Contacts of the strand formed by residues 137 - 142 (chain A) in PDB entry 2M3X
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 LYS 137 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A PHE* 3.5 35.6 - - - -
134A ASP* 2.6 55.2 + - - +
136A GLN* 1.3 81.9 - - + +
138A LEU* 1.3 61.6 + - - +
139A THR* 4.1 6.1 - - - +
77B GLU* 3.5 34.6 + - + +
78B ALA 3.6 15.5 - - - +
79B LYS* 4.4 5.6 - - + -
80B ILE 3.6 4.5 + - - +
83B ILE* 4.2 5.1 - - - +
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Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A VAL* 3.8 11.7 - - + -
132A ILE 3.9 1.8 - - - -
133A ILE* 3.5 26.7 - - + -
137A LYS* 1.3 77.0 - - - +
139A THR* 1.3 78.6 + - - +
140A LEU* 4.2 9.1 + - + +
77B GLU* 3.8 3.5 - - - +
78B ALA* 3.2 35.4 + - + +
80B ILE* 4.7 12.7 - - + +
83B ILE* 4.8 6.1 - - + -
86B VAL* 4.6 6.7 - - + -
93B ILE* 4.9 9.2 - - + -
95B VAL* 3.8 32.1 - - + -
109B LEU* 5.2 11.1 - - + +
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Residues in contact with THR 139 (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 TYR* 4.0 10.8 - - - +
117A PHE* 3.7 20.8 - - + -
131A VAL* 3.4 10.4 - - - +
132A ILE* 3.1 42.9 + - + -
134A ASP* 4.7 1.0 + - - -
137A LYS* 4.1 7.3 - - - +
138A LEU* 1.3 76.7 + - - +
140A LEU* 1.3 62.1 + - - +
141A ILE* 3.9 25.2 + - + +
75B VAL* 4.3 3.6 - - + -
76B LEU 3.9 3.4 - - - +
77B GLU* 4.0 27.1 + - + +
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Residues in contact with LEU 140 (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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129A LEU* 6.4 2.9 - - + -
130A VAL 4.4 0.4 - - - -
131A VAL* 3.8 23.3 - - + -
138A LEU* 4.2 4.0 + - + -
139A THR* 1.3 72.7 - - - +
141A ILE* 1.3 68.4 + - - +
142A ARG* 5.2 6.7 - - + +
74B ASP 3.7 3.6 - - - +
75B VAL* 3.8 0.3 - - - +
76B LEU* 3.0 46.4 + - + +
93B ILE* 3.5 28.3 - - + -
107B GLN* 3.0 35.0 - - + +
108B ASN 5.0 0.2 - - - -
109B LEU* 4.4 25.1 - - + -
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Residues in contact with ILE 141 (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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104A ILE* 4.0 22.2 - - + -
113A TYR* 4.1 19.1 - - + -
129A LEU* 4.3 4.0 - - - +
130A VAL* 3.1 49.2 + - + +
132A ILE* 3.6 35.9 - - + -
139A THR* 3.9 15.9 - - + +
140A LEU* 1.3 81.9 - - - +
142A ARG* 1.3 64.3 + - - +
143A THR* 4.1 5.5 + - + +
73B VAL* 4.2 24.9 - - + -
74B ASP 3.7 3.6 - - - +
75B VAL* 4.6 4.0 - - + -
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Residues in contact with ARG 142 (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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129A LEU* 3.8 19.5 - - + -
140A LEU* 4.1 6.5 - - + -
141A ILE* 1.3 73.8 - - - +
143A THR* 1.3 72.4 + - - +
73B VAL* 3.6 5.5 - - - +
74B ASP* 3.1 70.9 + - + +
76B LEU* 6.3 0.4 - - + -
107B GLN* 3.7 39.9 + - + +
108B ASN* 4.9 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