Contacts of the strand formed by residues 130 - 139 (chain B) in PDB entry 4A12
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 THR 130 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A THR* 4.1 25.1 - - + -
108A ILE* 6.4 0.7 - - + -
128B GLN* 4.4 0.7 - - - +
129B PRO* 1.3 78.1 - - - +
131B VAL* 1.3 63.2 + - - +
132B LEU* 4.4 7.0 - - - -
185B PHE* 3.8 5.8 - - - +
186B TYR* 3.4 6.8 - - - +
187B ASP* 3.0 55.5 + - - +
190B GLY 3.1 20.3 + - - +
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Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A PHE* 4.4 11.3 - - - -
123B VAL* 4.3 24.2 - - + +
126B ILE* 3.7 46.4 - - + +
128B GLN* 3.7 20.9 - - + +
129B PRO 4.2 1.0 + - - +
130B THR* 1.3 77.2 - - - +
132B LEU* 1.3 73.5 + - - +
184B MSE 3.7 30.3 - - + -
185B PHE 3.4 9.0 - - - +
186B TYR* 5.0 0.4 - - + -
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Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A PHE* 4.5 16.8 - - + -
106A THR* 5.2 3.8 - - + +
108A ILE* 4.1 31.4 - - + -
109A ALA 5.5 1.1 - - - +
143A LYS* 4.0 36.6 - - + +
123B VAL* 6.3 0.4 - - - -
130B THR* 5.3 5.4 - - - -
131B VAL* 1.3 84.1 - - - +
133B THR* 1.3 61.9 + - - +
134B HIS* 3.5 10.7 + - + +
184B MSE 3.6 6.4 - - - -
185B PHE* 2.7 65.1 + - + +
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Residues in contact with THR 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A GLY* 4.5 8.3 + - - +
140A PHE* 3.3 41.9 - - + +
119B ASN* 2.7 35.6 + - - +
123B VAL* 4.9 1.7 - - - +
132B LEU* 1.3 72.7 - - - +
134B HIS* 1.3 65.1 + - - +
135B GLU 3.9 15.0 - - - +
136B SER* 4.7 1.1 - - - -
182B PHE* 4.0 8.1 - - + -
184B MSE 3.4 30.3 - - - +
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Residues in contact with HIS 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A GLN* 4.5 0.2 - - - +
140A PHE* 2.8 45.0 + - + +
143A LYS* 6.1 2.4 - - - +
132B LEU* 3.5 11.7 + - + +
133B THR* 1.3 80.0 - - - +
135B GLU* 1.3 64.0 + - + +
163B HIS* 3.1 26.5 + + + +
183B LYS* 2.8 23.9 + - + +
185B PHE* 3.4 42.2 - + + +
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Residues in contact with GLU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ILE 3.5 6.3 - - - +
139A GLN* 3.9 32.4 + - + -
140A PHE* 4.7 1.6 - - - -
133B THR* 3.9 6.7 - - - +
134B HIS* 1.3 81.7 - - + +
136B SER* 1.3 63.8 + - - +
182B PHE* 3.7 0.9 - - - -
183B LYS* 2.9 65.7 + - + +
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Residues in contact with SER 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A SER 3.9 1.1 - - - +
137A SER* 3.6 1.9 + - - -
138A ILE* 2.8 55.8 + - - +
115B PHE* 3.4 17.2 - - - -
133B THR* 4.7 2.2 - - - -
135B GLU* 1.3 78.1 - - - +
137B SER* 1.3 61.7 + - - +
138B ILE* 3.4 9.2 - - - +
181B ASN 3.2 13.1 + - - -
182B PHE* 3.4 24.0 - - - -
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Residues in contact with SER 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A SER 3.5 6.1 - - - -
137A SER* 4.0 14.5 + - - -
136B SER* 1.3 73.2 + - - +
138B ILE* 1.3 60.1 + - - +
179B LYS 4.1 0.5 - - - +
180B GLY* 3.4 1.6 - - - -
181B ASN* 2.8 52.9 + - - -
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Residues in contact with ILE 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A PHE* 3.5 32.5 - - + -
135A GLU* 3.5 3.3 - - - +
136A SER* 2.8 46.5 + - - +
138A ILE* 6.0 1.3 - - + -
115B PHE* 3.7 20.2 - - + -
136B SER* 3.4 23.8 - - - +
137B SER* 1.3 75.7 - - - +
139B GLN* 1.3 64.4 + - - +
140B PHE* 3.6 25.1 - - + -
178B PHE* 3.5 25.6 - - + -
179B LYS 3.4 3.4 - - - -
180B GLY* 3.9 6.7 - - - -
182B PHE* 4.3 2.0 - - + -
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Residues in contact with GLN 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A HIS 3.5 3.8 - - - +
135A GLU* 3.8 27.1 - - + +
138B ILE* 1.3 76.7 - - - +
140B PHE* 1.3 63.7 + - - +
141B ILE* 3.4 17.5 - - + +
178B PHE* 3.5 4.2 - - - -
179B LYS* 2.8 75.5 + - + +
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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