Contacts of the strand formed by residues 150 - 158 (chain A) in PDB entry 2BGZ
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 150 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A THR* 3.2 18.1 - - - +
149A THR* 1.3 90.4 - - - +
151A ALA* 1.3 62.4 + - - +
258A PHE* 4.2 1.3 - - - -
259A SER* 3.4 13.7 - - - +
280A GLN* 3.3 13.1 - - - -
281A ASN* 3.1 23.7 + - - +
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Residues in contact with ALA 151 (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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150A THR* 1.3 79.6 - - - +
152A SER* 1.3 63.1 + - - +
183A VAL* 4.7 6.1 - - + -
185A VAL* 4.6 5.4 - - + -
258A PHE* 3.7 27.4 - - + -
259A SER 2.8 8.8 + - - +
260A LEU* 3.3 8.7 - - + -
261A SER* 2.9 24.6 + - - -
279A ASN 3.2 13.7 - - - +
280A GLN* 3.9 9.6 - - + +
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Residues in contact with SER 152 (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* 1.3 76.7 - - - +
153A MET* 1.3 62.8 + - - +
183A VAL* 5.0 3.1 - - - +
260A LEU* 4.3 4.0 - - - +
261A SER* 3.2 19.5 - - - +
263A LEU* 6.0 3.1 - - - -
277A ALA 5.4 0.2 - - - -
278A THR* 3.2 8.8 - - - -
279A ASN* 2.8 50.1 + - - +
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Residues in contact with MET 153 (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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152A SER* 1.3 78.8 - - - +
154A GLN* 1.3 61.7 + - - +
155A ILE* 5.1 0.7 - - + -
181A GLY* 3.9 3.6 - - - -
182A THR 3.9 32.8 - - - +
183A VAL* 4.5 6.3 - - + +
197A VAL* 3.6 31.2 - - + -
199A PHE* 3.9 31.2 - - + -
260A LEU* 4.8 5.2 - - + -
261A SER 3.0 6.0 + - - -
262A PHE* 3.3 38.8 - - + -
263A LEU 5.1 0.4 - - - -
265A SER* 3.5 3.8 + - - -
275A ILE* 4.0 26.0 - - + -
277A ALA 3.5 4.3 - - - -
278A THR* 4.1 8.7 - - + -
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Residues in contact with GLN 154 (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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152A SER 4.3 0.2 - - - -
153A MET* 1.3 71.0 - - - +
155A ILE* 1.3 60.5 + - - +
156A ASN* 5.2 6.0 + - - +
263A LEU 4.1 6.5 - - - +
264A ASN* 3.5 47.6 + - + +
265A SER* 3.6 3.4 - - - -
275A ILE* 3.7 4.1 - - - +
276A VAL* 3.0 47.1 + - + +
277A ALA* 2.9 31.8 + - + +
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Residues in contact with ILE 155 (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* 5.1 1.8 - - + -
154A GLN* 1.3 76.3 - - - +
156A ASN* 1.3 74.3 + - - +
157A LEU* 3.6 29.6 - - + -
179A LYS* 4.0 11.4 - - + -
199A PHE* 3.6 49.4 - - + -
229A LEU* 4.8 2.7 - - + -
262A PHE* 4.9 3.1 - - + -
265A SER* 3.0 25.8 + - - +
266A MET 3.0 24.9 + - - +
274A ASN 3.6 12.8 - - - +
275A ILE* 3.8 18.6 - - + -
276A VAL* 5.4 0.7 - - - -
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Residues in contact with ASN 156 (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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154A GLN* 5.2 5.9 + - - +
155A ILE* 1.3 76.9 - - - +
157A LEU* 1.3 61.9 + - - +
264A ASN 5.0 2.9 - - - +
266A MET* 3.4 28.7 + - - +
268A GLN* 3.9 31.5 + - + +
272A ALA 3.8 1.3 - - - +
273A ASN* 3.3 5.2 - - - -
274A ASN* 3.0 39.0 + - + +
276A VAL* 3.4 26.3 - - - +
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Residues in contact with LEU 157 (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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155A ILE* 3.6 39.5 - - + -
156A ASN* 1.3 75.8 - - - +
158A ASN* 1.3 58.6 + - - +
179A LYS* 4.9 0.7 - - + -
199A PHE* 4.3 16.8 - - + -
207A TRP* 3.7 58.6 - - + +
229A LEU* 4.5 2.2 - - + -
231A PHE* 3.9 21.5 - - + -
266A MET 2.9 11.0 + - - +
267A GLN* 3.2 7.6 - - + -
268A GLN* 2.8 32.4 + - - +
273A ASN* 3.6 13.5 - - + +
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Residues in contact with ASN 158 (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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156A ASN 4.3 0.2 + - - -
157A LEU* 1.3 71.5 - - - +
159A SER* 1.3 63.6 + - - +
160A THR* 2.9 30.9 + - - -
161A ASP* 2.7 50.6 + - - +
207A TRP* 3.5 8.9 - - - -
268A GLN* 4.0 3.1 - - - -
270A THR* 3.6 4.2 - - - -
271A GLY 2.9 45.0 + - - +
273A ASN* 2.9 15.1 + - - +
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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