Contacts of the helix formed by residues 107 - 129 (chain A) in PDB entry 1MUW
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 ASP 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A LYS* 5.6 3.8 + - - -
100A ASP* 6.0 1.7 - - - +
105A ALA* 3.2 2.6 - - + +
106A ASN* 1.3 78.8 - - - +
108A ARG* 1.3 64.9 + - - +
109A ASP* 3.5 17.0 - - - +
110A VAL* 3.2 26.5 + - + +
111A ARG* 3.2 14.8 + - - +
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Residues in contact with ARG 108 (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 ASN 3.4 4.4 + - - -
107A ASP* 1.3 71.2 - - - +
109A ASP* 1.3 63.6 + - - +
111A ARG* 3.1 35.4 + - + +
112A ARG* 3.1 63.6 + - + +
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Residues in contact with ASP 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ASP* 3.5 17.5 - - - +
108A ARG* 1.3 78.9 - - - +
110A VAL* 1.3 71.4 + - - +
112A ARG* 3.4 10.7 + - - +
113A TYR* 3.1 27.0 + - - +
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Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A VAL* 3.6 42.8 - - + +
98A PHE* 4.0 12.7 - - + -
101A GLY 3.6 19.3 - - - +
102A GLY 4.5 0.7 - - - +
105A ALA* 3.7 9.2 - - + -
107A ASP* 3.2 21.5 + - + +
108A ARG 3.2 0.6 - - - -
109A ASP* 1.3 92.0 + - - +
111A ARG* 1.3 58.8 + - - +
113A TYR* 3.3 7.2 + - + +
114A ALA* 2.9 27.9 + - - +
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Residues in contact with ARG 111 (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 GLY 3.4 20.2 - - - +
103A PHE* 3.2 23.3 - - - +
104A THR* 4.2 0.2 - - - +
105A ALA 2.8 43.9 + - - +
106A ASN* 2.9 22.2 + - - +
107A ASP 3.6 1.8 - - - +
108A ARG* 3.1 42.7 + - + +
110A VAL* 1.3 77.8 - - - +
112A ARG* 1.4 62.0 + - + +
114A ALA* 3.3 3.5 + - - +
115A LEU* 3.1 29.3 + - + +
156A ARG* 3.5 36.0 - - - +
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Residues in contact with ARG 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ARG* 3.1 59.4 + - + +
109A ASP* 3.7 10.5 - - - +
111A ARG* 1.4 75.1 - - + +
113A TYR* 1.3 64.7 + - - +
115A LEU* 3.2 13.1 + - + +
116A ARG* 3.0 28.7 + - + +
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Residues in contact with TYR 113 (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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60A PHE* 3.3 33.3 - + - -
97A VAL* 4.1 20.2 - - + -
98A PHE* 3.6 34.1 - + - -
109A ASP 3.1 17.5 + - - +
110A VAL* 3.6 6.5 - - - +
112A ARG* 1.3 72.0 - - - +
114A ALA* 1.3 65.7 + - - +
116A ARG* 3.1 9.5 + - + -
117A LYS* 2.9 39.0 + - + +
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Residues in contact with ALA 114 (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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92A LEU* 4.0 14.1 - - + +
98A PHE* 4.0 9.6 - - + -
102A GLY* 3.6 32.3 - - - -
103A PHE* 3.9 9.2 - - + -
110A VAL 2.9 17.8 + - - +
111A ARG 3.5 5.6 - - - +
113A TYR* 1.3 75.7 - - - +
115A LEU* 1.4 62.4 + - - +
117A LYS* 3.4 3.0 + - - +
118A THR* 3.0 27.4 + - - -
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Residues in contact with LEU 115 (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 PHE* 3.8 21.1 - - + -
111A ARG* 3.1 20.0 + - + +
112A ARG* 3.6 11.9 - - + +
114A ALA* 1.4 76.8 - - - +
116A ARG* 1.3 58.1 + - + +
118A THR* 3.3 2.2 + - - -
119A ILE* 2.9 41.5 + - + +
160A ALA* 3.8 26.5 - - + +
163A LEU* 3.7 31.0 - - + -
164A LEU* 3.8 25.1 - - + -
