +
184B THR* 3.3 13.5 - - - +
185B LYS 3.3 0.2 - - - -
186B ASP* 1.3 75.2 - - - +
188B GLY* 1.3 61.0 + - - +
190B ILE* 4.4 0.2 - - - -
191B ALA* 3.0 19.6 + - - +
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Residues in contact with GLY 188 (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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150B LEU* 3.5 15.4 - - - +
184B THR 3.2 4.2 + - - -
185B LYS 3.1 9.5 + - - -
187B ALA* 1.3 79.1 - - - +
189B THR* 1.3 59.3 + - - +
191B ALA* 3.0 9.7 + - - -
193B LEU* 2.8 40.2 + - - +
195B VAL* 3.9 12.1 - - - -
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Residues in contact with THR 189 (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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185B LYS* 3.0 14.7 + - - +
186B ASP* 3.1 12.5 + - - -
188B GLY* 1.3 73.7 - - - +
190B ILE* 1.3 61.8 + - + +
192B GLY* 2.9 21.0 + - - -
193B LEU 3.4 10.3 + - - +
194B ASN* 5.7 0.7 - - - -
195B VAL 5.7 0.7 + - - -
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Residues in contact with ILE 190 (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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143B GLU* 4.1 28.0 - - + +
144B GLU* 4.3 21.1 - - + +
147B ALA* 3.5 20.0 - - + -
186B ASP* 2.9 26.5 + - + +
189B THR* 1.3 79.2 - - + +
191B ALA* 1.3 55.8 + - - +
192B GLY 3.2 3.8 + - - -
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Residues in contact with ALA 191 (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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147B ALA* 3.4 26.0 - - - +
150B LEU* 3.9 15.7 - - + -
151B THR* 3.5 17.6 + - - +
154B LYS* 3.7 22.3 + - - +
187B ALA 3.0 10.9 + - - +
188B GLY* 3.0 10.5 + - - +
190B ILE* 1.3 76.1 - - - +
192B GLY* 1.3 60.0 + - - +
193B LEU* 3.3 5.6 + - + +
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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