Contacts of the helix formed by residues 178 - 191 (chain B) in PDB entry 5EWL
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 GLY 178 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A SER* 5.2 0.4 + - - -
134B MET 5.4 0.7 - - - -
150B ILE* 3.8 10.3 - - - +
176B PHE 3.1 0.2 + - - -
177B PRO* 1.3 71.4 - - - +
179B TYR* 1.3 56.1 + - - +
180B GLN* 3.2 3.6 - - - -
181B ASP* 2.9 23.6 + - - +
182B PHE* 2.8 33.6 + - - +
231B TYR* 3.7 8.3 - - - -
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Residues in contact with TYR 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A SER* 3.1 21.8 - - - -
173B THR* 3.6 19.8 - - - +
174B THR 3.4 14.8 - - - +
175B TYR* 3.5 46.8 - + - -
176B PHE 3.1 10.5 + - - +
178B GLY* 1.3 77.8 - - - +
180B GLN* 1.3 81.5 + - + +
182B PHE* 3.4 3.4 + - - +
183B VAL* 3.0 35.0 + - + +
204B LEU* 3.7 22.3 - - + +
231B TYR* 3.5 19.7 - - + -
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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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178B GLY 3.2 0.8 - - - -
179B TYR* 1.3 100.6 - - + +
181B ASP* 1.4 59.4 + - - +
183B VAL* 3.3 17.3 + - - +
184B ASN* 2.8 64.7 + - - +
187B ARG* 5.7 1.0 + - - -
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Residues in contact with ASP 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ASP* 4.4 12.5 - - - +
150B ILE* 4.1 15.0 - - + +
151B GLU* 5.4 3.5 - - + +
178B GLY* 2.9 18.5 + - - +
180B GLN* 1.4 78.0 - - - +
182B PHE* 1.4 57.0 + - - +
184B ASN* 3.8 10.3 + - - +
185B LYS* 2.9 31.0 + - - +
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Residues in contact with PHE 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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150B ILE* 3.6 16.9 - - + +
153B GLN* 5.8 0.4 - - + -
154B ALA* 3.8 24.2 - - + -
157B MET* 3.7 40.4 - - + -
171B ILE* 3.9 26.9 - - + -
173B THR* 4.2 2.7 - - + -
178B GLY 2.8 14.7 + - - +
179B TYR 3.4 8.1 - - - +
181B ASP* 1.4 70.5 - - - +
183B VAL* 1.4 63.6 + - - +
185B LYS* 3.2 15.1 + - - +
186B ILE* 3.2 32.9 + - + +
229B LEU* 4.2 9.9 - - + -
230B LEU 5.4 0.2 - - - -
231B TYR* 3.6 46.9 - + + -
259B PRO* 5.3 4.3 - - + -
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Residues in contact with VAL 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ILE* 4.0 28.0 - - + -
173B THR* 4.2 10.8 - - + +
179B TYR* 3.0 20.3 + - + +
180B GLN* 4.0 17.0 - - - +
182B PHE* 1.4 73.9 - - - +
184B ASN* 1.3 59.4 + - - +
186B ILE* 3.3 3.5 + - - +
187B ARG* 2.9 59.7 + - + +
202B VAL* 4.0 29.6 - - + -
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Residues in contact with ASN 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 GLN* 2.8 60.8 + - - +
181B ASP* 3.9 10.9 + - - +
183B VAL* 1.3 70.2 - - - +
185B LYS* 1.4 59.0 + - - +
187B ARG* 3.8 9.7 + - - +
188B SER* 2.8 33.1 + - - -
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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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151B GLU* 3.7 48.6 + - + +
152B GLN* 5.6 0.4 - - - +
154B ALA* 4.0 12.6 - - + -
155B SER* 4.7 13.6 - - - +
158B LEU* 6.1 0.4 - - + -
181B ASP 2.9 18.6 + - - +
182B PHE 3.2 5.4 + - - +
184B ASN* 1.4 73.4 - - - +
186B ILE* 1.3 60.7 + - - +
188B SER* 3.2 9.2 + - - +
189B THR* 2.7 49.2 + - - +
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Residues in contact with ILE 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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154B ALA* 3.5 40.2 - - + +
158B LEU* 3.9 12.6 - - + -
169B PHE* 3.6 36.3 - - + -
171B ILE* 3.8 20.6 - - + -
182B PHE* 3.2 24.0 + - + +
183B VAL 3.6 4.7 - - - +
185B LYS* 1.3 76.8 - - - +
187B ARG* 1.3 53.8 + - - +
189B THR* 3.1 2.3 + - - -
190B ILE* 2.9 44.4 + - + +
199B LEU* 4.9 2.9 - - + -
229B LEU* 4.1 16.8 - - + -
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Residues in contact with ARG 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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180B GLN* 5.7 1.0 + - - -
183B VAL* 2.9 40.3 + - + +
184B ASN* 3.8 10.5 + - - +
186B ILE* 1.3 72.8 - - - +
188B SER* 1.3 61.2 + - - +
190B ILE* 3.6 7.5 + - + +
191B GLU* 3.0 49.0 + - - +
199B LEU* 3.8 24.7 + - + +
202B VAL* 3.6 28.6 - - - +
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Residues in contact with SER 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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184B ASN 2.8 20.1 + - - -
185B LYS* 3.2 16.2 + - - +
187B ARG* 1.3 74.4 - - - +
189B THR* 1.4 67.0 + - - +
191B GLU* 3.4 11.1 + - - +
192B ASN* 3.2 24.6 - - - +
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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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155B SER* 5.7 5.1 - - - -
158B LEU* 3.7 25.7 - - + +
185B LYS* 2.7 41.2 + - - +
186B ILE 3.4 4.0 - - - -
188B SER* 1.4 77.2 + - - +
190B ILE* 1.3 60.9 + - + +
192B ASN* 3.5 5.3 + - - +
193B SER* 3.4 23.0 + - - -
197B TRP* 5.7 2.2 - - + +
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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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158B LEU* 3.2 37.7 - - + -
169B PHE* 3.9 11.2 - - + -
186B ILE* 2.9 29.1 + - + +
187B ARG* 3.6 12.8 - - + +
189B THR* 1.3 72.1 - - + +
191B GLU* 1.4 72.6 + - + +
192B ASN 3.2 4.7 + - - -
193B SER* 3.5 18.5 + - - +
195B VAL 4.8 1.2 - - - +
197B TRP* 3.5 44.5 - - + +
199B LEU* 5.4 10.3 - - + +
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Residues in contact with GLU 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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187B ARG* 3.0 50.1 + - - +
188B SER* 3.4 7.1 + - - +
190B ILE* 1.4 81.0 - - + +
192B ASN* 1.3 68.1 + - - +
193B SER 3.7 1.3 - - - -
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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