Contacts of the strand formed by residues 179 - 186 (chain A) in PDB entry 2BGY
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 LYS 179 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ILE* 4.0 20.4 - - + -
157A LEU* 4.9 0.4 - - + -
177A TYR* 3.6 11.1 - - - -
178A ASN* 1.3 80.9 - - - +
180A LYS* 1.3 76.5 + - - +
198A TYR* 3.4 3.5 - - - -
199A PHE* 2.9 42.5 + - + -
273A ASN* 2.9 46.2 + - + +
274A ASN* 4.1 12.6 + - - +
275A ILE* 4.4 11.9 - - + +
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Residues in contact with LYS 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A VAL 6.0 0.2 + - - -
177A TYR* 3.8 23.4 + - + +
179A LYS* 1.3 85.3 - - - +
181A GLY* 1.3 67.2 + - - +
182A THR* 4.6 4.3 - - - -
196A ASN* 3.8 29.4 + - + +
197A VAL 3.3 5.6 - - - +
198A TYR* 3.4 31.6 + - + -
275A ILE* 3.9 9.6 - - - +
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Residues in contact with GLY 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A MET* 3.9 9.0 - - - -
180A LYS* 1.3 77.1 - - - +
182A THR* 1.3 67.3 + - - -
196A ASN* 3.5 3.6 + - - -
197A VAL* 2.8 32.7 + - - +
199A PHE* 4.9 1.2 - - - -
275A ILE* 3.4 23.2 - - - +
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Residues in contact with THR 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A MET* 3.9 9.8 - - - +
180A LYS* 4.6 5.9 - - - +
181A GLY* 1.3 75.0 - - - -
183A VAL* 1.3 72.7 + - - +
184A THR* 4.7 4.0 - - - +
194A ASP* 4.3 16.2 - - + -
195A MET 3.3 8.3 - - - +
196A ASN* 2.9 27.9 + - - +
275A ILE* 5.0 0.2 - - - +
278A THR* 4.1 11.3 + - - +
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Residues in contact with VAL 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ALA* 4.7 3.6 - - + -
152A SER 5.0 2.2 - - - +
153A MET* 4.6 11.2 - - + -
182A THR* 1.3 77.7 - - - +
184A THR* 1.3 72.3 + - - +
185A VAL* 3.7 8.6 + - + -
193A HIS 3.7 0.2 - - - +
195A MET* 2.9 46.1 + - + +
197A VAL* 4.6 6.3 - - + -
258A PHE* 5.5 2.5 - - + -
260A LEU* 5.0 15.3 - - + -
278A THR* 4.6 17.3 - - - +
279A ASN* 4.2 13.2 - - - +
280A GLN* 4.2 18.2 - - + -
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Residues in contact with THR 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A THR* 4.7 4.5 - - - +
183A VAL* 1.3 72.7 - - - +
185A VAL* 1.3 64.6 + - - +
186A TYR* 3.9 19.1 - - - +
192A ALA* 3.8 25.1 - - + -
193A HIS 3.4 5.2 - - - +
194A ASP* 2.8 27.7 + - - +
280A GLN* 3.3 24.8 - - - +
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Residues in contact with VAL 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A THR* 3.5 30.3 - - + +
151A ALA* 4.6 0.9 - - + -
183A VAL* 4.3 19.1 - - + +
184A THR* 1.3 76.4 - - - +
186A TYR* 1.3 68.1 + - - +
192A ALA* 3.4 6.1 - - - -
193A HIS* 2.8 37.7 + - + +
195A MET* 3.8 6.5 - - + -
247A THR* 3.7 30.1 - - + -
256A ALA* 4.8 0.2 - - + -
258A PHE* 4.0 24.0 - - + -
280A GLN* 3.8 5.8 - - + +
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Residues in contact with TYR 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LYS 3.9 17.3 - - - +
148A THR* 2.9 27.6 + - - +
184A THR* 3.9 25.3 - - + +
185A VAL* 1.3 75.5 - - - +
187A ASP* 1.3 62.7 + - - +
190A GLY* 3.7 21.3 - - - -
191A ASN 3.3 7.4 - - - +
192A ALA* 3.8 17.5 - - + +
193A HIS* 4.6 1.6 - - - -
256A ALA* 3.3 12.7 - - - +
280A GLN* 3.7 17.9 - - - -
282A GLY 3.6 21.1 - - - -
283A TYR* 3.6 20.6 - - + +
284A LYS* 5.2 3.6 - - + -
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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