Contacts of the strand formed by residues 144 - 154 (chain A) in PDB entry 5BZR
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 PHE 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A ASN 4.8 5.4 - - - +
143A SER* 1.3 76.2 + - - +
145A ASP* 1.3 84.2 + - - +
163A LYS 4.6 0.5 - - - +
164A GLY* 3.2 7.3 - - - -
165A GLU* 2.8 47.7 + - + -
166A TYR* 3.4 28.5 - - - -
167A ARG 3.4 23.8 - - - -
168A THR* 3.9 15.9 - - + -
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Residues in contact with ASP 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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144A PHE* 1.3 94.0 - - - +
146A GLY* 1.3 64.9 + - - +
163A LYS* 4.3 12.0 + - - -
164A GLY* 4.7 0.7 - - - -
165A GLU* 3.9 1.6 - - - +
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Residues in contact with GLY 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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144A PHE 3.4 2.6 + - - -
145A ASP* 1.3 85.4 + - - +
147A PRO* 1.3 67.1 - - - +
163A LYS* 2.8 34.2 + - - +
164A GLY* 3.4 17.3 + - - -
165A GLU* 4.0 2.9 - - - -
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Residues in contact with PRO 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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24A ASN* 4.0 27.5 - - - +
146A GLY* 1.3 84.9 - - - +
148A VAL* 1.3 68.0 + - + +
149A THR* 3.8 2.6 + - - -
163A LYS* 4.0 14.1 - - + +
164A GLY 4.0 2.7 - - - +
165A GLU* 4.6 7.6 - - + +
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Residues in contact with VAL 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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24A ASN* 3.4 37.0 - - - +
26A ILE* 3.8 31.6 - - + +
147A PRO* 1.3 82.1 - - + +
149A THR* 1.3 74.7 + - - +
150A ILE* 3.3 8.9 + - + +
163A LYS* 3.2 4.3 - - - -
164A GLY 2.8 39.0 + - - +
165A GLU* 3.6 25.6 - - - +
167A ARG* 3.7 9.6 - - - +
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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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24A ASN 2.9 16.1 + - - -
25A GLN* 2.8 47.1 + - - +
26A ILE 2.9 15.1 + - - -
147A PRO 3.8 2.7 + - - -
148A VAL* 1.3 70.6 - - - +
150A ILE* 1.3 55.8 + - - +
151A THR* 4.1 6.7 - - - +
161A SER* 4.5 13.7 - - - +
162A LYS 3.7 6.7 - - - +
163A LYS* 4.5 7.0 - - - +
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Residues in contact with ILE 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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26A ILE* 3.4 13.2 - - + +
28A LEU* 3.7 29.6 - - + -
140A LEU* 3.8 28.3 - - + -
143A SER* 4.8 1.8 - - - -
148A VAL* 3.8 17.5 - - + +
149A THR* 1.3 73.6 - - - +
151A THR* 1.3 63.3 + - - +
152A ILE* 4.1 4.5 + - + +
160A TYR* 3.8 1.4 - - - +
161A SER* 3.2 2.8 - - - -
162A LYS* 2.8 39.5 + - + +
164A GLY* 3.7 31.4 - - - +
165A GLU* 3.9 6.7 - - - +
166A TYR* 4.1 18.4 - - + -
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Residues in contact with THR 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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25A GLN* 2.8 26.8 + - - -
26A ILE 2.8 9.1 + - - -
27A ASP* 3.4 10.1 - - - -
28A LEU* 2.8 30.8 + - - +
149A THR* 4.1 1.4 - - - +
150A ILE* 1.3 73.2 - - - +
152A ILE* 1.3 72.4 + - - +
153A VAL* 3.7 2.8 + - + +
159A ARG* 3.8 35.8 + - + +
160A TYR 3.4 4.0 - - - +
161A SER* 2.8 24.7 + - - +
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Residues in contact with ILE 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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28A LEU* 3.5 31.0 - - + -
30A VAL* 3.8 29.4 - - + -
60A PHE* 3.8 16.4 - - + -
137A VAL* 4.0 24.2 - - + +
139A ASP 4.6 9.0 - - - +
140A LEU* 4.4 10.5 - - + -
150A ILE* 4.5 6.7 - - + +
151A THR* 1.3 73.1 - - - +
153A VAL* 1.3 62.5 + - - +
154A ASN* 4.4 2.0 - - - +
158A THR 3.8 0.6 - - - +
159A ARG* 3.2 10.6 - - - +
160A TYR* 2.7 57.0 + - + +
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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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27A ASP* 4.1 9.6 - - + +
28A LEU 2.8 9.0 + - - +
29A ASN* 3.3 24.8 - - - +
30A VAL* 3.0 25.7 + - - -
151A THR* 3.9 12.6 - - + +
152A ILE* 1.3 78.1 - - - +
154A ASN* 1.3 74.0 + - - +
157A GLY* 4.8 5.6 - - - +
158A THR 3.8 2.2 - - - +
159A ARG* 3.7 46.7 - - + +
202A 4XM 3.5 9.0 - - + -
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Residues in contact with ASN 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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30A VAL* 3.5 18.4 - - - +
31A THR 6.0 0.2 - - - -
33A ARG* 5.1 0.7 + - - -
136A SER* 3.4 13.3 - - - -
137A VAL* 2.8 44.1 + - - +
138A THR* 5.5 0.6 - - - +
152A ILE* 4.4 4.9 + - - +
153A VAL* 1.3 79.4 - - - +
155A ARG* 1.3 61.6 + - - +
156A ASP* 3.2 16.2 - - - +
157A GLY* 2.9 18.9 + - - -
158A THR* 3.0 36.6 + - - +
159A ARG* 4.9 1.0 - - - +
201A DMS 3.8 9.2 - - - +
202A 4XM 3.6 7.7 - - - -
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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