Contacts of the strand formed by residues 257 - 261 (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 THR 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A SER* 5.0 0.2 + - - -
148A THR 3.4 10.0 + - - +
149A THR* 3.8 11.3 - - - +
244A ASN* 5.2 12.1 - - + +
245A ILE 3.3 5.6 - - - +
246A THR* 3.2 28.8 + - - +
255A ALA* 4.1 3.1 + - - +
256A ALA* 1.3 74.2 + - - +
258A PHE* 1.3 63.0 + - - +
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Residues in contact with PHE 258 (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 20.0 - - + +
149A THR 3.4 22.4 - - - -
150A THR 3.8 1.8 - - - +
151A ALA* 3.7 28.9 - - + -
183A VAL* 5.5 2.5 - - + -
185A VAL* 4.0 19.3 - - + -
195A MET* 4.2 11.9 - - + -
244A ASN* 3.4 6.2 - - - -
245A ILE* 2.8 72.0 + - + -
247A THR* 3.9 21.1 - - + -
256A ALA* 4.4 5.6 - - + -
257A THR* 1.3 76.5 - - - +
259A SER* 1.3 63.7 + - - +
260A LEU* 3.6 15.9 + - + -
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Residues in contact with SER 259 (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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149A THR 3.0 13.0 + - - -
150A THR* 3.4 8.3 - - - -
151A ALA 2.8 28.2 + - - +
242A THR* 3.3 28.2 - - - +
243A VAL 3.7 1.5 + - - -
244A ASN* 3.6 19.9 + - - +
258A PHE* 1.3 71.2 - - - +
260A LEU* 1.3 57.3 + - - +
261A SER* 4.0 2.6 + - - -
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Residues in contact with LEU 260 (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* 3.3 24.9 - - + +
152A SER* 4.1 11.4 - - - +
153A MET* 4.5 6.1 - - + +
183A VAL* 5.0 9.4 - - + -
197A VAL* 4.8 9.0 - - + -
211A THR* 4.4 15.9 - - + -
241A GLY 3.6 1.2 - - - +
242A THR* 3.4 4.2 - - - -
243A VAL* 2.8 43.7 + - + +
245A ILE* 4.0 22.7 - - + -
258A PHE* 3.6 10.6 + - + -
259A SER* 1.3 73.2 - - - +
261A SER* 1.3 62.9 + - - +
262A PHE* 3.6 31.5 - - + -
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Residues in contact with SER 261 (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 2.9 13.1 + - - -
152A SER* 3.2 9.9 - - - -
153A MET 3.0 25.6 + - - +
241A GLY 3.3 6.5 + - - -
242A THR* 4.6 11.4 + - - +
259A SER* 5.2 2.2 - - - -
260A LEU* 1.3 74.5 - - - +
262A PHE* 1.3 64.0 + - - +
263A LEU* 3.3 24.9 + - - +
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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