Contacts of the helix formed by residues 121 - 141 (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 LYS 121 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A SER* 4.5 5.0 + - - -
119A PHE* 3.1 7.2 + - + +
120A GLY* 1.3 76.5 - - - +
122A PRO* 1.3 76.2 - - + +
123A SER* 3.0 28.9 + - - +
124A TYR* 3.3 50.6 + - + +
125A LEU* 4.3 2.8 + - - +
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Residues in contact with PRO 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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120A GLY 3.5 7.9 - - - +
121A LYS* 1.3 90.2 - - + +
123A SER* 1.3 62.6 + - - +
125A LEU* 3.3 21.7 + - + +
126A GLU* 3.4 18.3 + - - +
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Residues in contact with SER 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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121A LYS* 3.0 36.4 - - - +
122A PRO* 1.3 79.0 - - - +
124A TYR* 1.3 63.5 + - - +
125A LEU 3.3 0.2 - - - -
126A GLU* 3.4 18.1 + - - +
127A ALA* 3.0 27.5 + - - +
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Residues in contact with TYR 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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112A ARG* 3.4 45.1 - - - +
115A GLN* 3.7 41.8 + - + -
116A SER* 3.6 10.1 - - - -
119A PHE* 3.8 31.9 - + + -
121A LYS* 3.3 52.1 - - + +
122A PRO 3.2 0.4 - - - -
123A SER* 1.3 82.3 + - - +
125A LEU* 1.3 55.8 + - - +
127A ALA* 3.4 3.8 - - + +
128A ALA* 3.1 20.3 + - - +
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Residues in contact with LEU 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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113A ARG* 3.8 27.8 + - + +
116A SER* 3.6 22.9 - - - +
117A GLU* 6.0 0.7 - - - +
121A LYS 4.3 1.3 + - - +
122A PRO* 3.3 14.7 + - + +
124A TYR* 1.3 76.2 - - - +
126A GLU* 1.3 66.6 + - + +
127A ALA 3.1 1.3 - - - -
128A ALA* 3.2 4.6 + - + +
129A GLN* 3.0 28.6 + - - +
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Residues in contact with GLU 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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20A VAL* 5.1 2.5 - - + -
122A PRO* 3.4 10.5 + - - +
123A SER* 3.4 23.7 + - - +
125A LEU* 1.3 77.6 - - - +
127A ALA* 1.3 64.1 + - - +
129A GLN* 3.1 23.5 - - - +
130A ALA* 3.0 22.7 + - - +
133A ARG* 4.5 1.4 + - - -
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Residues in contact with ALA 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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20A VAL* 3.6 35.6 - - + +
21A VAL* 3.8 5.4 - - - +
112A ARG* 3.6 24.2 - - + +
123A SER 3.0 13.6 + - - +
124A TYR* 3.4 11.4 - - + +
125A LEU 3.1 0.2 - - - -
126A GLU* 1.3 77.8 - - - +
128A ALA* 1.3 62.3 + - - +
130A ALA* 3.0 5.0 + - - +
131A ALA* 3.0 20.6 + - - +
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Residues in contact with ALA 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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109A GLU* 3.4 22.4 - - + +
112A ARG* 3.9 17.7 - - + +
113A ARG* 3.8 31.6 - - + +
124A TYR 3.1 14.5 + - - +
125A LEU* 3.2 10.5 + - + +
127A ALA* 1.3 75.6 - - - +
129A GLN* 1.3 64.0 + - - +
131A ALA* 3.3 3.4 + - - +
132A ARG* 3.2 18.4 + - - +
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Residues in contact with GLN 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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113A ARG* 4.6 4.4 - - - +
125A LEU* 3.0 14.4 + - - +
126A GLU* 3.1 37.8 - - - +
128A ALA* 1.3 76.9 - - - +
130A ALA* 1.3 56.5 + - - +
132A ARG* 3.3 21.4 + - - +
133A ARG* 3.0 62.9 + - - +
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Residues in contact with ALA 130 (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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15A ASP* 3.5 27.5 - - + +
20A VAL* 4.3 4.5 - - + -
21A VAL* 3.7 16.4 - - + -
126A GLU 3.0 14.8 + - - +
127A ALA* 3.1 12.8 - - - +
129A GLN* 1.3 77.3 - - - +
131A ALA* 1.3 56.4 + - - +
133A ARG* 3.3 14.3 + - - +
134A LEU* 3.0 32.1 + - - +
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Residues in contact with ALA 131 (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* 3.7 25.7 - - + +
105A LEU* 3.8 25.5 - - + +
108A ARG* 4.7 2.2 - - + -
109A GLU* 3.8 16.6 - - + +
112A ARG* 6.0 0.7 - - + -
127A ALA 3.0 11.6 + - - +
128A ALA* 3.7 7.6 - - - +
129A GLN 3.3 0.2 - - - -
130A ALA* 1.3 75.9 - - - +
