Contacts of the strand formed by residues 164 - 169 (chain C) in PDB entry 4DQ0
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 GLU 164 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163C TRP* 1.3 73.3 - - - +
165C MET* 1.3 64.6 + - - +
166C VAL* 3.4 32.3 + - + +
194C ALA* 3.2 6.4 - - - +
195C ARG* 2.7 61.6 + - + +
197C LYS* 3.6 32.2 + - - +
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Residues in contact with MET 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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157C ARG* 4.0 28.3 - - + +
160C TYR* 4.1 20.9 - - + +
161C GLU* 5.8 0.4 - - - -
163C TRP 3.6 8.9 + - - +
164C GLU* 1.3 75.7 - - - +
166C VAL* 1.3 63.7 + - - +
167C LYS* 3.3 5.1 + - - +
168C TYR* 3.3 36.3 - - + -
192C MET* 3.8 32.5 - - - +
193C LEU 4.2 1.1 - - - -
194C ALA* 4.6 3.6 - - - -
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Residues in contact with VAL 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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28C VAL* 4.8 12.1 - - + -
129C TYR* 4.2 22.9 - - + +
164C GLU* 3.4 33.5 + - + +
165C MET* 1.3 74.3 - - - +
167C LYS* 1.3 61.6 - - + +
193C LEU* 3.0 35.3 + - + +
195C ARG* 4.3 4.9 - - + -
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Residues in contact with LYS 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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21C GLU* 3.0 31.2 + - - +
24C GLU* 4.1 22.9 + - - +
165C MET* 3.9 6.3 - - - +
166C VAL* 1.3 81.7 - - + +
168C TYR* 1.3 70.0 + - - +
169C ASN* 4.3 12.3 - - - +
191C THR* 4.2 16.4 - - + -
192C MET* 3.4 1.6 - - - -
193C LEU* 2.9 47.2 + - + +
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Residues in contact with TYR 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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136C MET* 5.2 0.2 - - - +
152C LYS 5.4 0.2 + - - -
154C GLY* 4.2 2.6 + - - -
156C LEU* 4.0 23.6 + - + +
157C ARG* 3.5 63.1 + - + +
165C MET* 3.3 24.9 - - + -
167C LYS* 1.3 80.4 - - - +
169C ASN* 1.3 69.6 + - - +
170C GLU* 2.6 39.7 + - + +
190C ALA* 4.6 3.6 - - + +
191C THR 3.1 15.9 - - - -
192C MET* 3.7 16.6 - - + -
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Residues in contact with ASN 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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21C GLU* 5.5 1.2 + - - -
167C LYS* 4.3 13.5 - - - +
168C TYR* 1.3 83.4 - - - +
170C GLU* 1.3 64.7 + - - +
171C ASP* 3.1 43.3 + - - +
189C PHE 3.4 3.6 - - - +
190C ALA* 3.5 2.8 - - - -
191C THR* 2.9 52.9 + - - +
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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