Contacts of the strand formed by residues 126 - 135 (chain A) in PDB entry 2JK4
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 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ALA 4.0 2.4 + - - -
6A VAL* 4.2 5.6 + - - +
121A TYR 5.4 1.1 - - - +
122A LYS* 4.2 0.8 - - - +
123A ARG* 3.4 32.3 + - + +
124A GLU 3.3 3.1 + - - +
125A HIS* 1.3 80.7 - - - +
127A ASN* 1.3 76.0 + - - +
128A LEU* 4.5 13.9 - - + +
146A VAL* 2.8 25.4 - - - +
147A LEU* 3.0 32.8 - - + -
148A GLY* 3.9 4.0 - - - +
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Residues in contact with ASN 127 (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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6A VAL* 3.4 10.8 - - + +
7A PRO 2.6 28.5 - - - +
8A PRO* 3.1 30.5 - - - +
121A TYR 3.3 9.9 - - - +
122A LYS* 3.7 21.8 - - + -
126A ILE* 1.3 86.2 - - - +
128A LEU* 1.3 74.8 + - - +
129A GLY 5.2 0.6 - - - +
144A ALA* 6.3 0.2 - - - +
146A VAL* 3.3 17.7 + - - +
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Residues in contact with LEU 128 (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 GLY* 3.7 1.0 - - - -
121A TYR* 3.1 31.0 + - + +
126A ILE* 4.5 13.2 - - + +
127A ASN* 1.3 94.5 - - - +
129A GLY* 1.3 61.7 + - - +
130A CYS* 4.3 5.0 - - - -
144A ALA* 2.8 10.8 - - - +
145A LEU* 3.1 35.9 - - + -
146A VAL 2.8 44.6 - - - +
147A LEU* 6.4 0.2 - - + -
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Residues in contact with GLY 129 (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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119A THR 4.2 0.2 - - - -
120A GLY* 4.1 9.4 - - - -
127A ASN* 5.2 1.8 - - - +
128A LEU* 1.3 75.2 - - - +
130A CYS* 1.3 61.5 + - - -
131A ASP* 3.4 19.7 - - - -
143A GLY* 3.5 22.3 - - - -
144A ALA* 3.6 16.1 + - - +
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Residues in contact with CYS 130 (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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119A THR* 3.1 43.7 + - + +
120A GLY* 4.0 4.5 - - - -
121A TYR* 5.0 5.2 - - - -
128A LEU* 4.3 7.4 - - - -
129A GLY* 1.3 76.6 - - - -
131A ASP* 1.3 68.0 + - - +
132A MET* 3.0 21.0 + - + +
142A ARG 3.9 6.3 - - - -
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Residues in contact with ASP 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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117A ILE 3.9 4.3 - - - -
118A LYS* 3.1 37.4 - - - +
119A THR 3.2 22.0 + - - +
129A GLY* 3.4 9.5 + - - -
130A CYS* 1.3 72.5 + - - +
132A MET* 1.3 55.2 + - - +
142A ARG* 2.7 59.4 + - + +
143A GLY 5.4 1.2 + - - +
144A ALA* 5.8 1.9 - - - +
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Residues in contact with MET 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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116A LYS* 2.8 5.2 - - - +
117A ILE* 2.8 60.7 + - + +
118A LYS* 4.3 3.6 - - - +
119A THR* 4.7 4.9 - - - +
130A CYS* 3.0 17.2 + - + +
131A ASP* 1.3 73.4 - - - +
133A ASP* 1.3 59.8 + - - +
134A PHE* 3.0 48.2 + - + -
140A SER 4.0 3.8 - - - +
141A ILE* 4.1 19.1 - - + -
142A ARG 4.6 0.2 - - - +
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Residues in contact with ASP 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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114A ASN* 3.5 9.5 + - - -
115A ALA 3.0 12.5 - - - +
116A LYS* 2.8 40.5 + - + +
118A LYS* 4.9 5.4 - - - +
131A ASP 4.2 1.2 + - - -
132A MET* 1.3 71.0 - - - +
134A PHE* 1.3 56.9 + - - +
135A ASP* 3.1 24.5 + - - +
139A PRO* 3.8 0.2 - - - +
140A SER* 2.5 57.2 + - - +
142A ARG* 5.1 0.8 - - + +
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Residues in contact with PHE 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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114A ASN* 4.3 0.9 - - - +
115A ALA 3.6 21.6 + - - +
116A LYS* 4.4 3.1 - - - -
117A ILE* 3.1 44.6 - - + -
132A MET* 3.0 49.9 + - + -
133A ASP* 1.3 72.6 + - - +
135A ASP* 1.3 63.7 + - - +
139A PRO* 3.9 19.1 - - + -
141A ILE* 4.7 9.6 - - + -
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Residues in contact with ASP 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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113A LYS 4.9 0.4 - - - -
114A ASN* 3.0 36.1 - - + +
133A ASP* 3.1 22.8 + - - +
134A PHE* 1.3 78.9 - - - +
136A ILE* 1.3 67.5 + - - +
137A ALA 3.6 2.9 + - - +
138A GLY 2.3 37.6 - - - +
139A PRO* 3.4 4.3 - - - +
140A SER* 4.4 3.2 - - - -
161A GLU* 4.3 12.3 - - - +
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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