Contacts of the helix formed by residues 176 - 190 (chain B) in PDB entry 2CAR
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 SER 176 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136B THR* 3.5 0.2 - - - -
164B TYR* 4.0 8.7 - - - -
172B LYS* 2.8 25.6 + - - -
173B ASN* 3.5 6.6 + - - -
175B VAL* 1.3 74.7 - - - +
177B HIS* 1.3 68.4 + - - +
178B ARG* 3.0 22.5 + - - +
179B PHE* 3.3 29.5 + - - +
180B ARG* 3.0 25.7 + - - +
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Residues in contact with HIS 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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73B THR* 4.0 17.7 - - + +
114B ALA* 3.5 33.7 - - + +
115B LEU 4.0 10.1 - - - -
116B CYS* 3.6 20.0 - - + +
134B GLY* 3.5 23.1 - - - +
135B ARG 4.3 0.2 - - - +
136B THR* 2.8 19.7 + - - +
151B TRP* 3.9 9.0 - + - -
164B TYR* 3.0 40.3 + + - -
172B LYS* 4.8 7.9 - - - -
176B SER* 1.3 75.6 - - - +
178B ARG* 1.3 69.0 + - + +
180B ARG* 3.4 2.8 + - - -
181B ALA 3.0 21.7 + - - -
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Residues in contact with ARG 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LYS* 3.6 24.0 + - - +
22B GLU* 3.0 37.2 + - - +
23B VAL* 3.2 31.0 - - - +
26B ILE* 4.6 8.6 - - + +
71B GLU* 2.8 38.7 + - - +
73B THR* 5.9 0.4 - - - -
116B CYS* 3.9 15.0 - - + -
118B PHE* 4.4 0.6 - - + -
176B SER* 3.0 9.8 + - - +
177B HIS* 1.3 84.2 - - + +
179B PHE* 1.3 71.6 + - + +
181B ALA* 3.3 2.1 + - - +
182B LEU* 3.0 36.0 + - + +
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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
----------------------------------------------------------
26B ILE* 3.5 50.4 - - + +
169B LYS* 4.2 8.1 - - - -
173B ASN* 3.3 58.6 - - + +
176B SER* 3.2 25.1 + - - +
178B ARG* 1.3 83.6 - - + +
180B ARG* 1.3 58.7 + - + +
182B LEU* 3.3 6.3 + - - +
183B LEU* 2.9 30.1 + - - +
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Residues in contact with ARG 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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133B ARG 4.3 0.2 - - - -
134B GLY* 3.7 13.0 - - - -
135B ARG 2.7 29.1 + - - +
136B THR* 3.6 10.9 + - - +
137B SER 4.9 1.2 - - - +
174B ALA 4.5 5.0 + - - +
175B VAL* 3.4 45.1 + - - +
176B SER 3.0 19.5 + - - +
177B HIS 3.7 4.9 - - - +
178B ARG 3.3 0.2 - - - -
179B PHE* 1.3 78.5 - - + +
181B ALA* 1.3 62.7 + - - +
183B LEU* 3.3 13.2 + - + +
184B GLU* 3.3 23.7 + - - +
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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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116B CYS* 3.5 26.0 - - - +
118B PHE* 4.0 6.3 - - + -
132B PHE* 3.8 15.7 - - - +
133B ARG 3.6 5.6 - - - -
134B GLY* 3.4 23.9 - - - +
177B HIS 3.0 13.7 + - - +
178B ARG 3.3 4.2 + - - +
180B ARG* 1.3 75.4 - - - +
182B LEU* 1.3 64.3 + - - +
184B GLU* 3.1 15.2 + - - +
185B LEU* 3.1 9.7 + - - +
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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
----------------------------------------------------------
23B VAL* 3.9 29.4 - - + -
26B ILE* 3.9 42.6 - - + -
27B LEU* 3.4 24.1 - - + +
118B PHE* 3.6 35.2 - - + -
178B ARG* 3.0 25.9 + - + +
179B PHE 3.7 3.8 - - - +
181B ALA* 1.3 74.5 - - - +
183B LEU* 1.3 58.3 + - - +
185B LEU* 3.1 17.4 + - + +
186B GLN* 2.8 25.7 + - - +
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Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ILE* 5.4 1.2 - - - +
