Contacts of the helix formed by residues 125 - 141 (chain A) in PDB entry 2O1S
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 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A ASP* 3.3 1.3 + - - -
78A VAL 5.6 0.2 + - - -
118A LEU* 3.6 16.3 - - - +
120A VAL* 3.9 13.2 - - - +
122A HIS 4.1 10.9 + - - +
123A SER 3.5 13.7 - - - +
124A SER* 1.3 76.7 - - - +
126A SER* 1.3 66.8 + - - +
127A ILE 3.5 0.4 - - - -
128A SER 3.4 2.6 + - - -
129A ALA* 3.2 23.7 + - - +
159A MSE 3.9 14.6 - - - -
398A ARG* 4.1 6.7 - - - +
375B THR* 3.7 5.2 - - - +
405B HIS* 4.5 5.5 - - - +
406B ASP* 3.4 36.8 + - - +
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Residues in contact with SER 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ILE* 3.6 29.7 - - - +
77A ASP* 2.7 39.1 + - - +
118A LEU* 4.5 1.6 - - - -
120A VAL* 5.9 0.2 - - - -
125A THR* 1.3 80.9 + - - +
127A ILE* 1.3 68.1 + - - +
129A ALA* 4.0 1.0 - - - +
130A GLY* 2.8 28.2 + - - -
148A CYS* 3.4 16.5 - - - +
149A VAL 4.6 0.7 - - - -
150A ILE* 3.8 13.2 - - - +
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Residues in contact with ILE 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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124A SER 4.6 2.5 + - - +
125A THR 3.5 0.4 - - - -
126A SER* 1.3 82.2 + - - +
128A SER* 1.3 57.9 + - - +
130A GLY* 3.2 1.2 + - - -
131A ILE* 2.8 38.7 + - + +
148A CYS* 4.2 8.5 - - + -
150A ILE* 4.1 23.6 - - + -
155A ILE* 4.6 1.6 - - + -
160A ALA* 4.4 13.2 - - + +
163A ALA* 3.7 19.5 - - + -
164A MSE 3.8 34.3 - - + +
174A MSE 4.1 3.2 - - + +
176A VAL* 4.0 37.9 - - + -
248A PHE* 5.1 2.0 - - + -
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Residues in contact with SER 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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124A SER 4.6 2.5 + - - -
125A THR 3.4 3.6 + - - -
126A SER 3.3 0.6 - - - -
127A ILE* 1.3 75.3 - - - +
129A ALA* 1.3 66.8 + - - +
131A ILE* 3.1 13.5 + - - +
132A GLY 3.2 8.7 + - - -
159A MSE 3.8 17.6 + - - +
163A ALA* 3.4 9.6 - - - +
372B HIS* 3.0 36.3 - - - -
375B THR* 3.5 28.9 - - - -
376B PHE* 3.8 8.3 - - - -
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Residues in contact with ALA 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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75A ILE* 4.7 0.9 - - + -
118A LEU* 3.6 37.0 - - + -
125A THR 3.2 7.2 + - - +
126A SER 4.0 0.9 - - - +
128A SER* 1.3 77.7 - - - +
130A GLY* 1.3 59.2 + - - +
132A GLY* 3.0 4.0 + - - -
133A ILE* 2.8 39.2 + - + +
375B THR* 3.4 21.8 - - + +
378B ALA* 5.3 1.3 - - + -
379B GLY* 3.5 10.5 - - - +
382B ILE* 5.0 1.6 - - + -
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Residues in contact with GLY 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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75A ILE* 3.7 17.4 - - - +
126A SER 2.8 19.3 + - - -
127A ILE 3.4 2.0 - - - -
128A SER 3.0 0.2 - - - -
129A ALA* 1.3 77.0 - - - +
131A ILE* 1.3 55.8 + - - +
133A ILE* 3.2 4.6 + - - +
134A ALA* 2.8 29.6 + - - +
146A THR* 3.7 5.0 - - - +
148A CYS* 3.9 10.5 - - - -
174A MSE 3.8 6.7 - - - -
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Residues in contact with ILE 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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127A ILE* 2.8 23.7 + - + +
128A SER 3.1 5.8 + - - +
130A GLY* 1.3 71.9 - - - +
132A GLY* 1.3 57.3 + - - +
134A ALA* 3.3 2.8 + - - +
135A VAL* 2.9 28.9 + - - +
163A ALA* 3.0 37.0 - - + +
166A HIS* 4.1 3.4 - - - +
167A ALA* 3.5 15.9 - - + +
