Contacts of the helix formed by residues 168 - 176 (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 PRO 168 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162B GLN* 3.8 8.7 - - - +
166B GLU 3.5 4.4 - - - +
167B MET* 1.3 85.9 - - - +
169B LYS* 1.3 65.7 + - - +
170B ALA* 3.3 5.8 - - + +
171B GLU* 3.0 54.4 + - + +
172B LYS* 3.0 11.1 + - - +
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Residues in contact with LYS 169 (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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22B GLU* 5.9 6.7 - - - +
167B MET 3.6 2.2 + - - -
168B PRO* 1.3 71.0 - - - +
170B ALA* 1.3 64.9 + - - +
171B GLU 3.1 0.2 + - - -
172B LYS* 3.2 14.7 + - + +
173B ASN* 2.5 68.0 + - - +
179B PHE* 4.2 9.7 - - - -
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Residues in contact with ALA 170 (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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168B PRO* 3.2 4.4 + - + +
169B LYS* 1.3 78.8 - - - +
171B GLU* 1.3 62.6 + - + +
173B ASN* 3.4 24.0 - - - +
174B ALA* 3.4 9.5 + - - +
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Residues in contact with GLU 171 (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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160B TYR* 3.6 27.7 + - + +
162B GLN* 3.1 22.7 - - - +
167B MET* 3.6 13.0 - - + +
168B PRO* 3.0 34.2 + - + +
170B ALA* 1.3 76.0 - - + +
172B LYS* 1.3 65.8 + - - +
173B ASN 3.1 1.6 - - - -
174B ALA* 3.0 22.2 + - - +
175B VAL 3.7 1.6 + - - -
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Residues in contact with LYS 172 (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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152B ASP* 2.7 33.6 + - - +
164B TYR* 3.7 47.5 - - + +
167B MET* 3.6 21.2 - - + +
168B PRO 3.0 11.0 + - - +
169B LYS* 3.6 20.0 - - + +
171B GLU* 1.3 74.4 - - - +
173B ASN* 1.3 61.5 + - - +
175B VAL* 3.1 5.4 + - - +
176B SER* 2.8 33.8 + - - -
177B HIS* 4.8 8.6 - - - -
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Residues in contact with ASN 173 (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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169B LYS* 2.5 60.2 + - - +
170B ALA* 3.4 16.2 - - - +
171B GLU 3.1 0.2 - - - -
172B LYS* 1.3 79.9 - - - +
174B ALA* 1.3 60.4 + - - +
175B VAL 3.3 1.0 + - - -
176B SER* 3.5 13.3 + - - -
179B PHE* 3.3 49.5 - - + +
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Residues in contact with ALA 174 (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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160B TYR* 3.9 12.3 - - - +
170B ALA 3.4 7.9 + - - +
171B GLU* 3.0 16.6 + - - +
173B ASN* 1.3 78.3 - - - +
175B VAL* 1.4 60.0 + - + +
180B ARG* 4.5 6.9 + - - +
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Residues in contact with VAL 175 (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 THR* 2.8 33.1 + - + +
157B PRO* 4.2 16.4 - - + -
158B ASP 4.5 7.4 - - - +
160B TYR* 3.4 36.3 - - + +
164B TYR* 4.4 6.5 - - + -
167B MET* 4.2 9.4 - - + -
171B GLU 4.1 3.1 - - - +
172B LYS 3.6 9.2 - - - +
174B ALA* 1.4 78.6 - - + +
176B SER* 1.3 54.7 + - - +
180B ARG* 3.4 29.5 - - - +
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Residues in contact with SER 176 (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 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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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