Contacts of the helix formed by residues 111 - 125 (chain B) in PDB entry 1MA1
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 SER 111 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B ILE* 3.8 6.7 + - - +
106B GLU* 4.0 9.8 + - - +
109B PHE* 3.2 10.4 + - - +
110B GLY* 1.3 79.9 - - - +
112B PHE* 1.3 63.8 + - - +
113B GLU* 3.2 16.0 + - - +
114B ARG* 2.9 24.8 + - - +
115B PHE* 3.2 16.3 + - - +
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Residues in contact with PHE 112 (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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95B GLY 4.2 6.1 - - - -
96B GLU* 3.6 45.5 - - + +
97B PRO* 3.3 32.5 - - + -
105B ILE* 3.9 13.9 - - + +
106B GLU* 5.2 3.6 - - - +
111B SER* 1.3 70.6 - - - +
113B GLU* 1.3 67.1 + - - +
115B PHE* 3.1 19.2 + + - +
116B ARG* 2.7 59.0 + - + +
188B TRP* 4.5 11.9 - + - -
193B TRP* 3.7 22.0 - + - -
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Residues in contact with GLU 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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96B GLU* 4.5 10.2 - - - +
111B SER* 3.2 13.2 + - - +
112B PHE* 1.3 87.7 + - - +
114B ARG* 1.3 63.7 + - - +
116B ARG* 3.1 12.4 + - - +
117B LYS* 2.9 26.2 + - - +
198C LYS* 6.4 2.0 - - + -
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Residues in contact with ARG 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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109B PHE* 3.0 31.0 - - + +
111B SER* 2.9 15.7 + - - +
113B GLU* 1.3 75.2 - - - +
115B PHE* 1.3 63.2 + - - +
117B LYS* 3.1 31.0 + - - +
118B GLU* 2.8 56.1 + - - +
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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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105B ILE* 3.6 29.4 - - + -
109B PHE* 3.8 37.6 - + + +
111B SER 3.2 3.7 + - - +
112B PHE* 3.1 22.5 + + - +
114B ARG* 1.3 79.8 - - - +
116B ARG* 1.3 64.2 + - - +
117B LYS 3.0 0.3 + - - -
118B GLU* 3.1 0.9 + - - +
119B PHE* 2.8 64.8 + + + +
134B LEU* 4.0 28.7 - - + -
145B ILE* 4.2 2.9 - - + -
163B LEU* 4.1 13.7 - - + -
188B TRP* 3.9 13.2 - + - -
193B TRP* 3.8 23.1 - + - -
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Residues in contact with ARG 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 PHE* 2.7 40.4 + - + +
113B GLU* 3.3 14.1 - - - +
115B PHE* 1.3 80.5 - - - +
117B LYS* 1.3 54.8 + - - +
120B SER* 2.7 39.9 + - - -
185B GLU* 2.9 38.2 + - - -
188B TRP* 3.4 58.9 - - + +
198C LYS* 5.4 7.6 - - - +
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Residues in contact with LYS 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 GLU 2.9 16.8 + - - +
114B ARG* 3.4 30.7 - - - +
116B ARG* 1.3 77.5 - - - +
118B GLU* 1.3 61.0 + - + +
120B SER* 3.1 7.6 + - - -
121B GLN* 2.9 53.5 + - + +
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Residues in contact with GLU 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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109B PHE* 3.5 26.6 - - - -
114B ARG* 2.8 57.5 + - - +
115B PHE* 3.7 3.8 - - - +
117B LYS* 1.3 77.6 - - + +
119B PHE* 1.3 62.8 + - - +
121B GLN* 3.2 15.5 + - - +
122B ALA* 2.9 23.0 + - - +
145B ILE* 4.1 12.4 - - + +
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Residues in contact with PHE 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* 2.8 40.8 + + + +
116B ARG 3.9 3.6 - - - +
118B GLU* 1.3 73.5 - - - +
120B SER* 1.3 57.8 + - - +
122B ALA* 3.2 6.4 + - - +
123B ALA* 3.1 23.7 + - - +
132B ALA* 3.3 29.9 - - + +
133B VAL* 3.8 7.0 - - - -
134B LEU* 3.7 27.8 - - + -
145B ILE* 3.8 19.2 - - + +
163B LEU* 3.9 22.4 - - + -
165B LEU* 3.8 30.3 - - + -
187B PHE* 4.6 2.0 - + - -
188B TRP* 3.6 25.4 - + + -
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Residues in contact with SER 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 ARG* 2.7 28.1 + - - +
117B LYS* 3.4 8.1 - - - -
118B GLU 3.1 0.2 - - - -
119B PHE* 1.3 76.4 - - - +
121B GLN* 1.3 60.7 + - - +
123B ALA* 3.2 1.8 + - - +
124B ILE* 2.9 42.0 + - - +
184B VAL* 3.7 16.6 - - - +
185B GLU* 5.6 0.3 + - - -
188B TRP* 3.1 25.2 + - - -
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Residues in contact with GLN 121 (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 LYS* 2.9 45.6 + - + +
118B GLU* 3.6 14.6 - - - +
120B SER* 1.3 72.6 - - - +
122B ALA* 1.3 55.9 + - - +
124B ILE* 4.4 6.1 - - - +
125B SER* 2.6 44.4 + - - +
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Residues in contact with ALA 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 GLU 2.9 13.8 + - - +
119B PHE 3.4 10.3 - - - +
120B SER 3.2 0.2 - - - -
121B GLN* 1.3 76.2 - - - +
123B ALA* 1.3 62.2 + - - +
125B SER* 4.1 0.4 - - - -
126B ALA* 3.8 1.7 + - - +
131B TRP 4.8 0.5 - - - +
132B ALA* 4.0 15.0 - - + +
145B ILE* 4.0 20.2 - - + -
147B GLN* 3.0 42.5 + - + +
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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 PHE 3.1 10.8 + - - +
120B SER 3.6 7.0 - - - +
121B GLN 3.1 0.2 - - - -
122B ALA* 1.3 76.1 - - - +
124B ILE* 1.3 66.6 + - - +
125B SER 3.3 0.3 + - - -
126B ALA* 3.4 4.3 + - - +
132B ALA* 3.9 11.4 - - + +
165B LEU* 3.8 21.1 - - + -
167B VAL* 3.6 25.2 - - + +
180B ARG* 3.4 14.0 + - - -
184B VAL* 3.8 21.3 - - + -
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Residues in contact with ILE 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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120B SER* 2.9 29.1 + - - +
121B GLN* 4.2 4.7 - - - +
123B ALA* 1.3 75.2 - - - +
125B SER* 1.3 61.8 + - - +
126B ALA 4.1 0.3 - - - +
180B ARG* 3.0 30.6 + - - +
181B PRO* 3.9 42.6 - - + +
184B VAL* 3.9 21.5 - - + -
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Residues in contact with SER 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 GLN* 2.6 26.7 + - - +
122B ALA* 4.1 0.3 - - - -
124B ILE* 1.3 78.6 - - - +
126B ALA* 1.3 65.1 + - - +
127B GLU* 3.2 12.0 + - - +
147B GLN* 3.0 16.9 + - - +
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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