Contacts of the strand formed by residues 130 - 137 (chain B) in PDB entry 4Y0F
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 VAL 130 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121B LYS* 4.3 21.2 - - + +
124B PHE* 3.9 17.3 - - + +
125B SER* 3.8 20.4 + - - +
128B GLY 3.8 0.2 + - - -
129B GLU* 1.3 81.1 - - - +
131B LEU* 1.3 69.2 + - - +
132B MET 3.4 25.6 - - - +
133B VAL* 3.6 18.4 - - + -
150B VAL* 4.2 4.5 - - + -
151B ARG 3.4 7.6 - - - +
152B PHE* 3.9 22.4 - - + +
153B THR* 4.4 0.2 - - - -
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Residues in contact with LEU 131 (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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121B LYS* 6.1 0.9 - - - -
129B GLU* 4.1 6.9 + - - +
130B VAL* 1.3 76.6 - - - +
132B MET* 1.3 65.3 + - - +
151B ARG* 2.7 25.6 + - + +
152B PHE 4.3 4.7 - - - +
153B THR* 3.2 42.8 - - + +
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Residues in contact with MET 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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105B ASP* 3.3 31.6 - - - +
121B LYS* 5.7 2.5 - - - +
130B VAL* 3.4 4.6 - - - +
131B LEU* 1.3 83.3 - - - +
133B VAL* 1.3 84.2 - - - +
134B GLN* 4.2 11.0 - - + +
149B PHE* 3.7 31.0 - - + +
150B VAL 4.2 1.6 - - - +
151B ARG* 3.0 41.9 + - + +
6D G 5.6 1.6 - - - +
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Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B GLU* 3.3 45.7 - - + +
120B LEU* 3.3 26.0 - - + -
121B LYS* 3.9 28.6 - - + +
130B VAL* 3.6 17.9 - - + -
132B MET* 1.3 84.6 - - - +
134B GLN* 1.3 68.8 + - - +
149B PHE 3.4 5.6 - - - +
150B VAL* 4.3 11.0 - - + -
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Residues in contact with GLN 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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117B GLU* 4.3 9.0 - - - +
120B LEU* 4.0 2.9 - - - +
132B MET* 4.2 11.5 - - - +
133B VAL* 1.3 80.2 - - - +
135B VAL* 1.3 74.3 + - - +
136B LYS* 3.7 23.9 - - + +
148B GLY* 2.8 5.2 - - - -
149B PHE* 2.8 63.3 + - + +
6D G 3.7 10.2 - - - -
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Residues in contact with VAL 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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111B LEU* 4.6 8.5 - - + -
115B THR 3.7 14.1 - - - +
116B THR* 3.4 11.9 - - - +
117B GLU* 3.4 40.2 + - + +
120B LEU* 3.8 13.7 - - + -
134B GLN* 1.3 81.3 - - - +
136B LYS* 1.3 65.5 + - - +
137B LYS* 3.3 26.7 - - - +
144B SER* 3.3 29.2 - - - +
147B PHE 4.0 6.7 - - - +
148B GLY* 4.2 0.2 - - - -
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Residues in contact with LYS 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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134B GLN* 3.7 27.0 + - + +
135B VAL* 1.3 74.5 - - - +
137B LYS* 1.3 65.4 + - - +
144B SER* 3.4 5.4 + - - -
145B LYS* 3.1 28.3 + - + -
147B PHE* 3.0 52.0 + - + +
149B PHE* 3.9 9.4 - - + -
6D G 2.7 50.9 + - - +
7D C 3.2 17.6 + - - +
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Residues in contact with LYS 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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117B GLU* 5.0 13.3 + - - +
135B VAL* 3.3 24.0 - - + +
136B LYS* 1.3 86.6 - - - +
138B ASP* 1.3 67.0 + - - +
139B LEU* 3.4 9.7 + - - +
142B GLY* 3.9 23.1 - - - +
143B HIS 3.1 15.5 - - - +
144B SER* 4.4 2.7 - - - +
145B LYS* 3.9 13.0 - - - -
7D C 5.4 2.3 + - - -
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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