Contacts of the strand formed by residues 165 - 169 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139G TYR 4.8 2.8 + - - +
140G PHE* 3.2 18.1 - - + -
141G TYR* 2.7 34.2 + - - +
163G GLU 3.8 0.2 - - - -
164G ARG* 1.3 96.0 - - + +
166G PHE* 1.3 58.3 + - - +
192G ARG* 3.6 35.7 - - + +
194G ARG* 3.3 45.1 - - + +
219G GLU* 4.1 3.4 - - - +
322G ASP 4.3 10.1 - - - +
323G GLY* 4.3 1.8 - - - -
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Residues in contact with PHE 166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141G TYR* 3.9 28.9 - + + -
143G LEU* 4.2 15.9 - - + -
155G ALA 3.6 19.5 - - - -
158G GLY 4.0 0.7 - - - -
159G HIS* 3.6 27.8 - - - -
163G GLU* 3.7 27.6 - - + -
165G VAL* 1.3 75.7 - - - +
167G TYR* 1.3 56.8 + - - +
168G LEU 4.1 0.2 - - - -
188G ILE* 3.7 29.6 - - + -
191G ALA* 3.8 18.6 - - + -
192G ARG 2.9 21.9 + - - +
193G LEU* 3.5 15.8 - - + +
194G ARG* 2.8 35.5 + - - +
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Residues in contact with TYR 167 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140G PHE* 3.3 40.8 - + + -
141G TYR 3.1 12.8 + - - +
142G PHE* 3.9 21.0 - + - -
143G LEU* 3.2 28.7 + - - +
165G VAL 3.9 0.4 + - - -
166G PHE* 1.3 72.1 - - - +
168G LEU* 1.3 61.6 + - - +
169G LYS* 4.4 2.6 + - + -
194G ARG* 3.5 27.4 - - + -
196G ASP* 3.4 38.5 + - + +
220G PHE* 4.9 1.6 - + - -
222G GLU* 2.8 45.0 + - + -
247G ASP* 4.6 0.7 + - - -
325G GLN* 3.2 15.2 + - - -
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Residues in contact with LEU 168 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143G LEU* 4.1 11.9 - - + -
151G LEU* 3.8 39.3 - - + -
166G PHE 4.1 0.2 - - - -
167G TYR* 1.3 76.3 - - - +
169G LYS* 1.3 77.1 + - - +
170G VAL* 3.7 0.6 + - + -
172G ARG* 4.1 1.3 - - - +
180G ILE* 4.0 9.0 - - + +
181G THR* 3.8 31.2 - - - +
184G VAL* 3.8 21.1 - - + -
193G LEU* 4.2 6.1 - - + -
194G ARG 2.8 8.9 + - - +
195G LEU* 3.2 26.7 - - + +
196G ASP* 2.8 26.9 + - - -
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Residues in contact with LYS 169 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G TYR* 6.0 2.2 - - - +
23G HIS 5.8 4.9 - - - +
142G PHE* 6.3 3.4 - - + -
143G LEU 5.7 2.9 + - - +
167G TYR* 4.4 2.2 + - + -
168G LEU* 1.3 76.8 - - - +
170G VAL* 1.3 73.2 + - - +
171G GLY 5.5 1.8 + - - -
172G ARG* 2.9 48.7 + - - +
180G ILE* 3.6 6.9 - - - +
196G ASP* 3.6 22.2 - - + +
198G ASN* 4.1 27.5 - - + +
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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