Contacts of the strand formed by residues 165 - 169 (chain C) in PDB entry 2PGW
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 VAL 165 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C TYR 4.7 3.8 + - - +
140C PHE* 3.3 17.9 - - + -
141C TYR* 2.7 33.9 + - - +
163C GLU* 3.9 0.6 + - - +
164C ARG* 1.3 93.5 - - + +
166C PHE* 1.3 58.3 + - - +
192C ARG* 3.6 35.0 - - + +
194C ARG* 3.4 45.8 - - + +
219C GLU* 4.2 4.0 - - - +
322C ASP 4.2 10.3 - - - +
323C GLY* 4.3 1.3 - - - -
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Residues in contact with PHE 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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141C TYR* 3.8 30.7 - + + -
143C LEU* 4.1 15.5 - - + -
155C ALA* 3.7 17.0 - - - -
158C GLY 4.1 0.4 - - - -
159C HIS* 3.6 30.1 - + - -
163C GLU* 3.7 25.8 - - + -
164C ARG 4.6 0.4 - - - -
165C VAL* 1.3 74.5 - - - +
167C TYR* 1.3 56.7 + - - +
188C ILE* 3.8 26.5 - - + -
191C ALA* 3.7 20.6 - - + -
192C ARG 3.0 21.6 + - - +
193C LEU* 3.8 16.8 - - + -
194C ARG* 2.8 35.2 + - - +
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Residues in contact with TYR 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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140C PHE* 3.3 35.7 - + + -
141C TYR 3.0 13.4 + - - +
142C PHE* 3.5 32.9 - + - -
143C LEU* 3.1 29.8 + - - +
165C VAL 3.8 0.2 + - - -
166C PHE* 1.3 72.1 - - - +
168C LEU* 1.3 63.0 + - - +
169C LYS* 5.5 1.1 - - + -
194C ARG* 3.5 26.5 - - + -
196C ASP* 3.1 40.1 + - + +
220C PHE* 4.8 3.4 - + - -
222C GLU* 3.0 41.5 + - + -
247C ASP* 4.6 0.3 + - - -
325C GLN* 3.4 14.4 + - - -
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Residues in contact with LEU 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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143C LEU* 4.1 12.1 - - + -
151C LEU* 3.8 39.7 - - + -
167C TYR* 1.3 76.4 - - - +
169C LYS* 1.3 74.8 + - - +
170C VAL* 3.6 1.9 + - + -
172C ARG* 4.1 1.3 - - - +
180C ILE* 4.1 5.2 - - + +
181C THR* 3.8 31.9 - - - +
184C VAL* 4.1 21.3 - - + -
193C LEU* 4.2 5.2 - - + -
194C ARG 2.9 9.2 + - - +
195C LEU* 3.2 30.2 - - + +
196C ASP* 2.9 25.0 + - - -
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Residues in contact with LYS 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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22C TYR* 5.4 10.8 + - - +
23C HIS 4.0 18.4 + - - -
24C TRP* 4.8 8.7 - - - +
25C SER* 5.5 2.0 + - - +
142C PHE* 5.5 13.8 - - + -
143C LEU 5.7 2.7 + - - +
167C TYR* 5.2 1.8 - - + -
168C LEU* 1.3 75.9 - - - +
170C VAL* 1.3 69.7 + - - +
172C ARG* 2.9 44.4 + - - +
180C ILE* 3.6 7.3 - - - +
196C ASP* 3.7 22.0 - - + +
198C ASN* 4.0 26.9 - - + +
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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