Contacts of the strand formed by residues 143 - 149 (chain A) in PDB entry 4B5G
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 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A ARG* 3.3 24.6 + - - +
103A LEU* 3.4 3.1 - - + +
104A SER 2.9 24.9 + - - -
142A ARG* 1.3 72.0 - - - +
144A ILE* 1.3 61.9 + - - +
226A THR* 3.6 3.6 - - - -
228A GLU* 3.3 28.4 - - - +
229A LEU* 3.7 31.2 + - + +
232A LYS* 5.9 2.2 - - - -
256A TYR* 2.8 34.4 + - - +
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Residues in contact with ILE 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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97A ARG* 4.1 16.6 - - - +
104A SER* 3.2 20.6 - - - +
106A ILE* 5.0 2.0 - - + -
137A MET* 3.4 63.5 - - + +
140A GLU* 4.1 1.1 - - - +
142A ARG* 3.4 19.9 + - + +
143A ASP* 1.3 79.3 - - - +
145A VAL* 1.3 68.1 + - - +
146A VAL* 4.1 7.4 - - + -
188A TRP* 3.5 11.8 - - + -
225A VAL* 3.5 5.0 - - - +
226A THR* 3.3 36.2 + - + -
229A LEU* 4.3 1.0 - - - +
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Residues in contact with VAL 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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4A ILE* 3.8 24.0 - - + -
103A LEU* 4.4 7.2 - - + -
104A SER 2.9 7.5 + - - +
105A VAL* 3.4 7.9 - - + +
106A ILE 2.9 25.3 + - - -
144A ILE* 1.3 76.1 - - - +
146A VAL* 1.3 65.5 + - - +
147A CYS* 3.6 15.9 + - - -
223A GLN* 3.5 31.6 - - + +
224A MET 3.6 2.0 - - - -
225A VAL* 4.3 9.2 - - + -
229A LEU* 3.6 24.0 - - + -
254A TYR* 4.0 9.4 - - + +
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Residues in contact with VAL 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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106A ILE* 3.8 22.7 - - + -
108A LEU* 4.5 7.9 - - + -
130A PHE* 4.8 8.1 - - + -
134A LEU* 4.7 8.1 - - + -
137A MET* 4.3 10.8 - - + -
144A ILE* 4.1 8.1 - - + -
145A VAL* 1.3 74.3 - - - +
147A CYS* 1.3 65.0 + - - +
150A TRP* 3.6 31.5 + - + -
188A TRP* 4.0 21.5 - - + -
222A TYR 3.5 2.4 - - - +
223A GLN* 3.3 1.8 - - - -
224A MET* 2.9 39.7 + - + +
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Residues in contact with CYS 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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4A ILE* 3.6 25.1 - - - -
6A SER* 3.6 19.7 - - - +
33A CYS* 3.8 21.8 - - + -
35A GLN* 4.2 0.7 - - - -
105A VAL* 4.1 4.3 - - - -
106A ILE 2.9 20.7 + - - +
107A SER* 3.6 0.7 - - - -
108A LEU* 2.9 17.8 + - - +
145A VAL* 3.6 24.9 - - - -
146A VAL* 1.3 74.3 - - - +
148A GLY* 1.3 59.4 + - - +
150A TRP* 4.6 2.0 - - - -
222A TYR 3.2 5.8 - - - +
223A GLN* 3.9 8.7 - - - +
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Residues in contact with GLY 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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6A SER* 3.3 13.1 + - - -
35A GLN* 3.6 10.8 - - - -
108A LEU* 3.1 11.4 - - - -
147A CYS* 1.3 77.0 - - - +
149A ASP* 1.3 61.4 + - - -
150A TRP* 3.1 10.5 - - - +
221A ASP* 3.4 5.1 - - - +
222A TYR 2.9 34.0 + - - -
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Residues in contact with ASP 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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8A ASN* 3.2 18.4 + - - +
35A GLN* 4.0 5.2 + - + +
108A LEU* 2.9 8.5 + - - +
109A TYR* 3.8 18.3 - - + -
110A LEU* 2.8 30.8 + - - +
148A GLY* 1.3 69.6 - - - -
150A TRP* 1.3 59.1 + - - +
151A ASN* 2.9 36.3 + - - +
220A ILE* 3.5 12.1 - - - +
221A ASP* 4.2 7.0 - - - +
247A HIS* 3.1 30.7 + - - -
36U 3DR 4.1 1.9 + - - -
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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