Contacts of the helix formed by residues 101 - 120 (chain A) in PDB entry 1O9H
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 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A ALA* 3.2 13.1 + - - +
99A LEU 3.1 3.2 - - - +
100A LEU* 1.3 80.1 - - - +
102A PRO* 1.3 75.3 - - - +
103A ALA* 3.0 8.8 + - - +
104A GLY* 3.0 17.3 + - - -
105A LEU* 3.2 9.2 + - - +
138A LEU* 3.6 4.7 - - - -
144A ALA* 3.8 13.0 - - - -
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Residues in contact with PRO 102 (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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101A SER* 1.3 85.8 - - - +
103A ALA* 1.3 56.5 + - - +
105A LEU* 3.5 2.7 + - + +
106A THR* 2.9 30.5 + - - -
135A ARG* 3.3 23.1 - - + -
138A LEU* 3.5 18.8 - - + -
139A THR* 3.8 20.2 - - - +
143A GLY* 4.6 3.4 - - - -
144A ALA* 3.6 22.4 - - + +
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Residues in contact with ALA 103 (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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101A SER* 3.1 7.5 + - - +
102A PRO* 1.3 77.9 - - - +
104A GLY* 1.3 65.8 + - - +
106A THR* 3.3 8.9 + - - -
107A ALA* 3.2 21.8 + - - +
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Residues in contact with GLY 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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98A ALA* 3.2 26.7 - - - -
99A LEU* 3.6 14.5 - - - +
101A SER* 3.0 9.5 + - - -
103A ALA* 1.3 77.0 - - - +
105A LEU* 1.3 62.4 + - - +
107A ALA* 3.4 6.8 + - - +
108A ARG* 3.1 17.7 + - - +
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Residues in contact with LEU 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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21A VAL* 4.1 18.2 - - + -
71A LEU* 4.3 7.4 - - + -
99A LEU* 3.4 45.5 - - + +
101A SER 3.2 5.0 + - - +
102A PRO 3.7 7.0 - - - +
103A ALA 3.3 0.4 - - - -
104A GLY* 1.3 76.8 - - - +
106A THR* 1.3 58.2 + - - +
108A ARG* 3.8 0.8 - - - +
109A GLU* 3.0 28.2 + - - +
131A ALA* 3.8 16.2 - - - +
134A LEU* 4.0 13.5 - - + +
135A ARG* 3.5 40.6 - - + +
138A LEU* 4.0 15.7 - - + -
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Residues in contact with THR 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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102A PRO 2.9 14.1 + - - -
103A ALA* 3.6 10.4 - - - +
104A GLY 3.1 0.6 - - - -
105A LEU* 1.3 75.6 - - - +
107A ALA* 1.3 60.9 - - - +
109A GLU* 3.3 7.7 + - + +
110A LEU* 2.9 30.8 + - + +
135A ARG* 2.8 34.0 + - - +
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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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103A ALA 3.2 16.1 + - - +
104A GLY* 3.9 6.7 - - - +
106A THR* 1.3 75.8 - - - +
108A ARG* 1.3 59.2 + - - +
110A LEU* 3.8 9.1 - - - +
111A GLU* 2.9 29.3 + - - +
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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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19A GLY* 4.6 1.8 + - - -
21A VAL* 2.7 51.8 + - + +
22A LEU 4.0 5.1 + - - -
23A HIS* 3.5 37.9 + - - +
99A LEU* 3.9 11.4 - - + -
104A GLY 3.1 16.2 + - - +
105A LEU* 3.8 5.8 - - - +
107A ALA* 1.3 73.5 - - - +
109A GLU* 1.3 66.2 + - - +
111A GLU* 2.7 43.3 + - - +
112A ARG* 3.1 66.9 + - + +
115A GLN* 5.6 0.2 - - - +
131A ALA* 4.7 2.7 - - + -
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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 LEU 3.0 18.4 + - - +
106A THR* 3.4 7.6 - - - +
108A ARG* 1.3 77.1 - - - +
110A LEU* 1.3 61.1 + - - +
112A ARG* 3.3 5.4 + - - +
113A ARG* 3.2 53.7 + - - +
128A ALA* 3.4 21.6 - - - +
131A ALA* 3.8 10.7 - - + +
132A ARG* 3.3 22.0 - - - +
135A ARG* 2.7 31.8 + - - -
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Residues in contact with LEU 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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106A THR* 2.9 19.5 + - + +
