Contacts of the helix formed by residues 103 - 120 (chain A) in PDB entry 2IMT
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 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A GLN* 2.8 11.2 + - + +
102A PRO* 1.3 79.0 - - - +
104A ALA* 1.3 55.6 - - - +
105A GLU* 3.5 7.0 + - - +
106A ASN* 2.5 39.1 + - - +
107A ALA* 2.8 35.3 + - - +
147A LEU* 4.4 6.2 - - - +
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Residues in contact with ALA 104 (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 THR* 1.3 74.7 - - - +
105A GLU* 1.4 58.0 + - - +
107A ALA* 3.4 2.3 + - - +
108A TYR* 2.9 30.8 + - - +
147A LEU* 4.6 4.1 - - + +
150A PHE* 3.7 31.0 - - + -
153A GLN* 5.9 0.9 - - + -
157A PHE* 4.2 3.6 - - + -
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Residues in contact with GLU 105 (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 THR* 3.2 7.4 + - - +
104A ALA* 1.4 76.6 - - - +
106A ASN* 1.3 60.9 + - - +
108A TYR* 3.4 15.2 + - - +
109A GLU* 2.9 58.9 + - - +
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Residues in contact with ASN 106 (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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100A LEU* 3.4 10.7 - - + +
101A GLN* 3.1 43.8 - - + +
103A THR* 2.5 28.2 + - - +
105A GLU* 1.3 74.8 - - - +
107A ALA* 1.3 64.2 + - - +
109A GLU* 3.4 14.9 + - - +
110A TYR* 2.9 27.9 + - - +
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Residues in contact with ALA 107 (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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100A LEU* 3.7 9.8 - - + +
103A THR 2.8 18.3 + - - +
104A ALA 3.5 5.2 - - - +
105A GLU 3.2 0.2 - - - -
106A ASN* 1.3 78.1 - - - +
108A TYR* 1.3 58.0 + - - +
110A TYR* 3.8 1.4 - - - +
111A PHE* 2.8 31.0 + - - +
138A LEU* 4.0 18.7 - - + +
142A VAL* 4.6 7.9 - - + -
150A PHE* 3.8 26.7 - - + -
157A PHE* 4.0 4.3 - - + -
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Residues in contact with TYR 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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104A ALA 2.9 17.5 + - - +
105A GLU* 3.7 21.3 - - - +
107A ALA* 1.3 76.2 - - - +
109A GLU* 1.3 70.6 + - + +
111A PHE* 3.3 4.3 + + - +
112A THR* 2.9 56.6 + - + +
157A PHE* 3.6 37.9 - + + -
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Residues in contact with GLU 109 (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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105A GLU* 2.9 49.6 + - - +
106A ASN* 3.8 14.3 - - - +
108A TYR* 1.3 84.4 - - + +
110A TYR* 1.3 60.9 + - - +
112A THR* 3.9 3.0 - - - -
113A LYS* 3.1 39.5 + - - +
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Residues in contact with TYR 110 (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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96A MET* 3.2 40.8 + - + +
97A LEU* 3.6 35.9 - - + -
99A HIS* 3.3 30.7 - + - -
100A LEU* 3.9 17.3 - - + -
106A ASN 2.9 16.9 + - - +
107A ALA 3.9 2.9 - - - +
109A GLU* 1.3 72.1 - - - +
111A PHE* 1.3 65.8 + - - +
113A LYS* 3.4 25.1 + - - +
114A ILE* 3.1 52.2 + - + +
134A PHE* 3.7 11.0 - + - -
138A LEU* 5.3 0.4 - - + -
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Residues in contact with PHE 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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107A ALA 2.8 19.2 + - - +
108A TYR* 3.6 6.1 - + - +
110A TYR* 1.3 76.6 - - - +
112A THR* 1.3 68.8 + - - +
114A ILE* 3.5 0.3 + - - -
115A ALA* 2.9 38.3 + - + +
131A LEU* 4.0 24.7 - - + -
134A PHE* 3.6 26.1 - + - -
135A GLY* 5.0 4.0 - - - -
138A LEU* 4.0 17.7 - - + +
154A VAL* 5.4 0.9 - - + -
157A PHE* 3.5 50.9 - + + -
158A VAL* 3.8 25.6 - - + -
