Contacts of the strand formed by residues 133 - 137 (chain A) in PDB entry 1MTL
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 THR 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A ILE* 3.5 30.1 - - + +
100A GLN* 3.5 9.4 - - - +
101A PRO* 2.6 35.0 + - + +
102A GLN 3.7 1.3 - - - -
103A ALA 3.8 2.5 - - - -
104A LEU* 3.7 18.8 - - + +
129A THR* 3.1 24.6 - - - -
130A ILE* 3.1 18.8 + - + -
132A SER* 1.3 78.0 + - - +
134A GLN* 1.3 74.6 + - - +
135A ILE* 5.5 0.2 - - + -
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Residues in contact with GLN 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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102A GLN 3.1 14.9 + - - +
103A ALA* 4.3 1.3 - - + -
104A LEU 2.9 25.3 + - - -
125A LYS* 2.8 37.7 + - + +
126A GLN 5.9 0.7 - - - +
129A THR* 4.6 9.2 - - + -
132A SER 4.3 6.1 - - - +
133A THR* 1.3 80.9 - - - +
135A ILE* 1.3 61.4 + - - +
136A TRP* 3.0 24.0 + - + +
162A ALA 5.3 2.4 + - - -
163A LEU* 3.8 24.2 - - - +
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Residues in contact with ILE 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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104A LEU* 3.6 8.7 - - + +
106A ILE* 4.6 7.9 - - + -
112A TYR* 3.6 27.4 - - + -
116A PHE* 4.3 10.5 - - + -
125A LYS* 4.4 0.3 - - - +
126A GLN* 2.9 38.7 + - + +
128A LEU* 3.6 50.4 + - + +
129A THR* 4.3 3.8 - - - -
130A ILE* 3.9 31.9 - - + -
133A THR 5.3 0.2 - - - -
134A GLN* 1.3 79.3 - - - +
136A TRP* 1.3 70.9 + - - +
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Residues in contact with TRP 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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103A ALA* 4.2 6.5 - - + +
104A LEU 2.7 13.8 + - - +
105A ALA* 3.1 4.8 - - + -
106A ILE* 2.6 35.2 + - - +
124A GLY* 3.5 11.9 - - - -
125A LYS* 3.7 47.6 - - + +
134A GLN* 3.0 31.2 + - + +
135A ILE* 1.3 82.3 - - - +
137A VAL* 1.3 58.1 + - - +
138A LEU* 3.9 10.5 - - + -
155A ALA 5.2 1.6 - - - -
158A GLU* 4.3 15.3 - - + -
159A LEU* 3.7 57.1 - - + +
162A ALA* 3.6 32.5 - - + -
163A LEU* 5.2 0.2 - - - +
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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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106A ILE* 3.5 5.8 - - + -
108A GLY 4.1 4.0 - - - +
109A LYS* 4.0 19.5 - - + -
112A TYR* 3.3 51.4 - - + -
121A ALA* 6.0 0.7 - - + -
122A GLN 4.6 2.0 - - - +
123A TRP* 3.4 32.4 - - + -
124A GLY* 2.9 33.8 + - - +
126A GLN* 3.8 15.9 - - + +
136A TRP* 1.3 76.4 - - - +
138A LEU* 1.3 61.8 + - - +
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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