Contacts of the strand formed by residues 131 - 138 (chain A) in PDB entry 2JQZ
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 GLN 131 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ALA* 3.3 0.5 - - - -
22A LYS* 2.8 43.1 + - + +
23A ASN* 3.1 23.1 + - - +
114A ARG* 6.1 3.1 - - + -
115A LEU 4.8 0.4 - - - -
116A ASP* 3.6 27.4 + - - +
117A LEU* 3.2 24.4 - - - +
118A CYS* 6.1 0.2 - - - -
129A ARG 2.8 25.9 + - - -
130A GLY* 1.3 79.7 + - - +
132A ILE* 1.3 63.1 + - - +
133A VAL* 6.5 0.2 - - + -
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Residues in contact with ILE 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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18A VAL* 3.5 28.0 - - + -
20A CYS 3.0 21.1 - - - +
21A ALA* 3.7 10.1 - - + +
22A LYS* 4.5 0.8 - - - +
61A TRP* 3.6 8.5 - - + -
77A ILE* 5.6 0.2 - - + -
79A VAL* 3.6 29.8 - - + -
97A VAL* 3.9 17.7 - - + -
113A GLN 3.6 0.9 - - - +
114A ARG* 3.3 3.0 - - - -
115A LEU* 2.8 58.4 + - + +
117A LEU* 3.6 14.4 - - + -
131A GLN* 1.3 77.2 - - - +
133A VAL* 1.3 63.3 - - - +
134A VAL* 4.3 4.0 - - + -
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Residues in contact with VAL 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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18A VAL* 3.8 0.3 - - - -
19A LEU* 2.9 46.2 + - + +
20A CYS* 2.7 27.1 + - - +
21A ALA* 4.7 0.2 - - - +
22A LYS* 4.0 24.5 - - + +
112A TYR* 4.4 7.9 - - + -
113A GLN 3.6 3.1 - - - +
114A ARG* 3.5 42.8 - - + +
131A GLN* 6.5 0.2 - - + -
132A ILE* 1.3 73.2 - - - +
134A VAL* 1.3 73.5 + - - +
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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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16A LEU* 3.4 27.8 - - + -
17A THR 2.9 14.4 - - - +
18A VAL* 3.9 17.9 - - + -
19A LEU* 4.0 1.6 - - - +
77A ILE* 5.7 1.3 - - + -
97A VAL* 5.6 3.6 - - + -
99A LEU* 5.9 0.7 - - + -
112A TYR* 3.1 14.5 - - - -
113A GLN* 2.8 40.3 + - + +
115A LEU* 3.4 24.0 - - + -
132A ILE* 4.3 11.0 - - + -
133A VAL* 1.3 80.3 - - - +
135A SER* 1.3 62.4 + - - +
136A LEU* 3.7 12.3 - - + -
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Residues in contact with SER 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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15A ARG 3.3 3.3 - - - +
16A LEU* 3.8 0.3 - - - -
17A THR* 2.8 64.9 + - - +
19A LEU* 6.1 0.4 - - - -
111A GLY* 2.9 27.6 - - - -
112A TYR* 3.4 14.8 - - - +
134A VAL* 1.3 75.4 - - - +
136A LEU* 1.3 63.1 + - - +
137A GLN* 3.8 2.2 + - - +
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Residues in contact with LEU 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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14A LEU* 3.5 31.0 - - + -
15A ARG 3.8 0.2 - - - -
16A LEU* 3.5 32.1 - - + -
99A LEU* 5.3 6.1 - - + -
104A ILE* 4.9 8.5 - - + -
107A LEU* 2.7 49.9 - - + +
108A LYS* 2.5 24.6 - - - +
110A THR* 4.4 0.4 - - - +
111A GLY* 3.4 15.6 + - - -
113A GLN* 3.9 17.7 - - + -
134A VAL* 3.7 14.6 - - + -
135A SER* 1.3 77.8 - - - +
137A GLN* 1.3 56.0 + - - +
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Residues in contact with GLN 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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14A LEU* 3.6 4.6 - - - +
15A ARG* 3.2 57.3 + - + +
17A THR* 5.9 1.8 - - - +
108A LYS 2.9 7.6 - - - +
109A ASP* 5.8 0.7 - - - +
111A GLY* 5.4 4.3 - - - -
135A SER* 3.8 3.5 + - - +
136A LEU* 1.3 74.8 - - - +
138A SER* 1.3 73.9 + - - +
140A ASP* 4.8 7.5 + - - -
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Residues in contact with SER 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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12A VAL* 6.5 0.4 - - - -
13A LYS 3.9 11.7 - - - -
14A LEU* 3.8 7.8 - - - +
15A ARG* 3.9 7.0 + - - -
108A LYS* 3.3 40.8 + - - +
137A GLN* 1.3 91.4 + - - +
139A ARG* 1.3 65.5 + - - +
140A ASP* 4.0 4.3 + - - +
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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