Contacts of the strand formed by residues 130 - 138 (chain A) in PDB entry 5Y03
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 ILE 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A SER* 5.2 0.2 - - - -
6A VAL* 3.8 21.0 - - + +
22A ILE* 5.1 0.2 - - + -
25A THR 3.3 8.5 - - - +
26A PRO* 4.5 0.2 - - + -
27A ILE* 3.5 9.6 - - - +
35A GLN 4.1 2.0 - - - +
36A LEU* 3.5 37.0 - - + -
58A PHE* 4.2 4.7 - - + -
89A PHE* 4.0 24.5 - - + -
126A VAL* 3.4 33.2 - - + -
127A SER 4.2 4.5 - - - +
128A ARG 2.9 15.7 + - - +
129A ASP* 1.3 80.4 - - - +
131A SER* 1.3 59.6 + - - +
132A LEU* 3.7 21.3 - - + -
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Residues in contact with SER 131 (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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2A SER* 3.2 32.2 + - - -
24A GLY* 2.9 5.4 - - - -
25A THR* 2.6 49.8 + - - -
27A ILE* 3.5 11.4 - - - +
130A ILE* 1.3 73.9 - - - +
132A LEU* 1.3 59.3 - - - +
133A THR* 3.7 1.6 + - - -
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Residues in contact with LEU 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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2A SER* 2.8 16.5 + - - +
3A SER 3.2 22.2 + - - -
4A LEU* 3.4 20.0 + - + +
6A VAL* 4.0 16.6 - - + -
8A TYR* 3.6 37.0 - - + -
22A ILE* 3.6 31.2 - - + -
23A LYS 3.6 10.3 - - - +
126A VAL* 3.9 9.2 - - + -
130A ILE* 3.7 16.9 + - + -
131A SER* 1.3 69.4 - - - +
133A THR* 1.3 62.5 + - - +
135A VAL* 3.9 19.1 - - + -
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Residues in contact with THR 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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3A SER* 3.4 26.3 + - - +
4A LEU* 4.7 2.1 - - - +
23A LYS* 2.7 20.3 + - + -
24A GLY* 3.9 7.4 - - - -
25A THR* 4.8 2.8 + - - -
88A GLN* 3.2 31.3 + - - +
131A SER* 3.7 2.3 + - - -
132A LEU* 1.3 73.3 - - - +
134A SER* 1.3 65.5 + - - +
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Residues in contact with SER 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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4A LEU* 4.2 7.0 - - - -
21A ILE* 3.8 2.1 + - - +
22A ILE* 3.6 0.2 - - - -
23A LYS* 2.8 53.0 + - - +
132A LEU 3.6 1.2 - - - -
133A THR* 1.3 84.9 - - - +
135A VAL* 1.3 70.8 + - - +
136A CYS* 4.9 10.7 - - - -
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Residues in contact with VAL 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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4A LEU* 4.1 9.7 - - + +
8A TYR* 4.2 19.9 + - + -
10A LEU* 3.8 26.7 - - + +
20A VAL* 4.5 7.0 - - + -
21A ILE 3.1 9.2 - - - +
22A ILE* 4.1 19.5 - - + -
124A VAL* 5.8 1.8 - - + -
126A VAL* 4.5 5.8 - - + -
132A LEU* 3.9 32.8 - - + -
134A SER* 1.3 80.3 - - - +
136A CYS* 1.3 71.5 + - - +
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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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10A LEU* 5.8 0.2 - - - -
19A CYS 3.6 0.6 - - - +
20A VAL* 3.4 5.5 - - - +
21A ILE* 2.7 58.4 + - + +
134A SER* 4.9 11.7 - - - -
135A VAL* 1.3 79.3 - - - +
137A VAL* 1.3 64.8 + - - +
138A CYS* 4.1 10.5 - - - -
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Residues in contact with VAL 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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10A LEU* 3.9 25.8 - - + -
12A VAL* 3.9 15.7 - - + -
13A SER 4.7 9.0 - - - +
14A LEU* 4.0 23.3 - - + -
18A SER* 4.9 3.1 - - - -
19A CYS 3.2 8.3 - - - +
20A VAL* 4.6 11.2 - - + -
136A CYS* 1.3 78.3 - - - +
138A CYS* 1.3 69.6 + - - +
139A ASN* 4.9 5.6 + - - +
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Residues in contact with CYS 138 (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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17A GLY 4.0 0.4 - - - +
18A SER* 3.3 5.7 - - - -
19A CYS* 2.8 37.0 + - + +
21A ILE* 3.5 26.7 - - + -
136A CYS* 4.3 11.2 - - - -
137A VAL* 1.3 77.6 - - - +
139A ASN* 1.3 67.4 + - - +
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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