Contacts of the helix formed by residues 127 - 138 (chain A) in PDB entry 3MTG
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 MET 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A ALA* 2.8 18.3 + - + +
124A GLU* 3.7 6.6 + - - +
125A GLN 3.6 0.2 - - - -
126A ASP* 1.4 75.7 - - - +
128A SER* 1.4 53.8 + - - +
129A ALA 3.1 3.1 - - - -
130A LEU* 2.8 49.7 + - + +
131A ILE* 3.2 9.2 + - - +
157A GLN* 3.2 38.6 - - + +
160A VAL* 3.7 30.3 - - + -
452A THR* 3.7 31.4 - - + +
455A LEU* 4.6 2.9 - - + +
456A SER* 4.4 16.2 - - - +
459A ALA* 4.4 11.4 - - + -
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Residues in contact with SER 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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124A GLU 3.5 10.0 + - - -
125A GLN* 4.1 15.3 + - - -
126A ASP 3.3 5.6 + - - -
127A MET* 1.4 72.9 - - - +
129A ALA* 1.3 56.7 + - - +
130A LEU 3.3 0.2 - - - -
131A ILE* 3.6 9.6 + - - +
132A SER* 3.1 30.1 + - - -
499A SER* 5.3 9.5 - - - -
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Residues in contact with ALA 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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127A MET 3.0 0.4 + - - -
128A SER* 1.3 78.8 + - - +
130A LEU* 1.4 58.5 + - - +
132A SER* 3.6 5.9 + - - -
133A LEU* 3.2 24.4 + - - +
456A SER* 3.6 11.0 + - - +
460A THR* 4.3 2.6 + - - +
495A LEU* 3.5 36.2 - - + +
496A HIS* 3.6 32.3 - - + +
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Residues in contact with LEU 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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127A MET* 2.8 34.7 + - + +
129A ALA* 1.4 75.0 - - - +
131A ILE* 1.3 53.5 + - - +
132A SER 3.2 1.6 - - - -
133A LEU* 3.2 21.1 + - + +
134A ARG* 2.8 33.8 + - - +
160A VAL* 4.1 8.3 - - + -
161A LEU* 4.0 24.2 - - + +
164A THR* 3.8 24.0 - - + +
456A SER* 4.9 3.1 + - - +
459A ALA* 3.5 28.3 - - + +
460A THR* 4.1 27.1 - - - +
463A ALA* 4.6 0.4 - - + -
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Residues in contact with ILE 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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124A GLU* 3.6 54.1 - - + +
127A MET 3.2 6.8 + - - +
128A SER* 3.9 12.3 - - - +
129A ALA 3.5 0.2 - - - -
130A LEU* 1.3 77.6 - - - +
132A SER* 1.3 55.1 + - - +
134A ARG* 3.2 24.5 - - - +
135A LYS* 2.8 36.8 + - + +
160A VAL* 5.0 2.2 - - + -
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Residues in contact with SER 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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128A SER 3.1 18.0 + - - -
129A ALA* 3.7 8.2 - - - -
130A LEU 3.2 0.2 - - - -
131A ILE* 1.3 75.2 - - - +
133A LEU* 1.4 55.7 + - - +
135A LYS* 3.2 10.5 + - - +
136A ARG* 2.7 67.5 + - - +
495A LEU* 3.9 10.1 - - - -
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Residues in contact with LEU 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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129A ALA 3.2 12.8 + - - +
130A LEU* 3.2 17.0 + - + +
132A SER* 1.4 76.3 - - - +
134A ARG* 1.3 63.1 + - - +
136A ARG* 4.4 0.2 - - - +
137A ALA* 3.3 24.0 + - + +
164A THR* 4.7 5.2 - - + -
168A LEU* 4.3 4.4 - - + +
460A THR* 4.1 25.8 - - + +
463A ALA* 3.8 29.2 - - + -
464A LEU* 3.8 26.0 - - + -
467A ILE* 4.7 9.4 - - + -
491A TYR* 3.9 22.0 - - + +
495A LEU* 3.9 11.5 - - + +
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Residues in contact with ARG 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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124A GLU* 3.6 22.5 + - - -
130A LEU 2.8 11.7 + - - +
131A ILE* 3.2 25.8 - - - +
133A LEU* 1.3 77.8 - - - +
135A LYS* 1.3 53.8 + - - +
137A ALA 3.8 0.5 - - - -
138A GLN* 2.9 44.3 + - - +
160A VAL* 3.1 38.2 + - - +
163A GLU* 3.5 24.4 + - - +
164A THR* 3.4 25.4 + - + +
167A ALA* 3.8 25.4 - - + +
168A LEU* 4.0 5.1 - - - +
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Residues in contact with LYS 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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131A ILE* 2.8 23.5 + - + +
132A SER* 3.5 10.5 - - - +
134A ARG* 1.3 72.2 - - - +
136A ARG* 1.3 77.2 + - + +
138A GLN* 3.4 34.8 + - - +
140A GLU* 5.2 0.2 - - - +
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Residues in contact with ARG 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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132A SER* 2.7 50.4 + - - +
133A LEU 4.4 1.3 - - - +
135A LYS* 1.3 91.2 - - + +
137A ALA* 1.3 58.1 + - + +
138A GLN 3.6 0.2 - - - -
140A GLU* 2.9 19.1 - - - +
491A TYR* 3.5 31.7 + - - +
495A LEU* 4.2 10.3 - - - +
498A PRO* 5.8 5.9 - - - +
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Residues in contact with ALA 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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133A LEU* 3.3 16.7 + - + +
134A ARG 3.3 2.4 + - - -
136A ARG* 1.3 76.2 - - + +
138A GLN* 1.4 64.2 + - - +
140A GLU* 3.2 27.9 + - + +
142A PRO* 3.4 22.7 - - + +
168A LEU* 3.5 22.4 - - + -
467A ILE* 5.3 1.8 - - + -
491A TYR* 6.0 0.4 - - - +
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Residues in contact with GLN 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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134A ARG* 2.9 22.1 + - + +
135A LYS* 3.4 42.0 - - - +
136A ARG 3.6 0.2 - - - -
137A ALA* 1.4 71.4 - - - +
139A GLY* 1.3 59.5 + - - +
140A GLU* 2.8 23.1 + - - +
141A LYS 4.8 1.1 - - - +
167A ALA* 4.4 17.4 + - - +
168A LEU* 4.3 5.6 - - - -
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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