Contacts of the helix formed by residues 162 - 167 (chain B) in PDB entry 3CEI
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 162 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 5.1 2.0 - - - -
157B VAL* 3.6 22.2 - - - -
158B TRP 3.6 10.5 - - - -
159B GLU* 3.0 22.4 + - + +
160B HIS 3.2 0.2 - - - -
161B ALA* 1.3 79.4 - - - +
163B TYR* 1.3 67.8 + + - +
164B ILE 3.3 3.1 + - - -
165B ASP 3.5 2.4 + - - +
166B HIS* 2.8 37.2 + - + +
167B LYS 3.1 28.0 - - - -
168B ASN* 4.4 4.3 + - - -
170B ARG* 3.0 56.7 + - + +
173B TYR* 3.3 48.0 - + + -
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Residues in contact with TYR 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 4.0 13.0 - - - +
30A HIS* 2.7 36.9 + + - -
160A HIS* 3.7 22.0 + - + +
163A TYR* 4.1 33.4 - - + -
164A ILE* 3.8 30.3 - - + -
159B GLU* 2.9 33.4 + - + +
160B HIS 4.4 1.6 + - - -
162B TYR* 1.3 80.0 - + - +
164B ILE* 1.3 61.3 + - - +
167B LYS* 2.8 67.8 + - + +
168B ASN* 3.4 7.5 + - - +
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Residues in contact with ILE 164 (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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163A TYR* 3.9 28.9 - - + -
167A LYS* 4.1 17.0 - - - -
19B SER* 4.6 1.3 - - - +
21B VAL* 4.3 15.3 - - + +
22B ALA* 4.0 25.8 - - + +
25B PHE* 3.9 32.8 - - + -
160B HIS 5.4 4.4 + - - +
162B TYR 3.3 1.2 - - - -
163B TYR* 1.3 77.7 - - - +
165B ASP* 1.3 71.3 + - - +
167B LYS* 3.5 16.7 + - - +
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Residues in contact with ASP 165 (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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17B PHE 4.1 2.0 - - - +
18B LEU* 3.4 11.8 - - + +
19B SER* 2.9 48.0 + - - -
22B ALA* 3.1 17.6 - - - +
162B TYR 3.5 2.2 + - - -
164B ILE* 1.3 81.4 - - - +
166B HIS* 1.3 86.2 + - + +
167B LYS* 3.9 1.6 - - - -
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Residues in contact with HIS 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ASP 4.6 4.9 - - - -
17B PHE* 2.8 28.0 + - - -
18B LEU* 5.0 0.9 - - + -
162B TYR* 2.8 20.0 + - + +
165B ASP* 1.3 97.9 + - + +
167B LYS* 1.3 74.6 + - - +
168B ASN* 4.4 0.3 + - - -
169B ALA* 2.8 38.2 + - + +
172B VAL* 3.8 26.1 - - + +
173B TYR* 3.8 32.0 - + + -
176B LYS* 4.5 10.3 - - + -
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Residues in contact with LYS 167 (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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21A VAL* 5.2 4.3 - - - -
25A PHE* 3.5 43.5 - - + -
164A ILE* 4.0 22.7 - - + +
162B TYR* 3.1 18.3 + - - -
163B TYR* 2.8 67.5 + - + +
164B ILE* 3.5 23.0 + - - +
165B ASP 5.6 0.9 - - - -
166B HIS* 1.3 75.7 - - - +
168B ASN* 1.3 61.1 + - - +
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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