132A ARG* 1.3 60.5 + - - +
134A LEU* 3.4 5.0 + - - +
135A ARG* 3.0 25.1 + - - +
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Residues in contact with ARG 132 (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* 3.3 23.9 + - - +
113A ARG* 4.8 10.3 - - - +
128A ALA 3.2 8.6 + - - +
129A GLN* 3.5 21.7 + - - +
131A ALA* 1.3 78.8 - - - +
133A ARG* 1.3 82.3 + - - +
135A ARG* 3.4 14.8 + - - +
136A GLU* 2.8 77.5 + - + +
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Residues in contact with ARG 133 (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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12A ASP* 4.9 4.9 + - - -
14A SER* 5.5 0.2 + - - -
15A ASP* 2.9 43.6 + - - +
126A GLU 4.5 1.0 + - - -
129A GLN* 3.0 59.1 + - - +
130A ALA* 3.5 13.7 - - - +
132A ARG* 1.3 93.2 - - - +
134A LEU* 1.3 59.3 + - - +
136A GLU* 3.4 10.4 + - - +
137A ARG* 3.0 38.8 + - - +
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Residues in contact with LEU 134 (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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15A ASP* 3.9 30.3 - - + +
16A LEU* 3.7 29.2 - - + -
21A VAL* 4.1 24.5 - - + -
22A LEU* 4.7 1.3 - - + -
71A LEU* 4.5 24.1 - - + +
105A LEU* 4.0 11.1 - - + +
130A ALA 3.0 20.1 + - - +
131A ALA* 3.7 4.3 - - - +
132A ARG 3.3 0.2 - - - -
133A ARG* 1.3 78.3 - - - +
135A ARG* 1.3 50.6 + - - +
137A ARG* 3.5 26.8 + - - +
138A LEU* 2.8 32.9 + - - +
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Residues in contact with ARG 135 (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* 3.3 31.6 - - + +
105A LEU* 3.5 22.1 - - + +
106A THR* 2.8 25.0 + - - +
109A GLU* 2.7 34.2 + - - -
131A ALA 3.0 15.9 + - - +
132A ARG* 3.7 11.6 + - - +
133A ARG 3.2 0.2 - - - -
134A LEU* 1.3 74.4 - - - +
136A GLU* 1.3 71.6 + - - +
138A LEU* 3.6 3.8 - - - +
139A THR* 2.7 41.6 + - - +
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Residues in contact with GLU 136 (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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132A ARG* 2.8 54.9 + - + +
133A ARG* 3.7 10.2 - - - +
135A ARG* 1.3 85.5 + - - +
137A ARG* 1.3 63.5 + - - +
139A THR* 3.5 5.5 + - - -
140A ALA* 3.1 24.4 + - - +
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Residues in contact with ARG 137 (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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12A ASP* 5.8 2.6 + - - -
15A ASP* 4.2 14.1 + - - +
71A LEU 4.5 14.2 + - - +
72A LEU* 5.3 11.6 - - - +
133A ARG* 3.0 26.8 + - - +
134A LEU* 3.7 28.9 - - - +
136A GLU* 1.3 74.6 - - - +
138A LEU* 1.3 64.9 + - - +
140A ALA* 3.3 5.5 + - + +
141A GLU* 3.1 52.0 + - + +
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Residues in contact with LEU 138 (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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70A GLY 4.8 3.4 - - - +
71A LEU* 4.2 20.2 + - + -
74A ARG* 3.8 24.1 - - + +
99A LEU 4.2 0.7 - - - +
100A LEU* 3.5 23.8 - - + +
101A SER 3.6 4.0 - - - -
102A PRO* 3.5 36.8 - - + -
105A LEU* 4.0 11.4 - - + -
134A LEU 2.8 21.8 + - - +
135A ARG* 3.6 6.5 - - - +
137A ARG* 1.3 72.4 - - - +
139A THR* 1.3 61.1 + - - +
141A GLU* 3.3 5.3 + - - +
142A GLY 3.2 8.0 + - - -
143A GLY 2.8 37.5 + - - +
145A LEU* 4.9 1.6 - - + -
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Residues in contact with THR 139 (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* 3.8 20.0 - - + +
135A ARG* 2.7 23.8 + - - +
136A GLU* 3.7 7.4 - - - -
138A LEU* 1.3 77.0 - - - +
140A ALA* 1.3 62.0 + - - +
141A GLU 3.4 0.7 + - - -
142A GLY 3.5 9.4 + - - -
143A GLY* 3.5 14.0 + - - +
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Residues in contact with ALA 140 (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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136A GLU 3.1 18.1 + - - +
137A ARG* 3.3 6.0 + - - +
139A THR* 1.3 77.4 - - - +
141A GLU* 1.3 62.7 + - + +
142A GLY 3.4 0.8 + - - -
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Residues in contact with GLU 141 (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 LEU 5.0 1.3 - - - -
72A LEU 4.0 5.3 - - - +
74A ARG* 3.6 38.8 + - + +
75A ARG* 2.8 79.1 + - + +
137A ARG* 3.1 45.1 + - + +
138A LEU 3.3 1.5 + - - +
139A THR 3.2 0.2 - - - -
140A ALA* 1.3 79.7 - - + +
142A GLY* 1.3 56.2 + - - +
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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