Contacts of the strand formed by residues 146 - 151 (chain A) in PDB entry 1BU8
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 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A LYS* 6.2 0.7 - - - -
70A THR* 3.4 7.6 - - - +
72A PHE* 3.8 20.0 - - + -
132A VAL* 4.4 15.9 - - + -
135A LEU* 5.4 2.7 - - + -
141A TYR* 4.0 20.6 - - + -
142A SER 4.2 0.2 - - - +
143A PRO* 2.9 27.4 + - + +
144A GLU 3.2 1.0 - - - -
145A ASN* 1.3 83.1 - - - +
147A HIS* 1.3 62.2 - - - +
148A LEU* 3.5 27.4 - - + -
169A VAL* 3.6 11.7 - - + +
170A GLY* 3.3 8.7 + - - -
171A ARG 3.2 20.8 + - - -
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Residues in contact with HIS 147 (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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69A LYS* 5.8 3.6 - - - +
70A THR 2.8 8.0 + - - +
71A ARG* 2.9 44.0 + - + +
72A PHE 2.8 27.2 + - - +
145A ASN 4.1 0.4 + - - +
146A VAL* 1.3 73.6 - - - +
148A LEU* 1.3 72.4 + - - +
149A ILE* 3.5 12.6 - - + +
171A ARG* 3.3 44.1 - - + +
173A THR* 2.7 29.6 + - - -
270A TYR* 3.3 26.2 - - - -
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Residues in contact with LEU 148 (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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72A PHE* 3.5 38.6 - - + -
128A ILE* 4.0 13.7 - - + -
132A VAL* 5.0 0.7 - - + -
146A VAL* 3.5 12.8 - - + -
147A HIS* 1.3 73.4 - - - +
149A ILE* 1.3 61.5 + - - +
150A GLY 4.0 0.4 - - - -
158A VAL* 3.8 28.9 - - + +
161A ALA* 3.9 27.6 - - + -
162A GLY 4.6 1.3 - - - +
165A LEU* 5.0 2.5 - - + -
169A VAL* 4.0 22.9 - - + -
171A ARG 2.8 12.6 + - - +
172A ILE* 3.2 13.2 - - + +
173A THR 2.9 25.5 + - - +
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Residues in contact with ILE 149 (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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71A ARG* 4.7 2.9 - - + -
72A PHE 2.8 15.3 + - - +
73A ILE* 3.4 18.6 - - + -
74A VAL* 2.8 29.1 + - - +
85A TRP* 5.5 0.4 - - + -
89A MET* 4.3 7.0 - - - -
93A MET* 3.6 31.9 - - + -
147A HIS* 3.5 35.2 - - + +
148A LEU* 1.3 71.0 - - - +
150A GLY* 1.3 61.1 + - - +
151A HIS 5.2 0.4 - - - +
158A VAL* 4.1 2.0 - - - +
173A THR* 3.5 11.0 - - + +
175A LEU* 3.7 32.3 - - + -
270A TYR* 3.8 12.8 - - + +
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Residues in contact with GLY 150 (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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74A VAL 3.6 3.8 - - - -
148A LEU 4.0 1.4 + - - -
149A ILE* 1.3 75.1 - - - +
151A HIS* 1.3 59.6 + - - -
154A GLY 3.3 22.4 - - - -
155A ALA* 3.4 18.0 - - - +
158A VAL* 4.0 6.6 - - - +
173A THR 3.0 9.5 + - - +
175A LEU* 2.8 24.7 + - - -
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Residues in contact with HIS 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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74A VAL 3.0 8.2 + - - +
75A HIS* 5.0 0.2 - - - -
76A GLY 3.6 9.3 + - - -
77A PHE 4.0 12.4 + - - -
85A TRP* 3.7 28.0 - - + -
150A GLY* 1.3 72.4 - - - -
152A SER* 1.3 76.8 + - - +
154A GLY* 2.7 26.2 + - - -
175A LEU* 3.2 25.6 - - + -
176A ASP* 4.6 0.7 - - + -
263A HIS* 3.0 28.0 + - - -
264A LEU* 3.8 14.4 - - + -
266A SER* 3.1 21.7 + - - -
267A TYR* 3.5 33.3 - + - -
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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