Contacts of the helix formed by residues 112 - 127 (chain B) 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 GLN 112 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108B LYS* 3.8 23.2 - - - +
109B ASN* 3.1 8.9 + - - +
110B ILE* 3.0 36.3 - - + +
111B LYS* 1.4 74.1 - - - +
113B ALA* 1.4 51.3 + - - +
114B GLU 3.2 0.9 - - - -
115B PHE* 3.2 11.1 + - + +
116B GLY* 2.7 35.0 + - - -
184B ASN* 4.1 13.2 - - - +
185B GLU* 4.0 39.1 + - + +
188B ALA* 3.7 17.7 - - + +
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ASN* 4.1 7.8 + - - +
111B LYS* 3.2 4.0 - - - +
112B GLN* 1.4 76.3 - - - +
114B GLU* 1.4 65.2 + - + +
116B GLY 3.9 0.2 - - - -
117B ARG* 3.3 27.0 + - - +
188B ALA* 3.6 18.7 - - - +
189B ALA* 3.7 15.5 - - - +
192B GLU* 3.7 32.8 - - + +
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Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B LYS* 3.6 13.8 + - + +
112B GLN 3.2 0.4 - - - -
113B ALA* 1.4 80.7 - - + +
115B PHE* 1.4 61.4 + - - +
117B ARG* 4.1 2.9 + - - +
118B ARG* 3.4 39.6 + - - +
192B GLU* 6.0 1.4 - - - +
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Residues in contact with PHE 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B LYS 4.7 0.6 + - - -
112B GLN* 3.2 11.6 + - + +
114B GLU* 1.4 76.4 - - - +
116B GLY* 1.3 64.1 + - - +
118B ARG* 3.1 28.5 + - + +
119B GLU* 3.2 46.5 + - + +
185B GLU* 3.6 43.3 - - + -
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Residues in contact with GLY 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B GLN 2.7 14.8 + - - -
114B GLU 3.5 0.2 - - - -
115B PHE* 1.3 72.8 - - - +
117B ARG* 1.3 59.3 + - - +
119B GLU* 3.2 8.3 + - - +
120B ILE* 3.2 23.3 + - - +
185B GLU* 3.2 35.0 - - - -
186B VAL* 3.9 3.4 - - - +
189B ALA* 3.6 8.5 - - - -
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Residues in contact with ARG 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ALA 3.3 19.2 + - - +
114B GLU* 4.6 3.6 - - - +
115B PHE 3.3 0.2 - - - -
116B GLY* 1.3 72.2 - - - +
118B ARG* 1.3 54.0 + - - +
120B ILE* 3.2 19.1 + - + +
121B GLU* 2.7 49.9 + - + +
124B GLU* 5.2 2.9 - - - +
163B GLU* 2.7 38.9 + - - -
189B ALA* 2.7 47.8 + - - +
190B LEU* 3.7 2.0 - - - +
192B GLU* 4.2 9.5 - - - +
193B ALA* 3.4 21.3 - - - +
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Residues in contact with ARG 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B GLU* 3.4 30.5 + - - +
115B PHE* 3.1 22.6 + - + +
117B ARG* 1.3 78.0 - - + +
119B GLU* 1.4 59.1 + - - +
121B GLU* 3.4 24.9 - - - +
122B ILE* 3.3 28.9 + - + +
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Residues in contact with GLU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B PHE* 3.2 45.6 + - + +
116B GLY* 3.2 8.9 + - - +
118B ARG* 1.4 74.9 - - - +
120B ILE* 1.4 60.2 + - - +
122B ILE* 3.4 30.8 + - - +
123B ALA* 3.2 18.7 + - - +
156B ALA* 3.6 13.6 - - + +
183B GLN* 6.0 1.1 - - - +
185B GLU* 6.0 1.3 - - + -
186B VAL* 4.4 12.8 - - + -
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Residues in contact with ILE 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B GLY 3.3 16.6 - - - +