107A ALA* 4.0 7.6 - - - +
109A GLU* 1.3 74.7 - - - +
111A GLU* 1.3 64.7 + - - +
113A ARG* 3.4 13.5 + - + +
114A GLU* 3.2 42.9 + - + +
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Residues in contact with GLU 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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23A HIS* 4.9 2.8 + - - -
107A ALA 2.9 17.3 + - - +
108A ARG* 2.7 44.3 + - - +
109A GLU 3.3 0.2 - - - -
110A LEU* 1.3 78.7 - - - +
112A ARG* 1.3 60.9 + - - +
114A GLU* 3.4 16.3 + - - +
115A GLN* 3.2 41.1 + - + +
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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
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19A GLY 2.8 28.9 + - - -
20A VAL 2.9 19.8 + - - +
21A VAL* 6.2 0.4 - - + -
108A ARG* 3.1 52.9 + - + +
109A GLU* 3.6 7.6 - - - +
111A GLU* 1.3 75.3 - - - +
113A ARG* 1.3 59.7 + - - +
115A GLN* 3.1 29.1 + - - +
116A SER* 3.0 28.2 + - - -
124A TYR* 3.4 36.6 - - - +
127A ALA* 3.6 22.7 - - + +
128A ALA* 3.9 9.6 - - + +
131A ALA* 6.0 0.4 - - + -
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Residues in contact with ARG 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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109A GLU* 3.2 44.6 + - - +
110A LEU* 3.7 17.9 - - + +
111A GLU 3.3 0.6 - - - -
112A ARG* 1.3 75.5 - - - +
114A GLU* 1.3 64.4 - - - +
116A SER* 3.6 7.6 - - - -
117A GLU* 3.2 28.2 + - - +
125A LEU* 3.8 25.7 - - + +
128A ALA* 3.8 22.8 + - + +
129A GLN* 4.6 5.1 - - - +
132A ARG* 4.8 10.9 - - - +
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Residues in contact with GLU 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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110A LEU* 3.2 41.2 + - + +
111A GLU* 3.4 15.8 + - - +
112A ARG 3.3 0.2 - - - -
113A ARG* 1.3 76.7 - - - +
115A GLN* 1.3 59.7 + - + +
117A GLU* 3.3 6.5 + - - +
118A ARG* 3.0 29.7 + - - +
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Residues in contact with GLN 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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108A ARG* 5.6 0.2 - - - +
111A GLU* 3.2 30.6 + - + +
112A ARG* 3.1 47.7 + - - +
114A GLU* 1.3 75.8 - - + +
116A SER* 1.3 59.6 + - - +
118A ARG* 4.3 2.9 - - - +
119A PHE* 2.9 51.3 + - + +
124A TYR* 3.7 23.8 + - + -
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Residues in contact with SER 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 18.4 + - - -
113A ARG* 3.6 9.9 - - - -
115A GLN* 1.3 76.9 - - - +
117A GLU* 1.3 64.0 + - - +
120A GLY* 2.7 29.6 + - - +
121A LYS 4.5 4.1 + - - -
124A TYR* 3.6 21.9 - - - +
125A LEU* 3.6 29.7 - - - +
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Residues in contact with GLU 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 ARG 3.2 15.6 + - - +
114A GLU* 3.3 9.8 + - - +
116A SER* 1.3 85.7 + - - +
118A ARG* 1.3 66.3 + - - +
119A PHE 3.4 0.3 + - - -
120A GLY* 4.1 2.6 + - - -
125A LEU* 6.0 0.9 - - - +
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Residues in contact with ARG 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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114A GLU 3.0 17.7 + - - +
115A GLN* 3.8 5.8 - - - +
117A GLU* 1.3 78.6 - - - +
119A PHE* 1.3 96.7 + - + +
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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 GLN* 2.9 40.0 + - + +
118A ARG* 1.3 126.8 - - + +
120A GLY* 1.3 59.4 + - - +
121A LYS* 3.1 9.4 + - + +
124A TYR* 3.8 31.4 - + + -
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Residues in contact with GLY 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 SER* 2.7 25.2 + - - -
117A GLU 4.1 2.7 + - - -
118A ARG 3.8 0.6 - - - -
119A PHE* 1.3 72.3 - - - +
121A LYS* 1.3 64.7 + - - +
122A PRO* 3.3 8.8 - - - +
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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