Contacts of the helix formed by residues 182 - 196 (chain B) in PDB entry 2C8U
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 TYR 182 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133B PRO* 3.7 27.4 + - - +
136B LEU* 3.6 32.4 - - + +
137B ASP* 3.3 25.5 + - - -
140B CYS* 3.5 29.8 - - - -
177B PHE* 4.3 15.2 - + - -
178B LEU* 4.0 19.3 - - + -
181B LYS* 1.3 101.8 - - + +
183B PRO* 1.4 73.6 - - - +
184B GLU 3.2 2.7 - - - -
185B ILE* 2.9 25.8 + - + +
186B HIS* 3.2 9.8 + - - +
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Residues in contact with PRO 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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180B GLY 5.8 0.2 - - - -
181B LYS* 3.2 5.4 - - - +
182B TYR* 1.4 89.8 - - - +
184B GLU* 1.3 75.7 + - - +
186B HIS* 3.3 13.2 + - + +
187B LYS* 2.8 31.7 + - - +
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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
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140B CYS* 4.3 25.1 - - - +
143B LEU* 3.6 14.8 - - + +
144B LYS* 3.7 39.8 - - + +
182B TYR 3.1 0.4 + - - -
183B PRO* 1.3 95.1 - - - +
185B ILE* 1.3 56.6 + - - +
187B LYS* 3.6 8.2 - - + +
188B HIS* 2.8 29.1 + - - +
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Residues in contact with ILE 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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136B LEU* 3.8 34.5 - - + +
139B ILE* 4.3 11.2 - - + -
140B CYS* 3.7 26.7 - - - -
143B LEU* 4.0 17.7 - - + -
163B LEU* 5.3 3.4 - - + -
167B ILE* 4.0 31.4 - - + -
178B LEU* 4.1 13.0 - - + -
182B TYR* 2.9 16.8 + - + +
184B GLU* 1.3 74.9 - - - +
186B HIS* 1.3 68.0 + - + +
188B HIS* 3.3 5.0 + - - +
189B ARG* 3.2 20.3 + - - +
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Residues in contact with HIS 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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178B LEU* 2.9 36.1 + - + +
179B THR* 4.7 3.4 - - - -
180B GLY* 4.7 2.5 + - - -
181B LYS 2.7 31.2 + - - -
182B TYR* 3.2 15.4 + - - +
183B PRO* 3.3 8.4 + - + +
185B ILE* 1.3 78.1 - - + +
187B LYS* 1.3 64.0 + - - +
189B ARG* 3.1 8.4 + - - +
190B GLU* 3.1 22.8 + - - +
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Residues in contact with LYS 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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183B PRO 2.8 19.1 + - - +
184B GLU* 3.6 9.2 - - + +
186B HIS* 1.3 76.7 - - - +
188B HIS* 1.3 61.0 + - - +
190B GLU* 3.4 29.1 + - - +
191B ASN* 2.9 53.1 + - - +
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Residues in contact with HIS 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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143B LEU* 3.8 20.4 - - + -
149B LYS 4.9 2.0 - - - -
150B LEU* 4.3 8.1 - - + -
151B ALA* 3.7 17.0 + - - +
160B ASP* 2.4 56.0 + - - -
163B LEU* 3.7 21.3 - - + +
164B ILE* 4.2 6.6 - - + +
184B GLU 2.8 21.4 + - - +
185B ILE* 3.5 7.2 + - - +
186B HIS 3.3 0.2 - - - -
187B LYS* 1.3 72.7 - - - +
189B ARG* 1.3 60.1 + - - +
191B ASN* 3.3 8.0 + - - +
192B LEU* 2.8 42.2 + - + +
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Residues in contact with ARG 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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164B ILE* 3.5 34.6 + - + +
167B ILE* 4.4 13.5 - - - +
168B ASP* 2.7 39.6 + - - -
185B ILE 3.2 8.2 + - - +
186B HIS* 3.1 11.4 + - - +
188B HIS* 1.3 81.3 + - - +
190B GLU* 1.3 68.1 + - - +
192B LEU* 3.2 4.7 + - - +
193B LEU* 3.1 44.5 + - + +
203B LEU* 4.1 22.2 - - - +
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Residues in contact with GLU 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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186B HIS 3.1 12.7 + - - +
187B LYS* 3.6 38.0 + - - +
189B ARG* 1.3 77.8 - - - +
191B ASN* 1.3 68.5 + - - +
193B LEU* 3.3 8.7 + - - +
194B ALA* 3.2 20.4 + - + +
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Residues in contact with ASN 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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149B LYS* 3.0 51.7 + - + +
150B LEU* 3.6 5.8 - - + -
187B LYS* 2.9 48.2 + - - +
188B HIS* 3.6 3.3 - - - +
190B GLU* 1.3 83.8 - - - +
192B LEU* 1.3 59.3 + - - +
194B ALA* 3.3 9.0 + - - +
195B SER* 2.8 28.7 + - - +
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Residues in contact with LEU 192 (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 9.6 - - + +
156B VAL* 3.7 27.1 - - + -
160B ASP* 3.7 41.3 - - + +
161B LEU* 4.1 3.4 - - + -
164B ILE* 3.7 26.0 - - + -
188B HIS* 2.8 23.5 + - + +
189B ARG* 3.2 6.3 + - + +
191B ASN* 1.3 74.2 - - - +
193B LEU* 1.3 64.7 + - + +
195B SER* 3.2 2.7 + - - -
196B SER* 3.1 21.9 + - - -
199B LEU* 3.6 31.1 - - + +
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Residues in contact with LEU 193 (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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189B ARG* 3.1 37.6 + - + +
190B GLU* 3.7 7.0 - - - +
192B LEU* 1.3 79.0 - - + +
194B ALA* 1.3 59.7 + - - +
196B SER 3.2 21.2 - - - +
197B PRO* 3.8 1.6 - - - +
199B LEU* 4.4 5.6 - - + -
200B ALA* 3.5 35.3 - - + +
203B LEU* 3.6 33.0 - - + -
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Residues in contact with ALA 194 (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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190B GLU* 3.2 11.8 + - + +
191B ASN* 3.5 12.8 - - - +
192B LEU 3.2 0.4 - - - -
193B LEU* 1.3 77.0 - - - +
195B SER* 1.3 61.1 + - - +
196B SER 3.2 0.6 + - - -
197B PRO* 4.0 9.7 - - - +
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Residues in contact with SER 195 (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* 3.6 27.8 - - - +
154B ASP 4.3 7.0 + - - -
155B LYS* 5.7 0.7 - - - -
156B VAL* 4.1 11.0 - - - +
191B ASN 2.8 18.2 + - - -
192B LEU 3.2 4.0 + - - -
194B ALA* 1.3 76.2 - - - +
196B SER* 1.3 57.7 + - - +
197B PRO* 3.7 5.8 - - - +
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Residues in contact with SER 196 (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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26B ALA* 4.0 21.8 + - - +
156B VAL* 4.4 13.4 - - - +
192B LEU 3.1 12.1 + - - +
193B LEU 3.2 10.8 - - - +
195B SER* 1.3 80.9 - - - +
197B PRO* 1.4 62.0 - - - +
198B ARG* 3.2 6.3 - - - +
199B LEU* 3.7 26.9 + - - +
200B ALA 2.9 21.8 + - - -
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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