117B ARG* 3.2 24.7 + - - +
119B GLU* 1.4 75.4 - - - +
121B GLU* 1.4 52.6 + - - +
123B ALA* 3.0 7.9 + - - +
124B GLU* 2.6 58.5 + - + +
156B ALA* 4.1 6.5 - - - +
159B ALA* 3.8 34.3 - - + -
160B VAL* 4.2 4.7 - - + +
163B GLU* 4.6 7.9 - - - +
186B VAL* 4.1 17.7 - - + +
189B ALA* 3.6 23.8 - - + -
190B LEU* 5.0 0.9 - - + +
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Residues in contact with GLU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ARG* 2.7 40.9 + - + +
118B ARG* 3.4 29.3 + - - +
120B ILE* 1.4 72.7 - - - +
122B ILE* 1.4 58.8 - - + +
124B GLU* 3.7 13.0 + - - +
125B GLN* 3.3 27.9 + - - +
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Residues in contact with ILE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ARG* 3.3 15.8 + - + +
119B GLU* 3.4 38.6 - - - +
120B ILE 3.2 0.6 - - - -
121B GLU* 1.4 75.1 - - + +
123B ALA* 1.4 61.2 + - - +
125B GLN* 3.2 27.0 + - - +
126B ASP* 3.3 27.6 + - - +
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Residues in contact with ALA 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B GLU 3.2 12.8 + - - +
120B ILE 3.0 8.6 + - - +
122B ILE* 1.4 73.7 - - - +
124B GLU* 1.4 53.7 + - - +
126B ASP* 2.8 29.0 + - - +
127B MET* 2.8 23.3 + - - +
156B ALA* 3.4 35.0 - - + +
157B GLN* 4.1 16.2 - - + +
160B VAL* 4.0 3.6 - - + -
452B THR* 5.5 0.2 - - - -
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ARG* 5.2 3.3 - - - +
120B ILE* 2.6 39.4 + - - +
121B GLU* 3.8 14.8 - - - +
123B ALA* 1.4 69.4 - - - +
125B GLN* 1.4 60.8 + - - +
127B MET 3.4 7.8 + - - +
128B SER* 3.7 6.8 + - - -
131B ILE* 3.3 36.3 - - + +
134B ARG* 4.3 19.5 + - - -
160B VAL* 3.7 19.9 - - + +
163B GLU* 3.7 14.6 - - - +
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Residues in contact with GLN 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B GLU 3.3 13.6 + - - +
122B ILE* 3.2 24.5 + - - +
123B ALA 3.2 0.2 - - - -
124B GLU* 1.4 76.4 - - - +
126B ASP* 1.3 65.4 + - - +
127B MET 3.5 0.2 - - - -
128B SER* 4.5 10.3 + - - -
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Residues in contact with ASP 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ILE* 3.3 26.6 - - - +
123B ALA* 2.8 12.1 + - - +
125B GLN* 1.3 84.9 - - - +
127B MET* 1.4 57.4 + - - +
128B SER* 3.7 1.9 + - - -
452B THR* 3.8 29.6 + - + +
453B PHE* 5.4 5.4 + - - -
456B SER* 5.5 0.9 - - - -
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Residues in contact with MET 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ALA 2.8 19.3 + - - +
124B GLU* 3.4 5.3 + - - -
126B ASP* 1.4 79.0 - - - +
128B SER* 1.4 54.4 + - - +
129B ALA 3.0 11.6 + - - +
130B LEU* 3.1 41.0 + - + +
131B ILE* 3.7 8.7 + - - +
157B GLN* 3.4 50.0 - - + +
160B VAL* 4.0 14.4 - - + -
452B THR* 3.9 15.3 - - + +
455B LEU* 4.9 1.3 - - + -
456B SER* 3.9 33.7 - - - +
459B ALA* 4.4 7.0 - - + -
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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