Contacts of the helix formed by residues 180 - 187 (chain B) in PDB entry 5ICN
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 180 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B HIS* 3.4 27.8 - - - -
172B TYR* 4.9 3.5 - - - -
174B ASP* 3.5 10.7 + - - -
178B HIS 3.4 3.4 + - - -
179B HIS* 1.3 76.4 + - - +
181B ASP* 1.3 57.7 + - - -
182B GLY 3.3 3.5 + - - -
183B VAL* 3.5 6.5 + - - +
184B GLU* 3.1 25.8 + - - +
195B THR* 5.7 0.7 - - - -
197B SER* 3.6 9.0 + - - -
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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
----------------------------------------------------------
167A ILE* 4.5 4.6 - - + +
140B HIS 4.2 0.4 + - - -
141B HIS* 3.6 16.6 + - - +
143B LYS* 3.0 29.1 + - - +
179B HIS* 2.7 21.9 + - + +
180B GLY* 1.3 69.3 - - - -
182B GLY* 1.3 84.3 + - - +
184B GLU* 3.7 3.8 - - - +
185B GLU* 2.8 33.3 + - + +
205B PHE* 4.7 1.9 - - - -
206B PRO* 3.0 31.9 - - - +
208B THR* 3.6 21.3 + - + +
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Residues in contact with GLY 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TYR* 4.6 2.1 + - - -
140B HIS 3.0 14.8 + - - -
141B HIS 4.3 0.7 - - - -
142B ALA 3.3 22.0 - - - +
143B LYS* 4.8 4.5 - - - -
154B ASN* 3.8 6.7 - - - -
157B VAL* 4.3 0.5 - - - +
181B ASP* 1.3 86.9 + - - +
183B VAL* 1.3 63.2 + - - +
185B GLU* 4.1 1.7 - - - +
186B ALA* 3.1 26.5 + - - +
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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
----------------------------------------------------------
140B HIS* 3.8 10.1 - - + -
154B ASN* 3.9 4.5 - - - +
156B ILE* 3.6 30.3 - - + -
157B VAL* 4.2 7.6 - - + -
160B ILE* 3.7 29.6 - - + -
172B TYR* 3.6 44.6 - - + +
180B GLY 3.5 3.0 + - - +
182B GLY* 1.3 75.4 - - - +
184B GLU* 1.3 63.3 + - - +
187B PHE* 3.1 37.5 + - + +
195B THR* 3.9 4.2 - - + +
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Residues in contact with GLU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 3.6 12.7 - - + +
179B HIS* 3.2 21.3 + - - -
180B GLY 3.1 18.4 + - - +
181B ASP* 3.8 7.0 - - - +
182B GLY 3.1 0.2 - - - -
183B VAL* 1.3 77.2 - - - +
185B GLU* 1.3 59.9 + - - +
187B PHE* 3.0 5.5 + - - +
188B TYR* 2.9 36.3 + - + -
195B THR* 3.5 28.9 + - - +
197B SER* 5.4 0.7 - - - -
213B ASP* 3.0 33.5 - - - +
223B ALA* 3.8 10.8 - - + +
225B ASN* 3.1 24.1 + - - +
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Residues in contact with GLU 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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166A GLU 4.7 1.7 - - - +
167A ILE* 3.7 18.7 - - + +
168A ARG* 3.4 39.8 + - - +
173A TYR* 3.3 37.6 - - + +
174A GLN* 2.7 31.8 + - - +
67B TYR* 5.1 1.8 + - - +
143B LYS* 4.3 31.7 + - + +
144B LYS 5.1 0.9 + - - -
181B ASP 2.8 21.6 + - - +
182B GLY* 4.1 2.9 - - - +
184B GLU* 1.3 73.4 - - - +
186B ALA* 1.3 61.6 + - - +
187B PHE 3.3 0.3 + - - -
188B TYR* 3.4 4.2 + - - -
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Residues in contact with ALA 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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173A TYR 3.9 10.1 - - - -
174A GLN* 3.6 4.6 - - - +
175A ALA* 2.8 29.6 + - - +
177A ILE* 5.1 1.2 - - - +
67B TYR* 3.6 21.3 + - + +
157B VAL* 3.5 28.5 - - + -
182B GLY 3.1 18.3 + - - +
185B GLU* 1.3 78.1 - - - +
187B PHE* 1.3 65.6 + - + +
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Residues in contact with PHE 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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174A GLN* 4.9 0.2 - - - -
175A ALA* 4.9 2.0 - - + -
177A ILE* 4.8 6.3 - - + -
157B VAL* 3.7 40.2 - - + -
160B ILE* 3.5 46.7 - - + -
161B LEU* 4.1 18.4 - - + -
164B LEU* 4.2 3.8 - - + -
183B VAL* 3.1 27.6 - - + +
184B GLU 3.0 5.3 + - - +
186B ALA* 1.3 79.9 - - + +
188B TYR* 1.3 58.4 + - - +
189B THR 3.1 4.5 + - - -
190B THR* 3.3 26.6 + - + +
193B VAL* 3.9 31.0 - - + -
195B THR* 4.5 3.4 - - + -
403B K 2.8 27.4 - - - -
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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
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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