161A PHE* 3.8 18.2 - + + -
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Residues in contact with THR 112 (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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108A TYR* 2.9 51.1 + - + +
109A GLU* 3.9 5.2 - - - -
111A PHE* 1.3 86.5 - - - +
113A LYS* 1.3 57.7 + - + +
115A ALA* 4.6 2.0 - - - -
116A THR* 2.5 44.9 + - - +
161A PHE* 5.2 6.7 - - + -
165A HIS* 5.9 2.9 - - + +
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Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A HIS* 5.7 1.4 + - - -
109A GLU* 3.1 33.5 + - - +
110A TYR* 3.7 28.0 - - - +
112A THR* 1.3 81.9 - - + +
114A ILE* 1.3 68.7 + - + +
116A THR* 3.8 3.9 - - - -
117A SER* 3.1 22.9 + - - -
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Residues in contact with ILE 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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93A PHE* 3.9 28.7 - - + -
96A MET* 3.5 24.9 - - + -
110A TYR* 3.1 47.5 + - + +
113A LYS* 1.3 80.5 - - + +
115A ALA* 1.3 60.9 + - - +
117A SER* 3.2 9.1 + - - -
118A LEU* 2.9 32.6 + - + +
134A PHE* 3.7 20.6 - - + -
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Residues in contact with ALA 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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111A PHE* 2.9 26.0 + - + +
114A ILE* 1.3 76.0 - - - +
116A THR* 1.3 63.8 + - - +
118A LEU* 3.2 12.9 + - - -
119A PHE* 3.2 21.7 - - - -
131A LEU* 3.7 29.4 - - + -
134A PHE* 4.9 1.1 - - + -
161A PHE* 3.6 28.4 - - + -
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Residues in contact with THR 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 THR* 2.5 32.1 + - - +
113A LYS* 3.8 4.5 - - - -
115A ALA* 1.3 76.1 - - - +
117A SER* 1.3 61.8 + - - +
119A PHE* 3.2 4.0 + - - +
120A GLU* 3.1 24.9 + - + +
161A PHE* 3.8 17.5 - - - -
165A HIS* 4.2 12.1 + - + +
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Residues in contact with SER 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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113A LYS 3.1 17.8 + - - -
114A ILE* 3.2 11.6 + - - -
116A THR* 1.3 77.2 - - - +
118A LEU* 1.3 62.8 + - - +
119A PHE 3.2 0.7 + - - -
120A GLU* 3.4 27.2 + - - +
121A SER 5.0 0.3 + - - -
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Residues in contact with LEU 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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89A TYR* 3.7 34.8 - - + +
93A PHE* 4.2 12.6 - - + -
114A ILE* 2.9 21.1 + - + +
115A ALA* 3.2 9.8 + - - +
117A SER* 1.3 75.9 - - - +
119A PHE* 1.3 69.8 + - + +
121A SER 5.0 0.5 + - - -
122A GLY 4.1 0.2 - - - +
127A ARG* 3.3 32.8 + - + +
130A ALA* 3.9 14.4 - - + +
131A LEU* 3.6 46.9 - - + +
134A PHE* 4.8 2.9 - - + -
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Residues in contact with PHE 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 ALA 3.2 22.0 - - - +
116A THR* 3.2 5.8 + - - +
117A SER 3.2 0.4 - - - -
118A LEU* 1.3 83.4 - - + +
120A GLU* 1.3 66.1 + - - +
121A SER 3.1 3.6 - - - -
122A GLY* 2.9 31.0 + - - +
123A ILE* 3.8 32.5 - - + +
127A ARG* 3.4 41.3 - - + -
128A VAL* 3.9 9.9 - - + -
131A LEU* 3.9 26.5 - - + -
161A PHE* 3.7 15.5 - + + -
165A HIS* 6.0 3.8 - - + +
167A ILE* 3.8 22.9 - - + -
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Residues in contact with GLU 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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116A THR* 3.1 13.7 + - + +
117A SER* 3.4 25.4 + - - +
119A PHE* 1.3 79.1 - - - +
121A SER* 1.3 61.3 + - - +
122A GLY 3.6 0.7 + - - -
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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