Contacts of the strand formed by residues 150 - 160 (chain A) in PDB entry 3UR9
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 ASP 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A VAL* 5.4 11.0 - - + +
146A LYS* 4.0 4.0 - - - -
147A ARG* 2.9 35.1 + - - +
148A GLY 3.2 1.8 - - - -
149A ASN* 1.3 99.7 + - - +
151A TRP* 1.3 67.8 + - - +
152A VAL* 3.7 7.9 + - + +
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Residues in contact with TRP 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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-1A HIS* 3.7 32.5 - - + -
0A MET 3.5 21.1 - - - -
1A ALA* 3.8 11.7 - - + -
2A PRO* 3.7 17.3 - - + +
5A LEU* 3.6 27.4 - - + -
71A MET* 3.4 38.1 - - + +
72A VAL 4.0 3.8 + - - -
84A SER* 5.3 4.5 - - - -
144A VAL* 3.8 23.3 - - + -
145A HIS* 3.6 20.9 - - - -
146A LYS* 3.8 44.0 - - + +
149A ASN 4.0 2.2 + - - -
150A ASP* 1.3 77.3 - - - +
152A VAL* 1.3 60.0 + - - +
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Residues in contact with VAL 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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71A MET* 3.9 3.4 - - - -
72A VAL* 3.5 19.3 - - + +
74A GLU* 3.8 28.7 - - + +
144A VAL* 3.1 5.9 - - - +
145A HIS* 2.7 57.7 + - + +
147A ARG* 3.8 34.5 - - + +
150A ASP* 4.0 11.9 - - + +
151A TRP* 1.3 78.7 - - - +
153A VAL* 1.3 69.8 + - - +
154A CYS* 4.8 0.4 - - + -
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Residues in contact with VAL 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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18A PHE* 3.8 24.0 - - + -
20A VAL* 4.1 12.3 - - + -
26A ILE* 3.9 15.9 - - + -
71A MET* 3.7 8.3 - - + +
72A VAL 3.0 17.4 + - - +
73A LEU* 3.4 20.0 - - + +
74A GLU 3.0 23.6 + - - -
142A PRO* 4.0 17.0 - - + -
143A TYR 3.5 11.4 - - - +
144A VAL* 4.1 2.7 - - + -
152A VAL* 1.3 73.2 - - - +
154A CYS* 1.3 65.5 + - - +
155A GLY 3.8 14.8 - - - +
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Residues in contact with CYS 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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55A PHE* 5.6 0.4 - - - -
73A LEU* 4.7 2.7 - - - -
74A GLU* 3.4 12.5 - - + +
76A GLY* 3.2 41.2 + - - +
77A CYS* 4.0 18.4 - - + -
83A CYS* 3.9 25.6 - - - -
101A MET* 6.0 0.7 - - - -
117A GLN* 5.2 0.7 - - - -
143A TYR* 2.9 22.3 + - - -
145A HIS* 4.1 11.7 - - + -
152A VAL* 4.8 0.2 - - + -
153A VAL* 1.3 76.9 - - - +
155A GLY* 1.3 59.0 + - - +
169A CYS* 4.7 2.9 - - - -
171A VAL* 3.3 11.7 - - - +
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Residues in contact with GLY 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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26A ILE* 5.5 0.2 - - - +
55A PHE* 4.6 7.0 - - - -
73A LEU* 5.2 0.6 - - - +
142A PRO* 3.4 5.2 - - - +
143A TYR* 2.9 26.4 + - - -
153A VAL* 3.8 7.3 - - - +
154A CYS* 1.3 78.5 - - - +
156A VAL* 1.3 65.0 + - - +
169A CYS* 4.0 13.0 - - - -
170A ALA 3.1 15.3 - - - -
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Residues in contact with VAL 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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18A PHE* 5.3 0.2 - - + -
26A ILE* 3.8 31.6 - - + +
27A THR* 3.5 24.2 - - - +
28A THR* 3.2 21.8 + - - +
55A PHE* 3.9 17.0 - - + -
140A GLY* 3.8 18.6 - - - +
141A ALA 3.4 4.0 - - - +
142A PRO* 4.7 3.1 - - + -
143A TYR* 4.2 0.2 - - - -
155A GLY* 1.3 79.3 - - - +
157A HIS* 1.3 67.5 + - - +
169A CYS* 3.1 3.6 - - - -
170A ALA* 2.8 35.8 + - + +
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Residues in contact with HIS 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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28A THR* 2.7 20.4 + - - -
85A VAL* 4.6 3.0 - - + +
87A ILE* 6.0 0.2 - - + -
134A THR* 3.6 22.6 + - + +
138A ASP* 3.8 24.7 - - + +
139A CYS* 3.3 26.7 - - - +
140A GLY 2.9 13.8 + - - +
141A ALA* 2.7 22.9 + - + +
143A TYR* 2.9 35.8 + + + -
156A VAL* 1.3 72.4 - - - +
158A ALA* 1.3 57.4 + - - +
159A ALA 3.2 26.2 + - - -
167A VAL* 4.1 4.0 - - + -
168A VAL 3.8 0.4 + - - -
203A K36 2.7 29.2 + - + +
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Residues in contact with ALA 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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28A THR* 4.1 15.7 - - + -
30A HIS* 3.8 1.9 - - + -
54A GLU* 4.9 2.9 - - + -
114A VAL* 4.5 16.8 - - + -
139A CYS* 3.4 12.3 - - - -
156A VAL 3.3 0.9 + - - +
157A HIS* 1.3 75.0 - - - +
159A ALA* 1.3 63.0 + - + +
168A VAL 2.8 16.0 + - - +
169A CYS 4.4 0.9 - - - -
170A ALA* 3.9 21.1 - - + +
203A K36 2.9 27.8 + - + +
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Residues in contact with ALA 159 (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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109A ILE* 3.9 31.6 - - + -
157A HIS* 3.2 16.0 + - - -
158A ALA* 1.3 82.6 - - + +
160A ALA* 1.3 63.0 + - - +
168A VAL* 2.9 32.0 + - + -
203A K36 3.2 27.6 - - + +
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Residues in contact with ALA 160 (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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134A THR* 3.4 13.7 - - - +
159A ALA* 1.3 77.6 - - - +
161A THR* 1.3 69.3 + - - +
165A ASN* 4.6 4.5 - - - +
166A THR 3.2 13.5 - - - +
167A VAL* 4.2 6.5 - - + +
168A VAL* 5.7 1.3 - - - -
203A K36 2.9 59.8 + - + +
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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