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Residues in contact with ARG 116 (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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112A ARG* 3.0 20.2 + - + +
113A TYR* 3.7 11.7 - - + +
115A LEU* 1.3 77.1 - - + +
117A LYS* 1.3 62.8 + - - +
119A ILE* 3.4 15.2 + - - +
120A ARG* 3.0 24.8 + - - +
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Residues in contact with LYS 117 (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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54A ASP* 2.8 32.2 + - - +
55A ASP* 2.8 31.3 + - - -
60A PHE* 4.0 22.4 - - - -
90A THR* 4.0 4.5 - - + +
91A ASN 2.9 22.5 + - - +
92A LEU* 4.1 2.2 - - + -
95A HIS* 6.1 0.4 - - - -
98A PHE* 3.9 26.2 - - + -
113A TYR* 2.9 30.8 + - + +
114A ALA 3.7 4.5 - - - +
116A ARG* 1.3 76.6 - - - +
118A THR* 1.3 63.0 + - - +
120A ARG* 3.5 7.9 + - - +
121A ASN* 3.3 20.4 + - - +
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Residues in contact with THR 118 (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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90A THR* 3.4 27.1 + - - +
92A LEU* 3.6 16.5 - - - +
103A PHE* 3.7 9.1 - - + -
114A ALA 3.0 18.1 + - - -
115A LEU 3.6 4.5 - - - -
117A LYS* 1.3 77.8 - - - +
119A ILE* 1.3 58.4 + - - +
121A ASN* 3.0 4.7 + - - +
122A ILE* 2.9 43.4 + - + +
133A TYR* 3.9 9.5 + - + -
164A LEU* 3.9 22.0 - - + -
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Residues in contact with ILE 119 (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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115A LEU* 2.9 29.0 + - + +
116A ARG* 3.4 16.4 + - - +
118A THR* 1.3 73.4 - - - +
120A ARG* 1.3 65.3 + - - +
122A ILE* 3.2 17.5 + - - +
123A ASP* 3.2 15.9 + - - +
163A LEU* 5.7 3.1 - - + +
164A LEU* 3.7 23.8 - - + -
167A TYR* 3.6 50.3 - - + +
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Residues in contact with ARG 120 (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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62A SER 5.4 6.3 + - - -
64A ASP* 3.6 20.8 + - - -
67A ARG* 3.4 58.8 + - - +
116A ARG 3.0 17.9 + - - +
117A LYS* 3.7 7.6 - - - +
118A THR 3.3 0.2 - - - -
119A ILE* 1.3 79.1 - - - +
121A ASN* 1.3 60.6 + - - +
123A ASP* 3.4 16.1 + - - +
124A LEU 3.5 7.8 + - - -
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Residues in contact with ASN 121 (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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52A PHE* 3.5 23.3 - - - -
54A ASP* 3.4 30.6 - - + +
58A ILE* 5.4 0.2 - - - +
67A ARG* 5.0 2.5 + - - +
88A ALA* 4.3 1.0 - - - +
89A THR 2.9 29.9 + - - +
90A THR* 4.8 0.4 - - - +
117A LYS 3.3 9.0 + - - +
118A THR 3.0 4.7 + - - +
120A ARG* 1.3 79.3 - - - +
122A ILE* 1.3 58.7 + - - +
124A LEU* 3.2 14.4 + - - +
125A ALA* 2.8 28.8 + - - +
133A TYR* 3.0 22.5 + - - +
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Residues in contact with ILE 122 (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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118A THR* 2.9 31.6 + - + +
119A ILE* 3.2 12.8 + - + +
121A ASN* 1.3 74.6 - - - +
123A ASP* 1.3 65.3 + - - +
125A ALA* 3.2 1.0 + - - +
126A VAL* 2.9 28.2 + - + +
133A TYR* 3.9 28.5 - - + -
164A LEU* 4.1 12.3 - - + -
167A TYR* 4.5 5.4 - - + -
168A VAL* 4.0 16.8 - - + -
173A TYR* 4.0 22.7 - - + -
175A ILE* 4.6 7.4 - - + -
