Contacts of the strand formed by residues 131 - 137 (chain A) in PDB entry 1AVU
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 TYR 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A PHE 3.5 10.0 + - - -
3A VAL* 3.6 43.7 - - + -
4A LEU* 3.3 28.6 + - - +
69A GLU* 4.2 8.5 + - + -
120A LEU* 4.6 4.0 - - + -
121A GLU 3.4 11.2 - - - +
122A ARG* 3.7 47.6 + - + -
123A VAL* 3.9 5.2 - - - -
129A ASN* 3.6 26.9 - - - -
130A ASN* 1.3 77.7 - - - +
132A LYS* 1.3 63.7 + - - +
170A VAL* 3.5 7.1 - - - +
171A VAL* 3.0 33.4 + - + +
173A PHE* 4.4 21.1 - + + -
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Residues in contact with LYS 132 (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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120A LEU* 3.3 10.2 - - - +
121A GLU* 2.8 68.6 + - + +
122A ARG 5.5 0.9 - - - -
123A VAL* 3.9 17.7 - - + +
131A TYR* 1.3 75.8 - - - +
133A LEU* 1.3 64.5 + - - +
134A VAL* 4.3 5.0 - - + +
147A ASP* 2.9 32.2 + - + +
148A ILE 5.6 0.2 - - - +
168A PRO* 3.7 23.1 - - + -
169A LEU 3.6 18.4 - - - +
170A VAL* 5.2 0.7 - - + -
171A VAL* 4.6 2.5 - - - -
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Residues in contact with LEU 133 (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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19A ILE* 5.3 8.1 - - + -
73A LEU* 5.3 0.9 - - + -
75A LEU* 3.9 17.0 - - + -
93A TRP* 3.5 34.1 - - + -
118A PHE* 3.5 34.8 - - + -
119A ARG 3.6 4.7 - - - +
120A LEU* 4.0 21.1 - - + -
132A LYS* 1.3 79.4 - - - +
134A VAL* 1.3 64.2 + - - +
147A ASP* 4.0 0.9 - - - -
148A ILE* 3.2 43.5 + - + +
161A LEU* 5.1 2.5 - - + -
169A LEU 4.6 2.2 + - - -
171A VAL* 5.1 9.5 - - + +
173A PHE* 5.9 1.6 - - + -
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Residues in contact with VAL 134 (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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118A PHE* 3.2 11.8 - - - -
119A ARG* 2.9 74.0 + - + +
121A GLU* 4.4 15.0 - - + +
132A LYS* 4.3 10.1 - - + +
133A LEU* 1.3 77.3 - - - +
135A PHE* 1.3 60.3 + - - +
145A CYS* 3.7 15.7 - - + +
146A GLY 3.4 17.9 - - - +
147A ASP* 3.8 20.2 - - - +
148A ILE* 4.5 0.9 - - - -
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Residues in contact with PHE 135 (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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94A SER* 6.3 0.2 - - - -
95A VAL* 3.6 33.0 - - + -
114A MET* 3.7 48.0 - - + -
115A ASP 4.1 5.6 - - - -
116A GLY* 3.4 22.0 - - - -
117A TRP 3.5 24.9 - - - -
118A PHE* 3.9 20.6 - + + -
134A VAL* 1.3 73.7 - - - +
136A CYS* 1.3 57.8 + - - +
137A PRO* 3.4 16.2 - - + +
145A CYS* 3.0 6.3 - - - -
146A GLY 2.9 34.7 + - - +
148A ILE* 4.1 17.6 - - + +
163A VAL* 4.5 6.3 - - + -
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Residues in contact with CYS 136 (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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116A GLY* 3.1 1.8 - - - -
117A TRP* 2.9 38.6 + - + +
119A ARG* 3.5 36.8 - - + -
134A VAL 4.8 0.7 - - - -
135A PHE* 1.3 71.9 - - - +
137A PRO* 1.3 72.8 - - - +
139A GLN 5.4 0.7 - - - -
143A ASP* 5.8 1.1 - - - -
144A LYS 5.0 0.2 - - - +
145A CYS* 2.0 44.6 - - - -
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Residues in contact with PRO 137 (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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114A MET* 4.1 27.6 - - + -
115A ASP 3.4 5.6 - - - +
116A GLY* 4.0 1.1 - - - -
135A PHE* 3.4 17.3 - - + +
136A CYS* 1.3 87.6 - - - +
138A GLN* 1.3 75.9 + - + +
139A GLN 4.6 2.8 - - - -
144A LYS 3.5 18.2 - - - +
145A CYS* 4.4 0.2 - - - -
146A GLY 5.1 0.7 - - - +
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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