179B PHE 2.9 13.6 + - - +
180B ARG* 3.5 15.9 - - + +
181B ALA 3.3 0.2 - - - -
182B LEU* 1.3 77.5 - - - +
184B GLU* 1.3 60.3 + - + +
186B GLN* 3.4 26.4 + - - +
187B GLU* 2.9 31.2 + - + +
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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
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132B PHE* 3.7 20.4 - - + -
133B ARG 3.6 25.4 + - - +
180B ARG 3.3 8.5 + - - +
181B ALA 3.1 7.6 + - - +
183B LEU* 1.3 80.5 - - + +
185B LEU* 1.3 63.2 + - - +
187B GLU* 3.3 15.9 + - - +
188B TYR* 3.0 22.5 + - - +
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Residues in contact with LEU 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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27B LEU* 4.2 15.3 - - + -
31B PHE* 4.4 7.6 - - + -
69B LEU* 4.1 30.7 - - + -
118B PHE* 4.9 4.0 - - + -
120B LEU* 4.4 6.7 - - + -
132B PHE* 3.6 39.4 - - + -
181B ALA 3.1 10.6 + - - +
182B LEU* 3.1 31.0 + - + +
184B GLU* 1.3 75.6 - - - +
186B GLN* 1.3 65.3 + - - +
188B TYR* 3.2 15.1 + - - +
189B PHE* 3.4 32.2 + - + -
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Residues in contact with GLN 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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26B ILE 3.8 8.7 + - - +
27B LEU* 2.9 44.6 + - + +
28B GLY* 4.7 1.8 - - - -
31B PHE* 4.8 10.7 - - + +
182B LEU 2.8 16.0 + - - +
183B LEU* 3.6 25.8 - - - +
185B LEU* 1.3 78.4 - - - +
187B GLU* 1.3 61.0 + - - +
189B PHE* 3.3 5.4 + - - +
190B GLY* 3.0 21.5 + - - +
191B SER* 4.8 15.2 + - - +
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Residues in contact with GLU 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 LEU* 2.9 20.5 + - + +
184B GLU* 3.7 16.1 - - - +
185B LEU 3.2 0.2 - - - -
186B GLN* 1.3 77.3 + - - +
188B TYR* 1.3 62.2 + - - +
189B PHE 4.0 0.2 - - - -
190B GLY* 3.2 13.2 + - - +
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Residues in contact with TYR 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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1B MET* 2.9 45.5 - - - +
2B ALA* 3.4 26.8 + - + +
120B LEU* 4.2 5.6 - - + -
130B ARG* 3.0 48.9 + - - -
132B PHE* 3.4 31.4 - + + -
184B GLU 3.0 5.9 + - - +
185B LEU 3.4 8.7 - - - +
187B GLU* 1.3 77.7 - - - +
189B PHE* 1.3 74.0 + + - +
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Residues in contact with PHE 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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2B ALA* 3.4 43.1 - - + +
5B LEU* 4.0 11.7 - - + -
6B VAL* 5.1 1.3 - - + -
10B ILE* 4.6 3.1 - - + -
31B PHE* 3.5 26.9 - + + -
32B PRO* 3.8 34.4 - - + +
33B CYS* 3.5 21.8 - - - -
120B LEU* 4.0 18.4 - - + -
185B LEU* 3.6 28.9 - - + -
186B GLN 3.3 6.7 + - - +
188B TYR* 1.3 87.1 - + - +
190B GLY* 1.3 63.3 + - - +
192B LEU 5.3 0.2 + - - -
193B ALA* 5.3 5.5 - - - +
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Residues in contact with GLY 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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30B LYS 4.1 11.4 - - - +
31B PHE* 5.3 0.5 - - - -
32B PRO* 4.3 3.8 - - - +
186B GLN* 3.0 15.9 + - - +
187B GLU* 3.2 11.4 + - - -
189B PHE* 1.3 88.2 - - - +
191B SER* 1.3 63.7 + - - -
192B LEU* 3.5 6.8 + - - -
193B ALA 5.0 1.6 + - - -
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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