Contacts of the helix formed by residues 162 - 169 (chain C) in PDB entry 4J47
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 162 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C ALA 4.3 2.9 + - - -
160C MET 3.3 0.8 - - - +
161C TYR* 1.3 78.0 - - - +
163C GLU* 1.3 63.6 + - - +
164C GLU* 3.2 23.9 + - - +
165C ALA* 3.0 25.5 + - - +
166C ARG* 3.1 16.6 + - - +
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Residues in contact with GLU 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C TYR 3.5 4.9 + - - -
162C SER* 1.3 70.9 + - - +
164C GLU* 1.3 57.2 + - - +
166C ARG* 3.4 21.5 + - - +
167C LEU* 3.0 40.7 + - + +
182C ARG 4.6 2.1 - - - +
185C ALA* 3.8 19.9 - - + +
186C SER* 3.5 32.1 + - - +
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Residues in contact with GLU 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C SER* 3.1 11.7 + - - +
163C GLU* 1.3 79.6 - - - +
165C ALA* 1.3 60.1 + - - +
167C LEU* 3.3 23.4 + - - +
168C LYS* 3.2 48.6 + - - +
182C ARG* 4.8 6.8 + - - -
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Residues in contact with ALA 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C ALA 3.1 27.8 - - - +
160C MET* 3.7 13.7 - - - +
162C SER* 3.0 17.9 + - - +
164C GLU* 1.3 76.0 - - - +
166C ARG* 1.3 65.1 + - - +
168C LYS* 3.4 14.8 + - + +
169C SER 3.3 15.1 + - - -
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Residues in contact with ARG 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C MET* 2.9 45.7 + - - +
161C TYR 2.8 30.1 + - - -
162C SER 3.1 4.2 + - - +
163C GLU* 3.6 29.6 + - - +
164C GLU 3.3 0.2 - - - -
165C ALA* 1.3 76.0 - - - +
167C LEU* 1.3 61.5 + - - +
169C SER* 2.5 25.3 + - - -
170C PHE* 3.2 8.8 - - - -
185C ALA* 2.9 37.7 + - + -
186C SER 4.6 1.4 + - - -
188C GLY* 3.6 35.5 - - - +
189C LEU 3.9 9.6 - - - +
190C TYR* 4.1 4.9 - - + -
201C PHE* 3.8 18.6 - - - -
229C PHE* 4.6 7.3 - - - -
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Residues in contact with LEU 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C GLU* 3.0 35.8 + - + +
164C GLU* 3.3 31.6 - - - +
166C ARG* 1.3 77.1 - - - +
168C LYS* 1.3 57.5 + - + +
170C PHE* 2.9 31.1 + - - +
181C PRO* 3.7 11.0 - - + +
182C ARG* 3.4 68.0 - - + +
185C ALA* 3.6 5.2 - - + -
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Residues in contact with LYS 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C GLU* 3.2 38.9 + - - +
165C ALA* 3.7 13.8 - - + +
166C ARG 3.3 0.2 - - - -
167C LEU* 1.3 76.8 - - + +
169C SER* 1.3 61.3 + - - +
170C PHE 3.0 1.4 + - - -
171C GLN* 3.3 33.6 + - - +
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Residues in contact with SER 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C MET* 3.9 26.5 - - - -
165C ALA 3.3 4.9 + - - -
166C ARG 2.5 20.9 + - - -
168C LYS* 1.3 75.6 - - - +
170C PHE* 1.3 56.1 + - - +
171C GLN* 3.1 14.0 + - - +
190C TYR* 3.3 3.6 - - - +
191C TYR* 2.9 47.1 + - - +
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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