Contacts of the strand formed by residues 143 - 149 (chain A) in PDB entry 1BT4
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 ALA 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A GLN* 4.5 5.3 + - - -
94A THR* 3.4 10.3 - - - +
96A ASN* 3.5 25.1 - - - +
139A LEU* 4.4 3.8 - - + -
140A GLN 3.4 18.6 + - - +
141A ASP 3.4 4.0 + - - +
142A ASN* 1.3 77.1 + - - +
144A ALA* 1.3 62.5 + - - +
145A TYR 4.4 2.2 - - - +
168A VAL* 4.1 29.8 - - + +
169A PRO* 5.4 0.3 - - - +
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Residues in contact with ALA 144 (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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88A PHE* 3.4 27.9 - - - +
89A LEU* 4.0 14.1 - - + -
93A GLN* 3.6 22.2 - - + +
94A THR 3.0 14.8 + - - +
142A ASN 3.5 2.0 + - - -
143A ALA* 1.3 72.0 - - - +
145A TYR* 1.3 74.3 + - + +
169A PRO* 3.4 19.3 - - - +
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Residues in contact with TYR 145 (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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84A ILE* 3.8 21.6 - - + +
85A PRO* 3.6 21.1 - - + +
88A PHE* 3.9 21.3 - - + -
89A LEU* 4.6 2.5 - - + -
94A THR 4.3 0.2 + - - -
95A ALA* 3.5 21.6 - - + +
96A ASN* 3.2 29.4 + - - +
97A TYR* 2.7 30.0 + + - -
143A ALA* 3.3 1.9 - - - +
144A ALA* 1.3 92.8 + - + +
146A LEU* 1.3 61.3 + - - +
147A HIS* 3.8 27.4 - - + -
168A VAL* 3.6 10.8 - - - -
169A PRO* 3.2 20.2 - - + +
171A ILE* 3.5 21.8 - - + -
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Residues in contact with LEU 146 (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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96A ASN* 3.3 21.1 - - + +
98A VAL* 4.0 16.8 - - + -
120A ALA* 3.7 17.0 - - + -
137A ILE* 3.9 16.6 - - + -
139A LEU* 3.2 35.7 - - + -
145A TYR* 1.3 75.0 - - - +
147A HIS* 1.3 54.7 + - - +
148A LEU* 5.5 0.4 - - + -
163A PRO* 4.3 8.3 - - + -
165A THR* 3.7 28.0 - - + -
168A VAL* 3.9 2.2 - - + +
169A PRO 2.9 7.5 + - - +
170A LEU* 3.5 14.7 - - + +
171A ILE 2.7 31.7 + - - +
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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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81A PHE* 5.0 0.2 - - - -
84A ILE* 4.5 5.8 - - + -
96A ASN 2.8 9.1 + - - +
97A TYR* 3.4 36.0 - + + -
98A VAL* 3.0 30.0 + - - +
99A MET* 6.1 0.2 - - - +
104A ALA* 5.6 1.2 - - - -
107A ALA* 3.5 23.3 - - + +
145A TYR* 3.8 15.2 - + + -
146A LEU* 1.3 73.1 - - - +
148A LEU* 1.3 74.9 + - - +
149A THR* 4.4 5.8 + - - -
171A ILE* 3.1 30.5 - - + -
173A ASP* 4.2 7.6 - - + +
192A TYR* 2.5 34.7 + + - -
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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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98A VAL* 4.0 24.7 - - + -
137A ILE* 5.5 1.8 - - + -
146A LEU* 5.5 0.2 - - + -
147A HIS* 1.3 82.6 + - - +
149A THR* 1.3 58.1 + - - +
150A SER* 3.9 14.1 - - - +
159A PHE* 4.4 19.1 - - + -
162A PHE* 4.0 28.5 - - + -
163A PRO* 4.1 26.7 - - + -
170A LEU* 4.1 19.7 - - + -
171A ILE 2.8 7.5 + - - +
172A GLY* 3.1 15.4 - - - -
173A ASP* 2.8 30.5 + - - -
188A PHE* 4.5 4.9 - - + -
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Residues in contact with THR 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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98A VAL 5.0 1.6 + - - -
100A THR* 4.1 8.5 + - - -
103A TRP* 4.0 3.9 + - + +
104A ALA* 3.4 26.0 + - - +
147A HIS* 4.4 4.2 - - - -
148A LEU* 1.3 73.4 + - - +
150A SER* 1.3 67.4 + - - +
151A ASN* 3.3 25.4 + - - +
152A GLU* 3.5 28.3 + - - +
159A PHE* 3.3 18.7 - - - -
173A ASP* 3.7 12.6 - - + +
363A PLP 3.9 19.5 - - + -
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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