177A PHE* 3.8 28.5 - - + -
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Residues in contact with ASP 123 (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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119A ILE* 3.2 12.0 + - - +
120A ARG* 3.6 11.6 - - - +
121A ASN 3.2 0.2 - - - -
122A ILE* 1.3 79.2 - - - +
124A LEU* 1.3 61.3 + - - +
126A VAL* 3.5 3.1 + - - +
127A GLU* 3.2 21.0 + - - +
167A TYR* 2.6 31.4 + - - -
173A TYR* 2.6 31.8 + - - +
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Residues in contact with LEU 124 (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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52A PHE* 4.1 12.1 - - + -
57A LEU* 4.1 5.4 - - + -
58A ILE* 3.8 27.6 - - + -
67A ARG* 4.1 9.6 - - - +
71A ILE* 3.9 29.8 - - + -
120A ARG 3.5 9.6 + - - +
121A ASN* 3.2 24.3 + - - +
123A ASP* 1.3 76.5 - - - +
125A ALA* 1.3 67.2 + - - +
127A GLU* 3.1 22.8 + - - +
128A LEU* 3.0 42.0 + - + +
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Residues in contact with ALA 125 (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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52A PHE* 4.6 6.2 - - + -
88A ALA* 3.8 27.8 - - + -
121A ASN 2.8 20.6 + - - +
122A ILE* 3.5 4.7 - - - +
124A LEU* 1.3 72.3 - - - +
126A VAL* 1.3 64.1 + - - +
128A LEU* 3.2 4.2 + - - +
129A GLY 3.1 5.5 + - - -
130A ALA* 2.9 34.2 + - + +
133A TYR* 3.9 15.7 - - + -
175A ILE* 4.3 3.4 - - + -
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Residues in contact with VAL 126 (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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122A ILE* 2.9 20.7 + - + +
123A ASP 3.7 5.2 - - - +
125A ALA* 1.3 75.9 - - - +
127A GLU* 1.3 65.5 + - - +
129A GLY* 3.1 13.7 + - - -
130A ALA 4.5 7.4 - - - +
131A LYS* 5.9 0.2 + - - -
173A TYR* 3.7 49.8 - - + -
174A ASP 6.1 0.2 - - - +
175A ILE* 3.8 25.4 - - + +
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Residues in contact with GLU 127 (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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71A ILE* 5.6 0.2 - - - +
75A ARG* 2.9 33.8 + - - +
123A ASP 3.2 10.0 + - - +
124A LEU* 3.1 27.3 + - - +
126A VAL* 1.3 82.2 - - - +
128A LEU* 1.3 63.2 + - + +
129A GLY 3.6 0.5 + - - -
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Residues in contact with LEU 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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52A PHE* 3.8 31.2 - - + -
57A LEU* 4.5 3.1 - - + -
71A ILE* 5.0 6.1 - - + -
74A PHE* 4.1 20.2 - - + -
75A ARG* 4.4 34.3 - - + +
78A LEU* 4.7 10.9 - - + +
85A VAL* 3.9 30.1 + - + +
124A LEU* 3.0 34.7 + - + +
125A ALA* 3.9 4.0 - - - +
127A GLU* 1.3 80.3 - - + +
129A GLY* 1.3 57.5 + - - +
130A ALA 3.7 0.7 - - - -
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Residues in contact with GLY 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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85A VAL 3.3 8.7 - - - +
86A PRO* 4.6 2.1 - - - +
125A ALA 3.1 2.2 + - - -
126A VAL 3.1 11.1 + - - -
127A GLU 3.3 1.2 - - - -
128A LEU* 1.3 78.1 - - - +
130A ALA* 1.3 68.3 + - - +
131A LYS* 3.3 25.9 + - - +
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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
------------------------------------------------------------
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