170A ILE* 3.8 23.8 - - + -
172A PRO* 4.0 6.3 - - + -
174A MSE 3.7 22.9 - - - -
372B HIS* 3.8 12.6 - - + +
376B PHE* 3.7 19.5 - - + -
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Residues in contact with GLY 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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128A SER 3.2 4.8 + - - -
129A ALA 3.0 8.0 + - - -
131A ILE* 1.3 79.0 - - - +
133A ILE* 1.3 60.5 + - - +
135A VAL 3.5 0.2 + - - -
136A ALA* 3.2 20.1 + - - +
376B PHE* 3.5 35.8 - - - -
379B GLY 3.6 8.4 - - - +
380B LEU* 3.6 14.6 - - - +
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Residues in contact with ILE 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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73A GLN* 3.7 30.5 - - + +
75A ILE* 3.4 29.6 - - + -
117A VAL* 3.4 23.1 - - + -
118A LEU* 5.8 0.4 - - + -
129A ALA* 2.8 16.6 + - + +
130A GLY* 3.5 7.4 - - - +
132A GLY* 1.3 75.2 - - - +
134A ALA* 1.3 59.8 + - - +
136A ALA* 3.3 5.0 + - - +
137A ALA* 3.0 26.0 + - - +
144A ARG* 5.4 3.3 - - - -
146A THR* 3.8 13.7 - - + +
379B GLY* 3.6 16.8 - - - +
382B ILE* 4.1 19.1 - - + -
383B GLY* 5.0 3.8 - - - +
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Residues in contact with ALA 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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130A GLY 2.8 19.0 + - - +
131A ILE* 3.3 2.4 + - - +
133A ILE* 1.3 70.8 - - - +
135A VAL* 1.3 65.7 + - - +
137A ALA* 3.3 3.9 + - - +
138A GLU* 3.0 24.6 + - - +
146A THR* 3.5 16.4 - - - +
172A PRO* 3.9 19.9 - - + +
173A ASP 3.5 25.7 + - - +
174A MSE 4.1 5.4 - - + -
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Residues in contact with VAL 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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131A ILE* 2.9 22.5 + - + +
132A GLY 3.8 4.9 - - - +
134A ALA* 1.3 77.0 - - - +
136A ALA* 1.3 63.6 + - - +
138A GLU* 3.3 8.4 + - - +
139A LYS* 3.1 36.2 + - + +
170A ILE* 3.8 28.0 - - + -
172A PRO* 4.7 6.5 - - + -
364B PHE* 3.9 26.5 - - + -
376B PHE* 4.1 9.6 - - + -
380B LEU* 3.9 13.9 - - + -
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Residues in contact with ALA 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 GLY 3.2 14.0 + - - +
133A ILE 3.7 4.0 - - - +
135A VAL* 1.3 82.3 - - - +
137A ALA* 1.3 56.7 + - - +
139A LYS* 3.3 4.3 + - - +
140A GLU* 2.9 29.6 + - - +
380B LEU* 4.6 4.3 - - + +
383B GLY* 3.7 26.1 - - - +
385B TYR* 3.5 35.3 - - + -
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Residues in contact with ALA 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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133A ILE* 3.0 17.4 + - + +
134A ALA* 3.6 9.2 - - - +
135A VAL 3.2 0.2 - - - -
136A ALA* 1.3 77.1 - - - +
138A GLU* 1.3 62.2 + - - +
140A GLU* 3.2 14.3 + - - +
141A GLY* 3.1 18.4 + - - -
142A LYS 4.3 3.3 + - - -
143A ASN* 4.9 1.0 + - - -
144A ARG* 3.5 45.6 + - + +
146A THR* 4.5 3.4 - - - +
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Residues in contact with GLU 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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134A ALA 3.0 17.0 + - - +
135A VAL* 3.6 7.8 - - - +
137A ALA* 1.3 75.7 - - - +
139A LYS* 1.3 81.0 + - - +
141A GLY* 3.5 11.7 + - - -
172A PRO* 6.5 1.3 - - + -
173A ASP* 5.5 12.3 - - + +
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Residues in contact with LYS 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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135A VAL* 3.1 32.2 + - + +
136A ALA* 3.3 4.7 + - - +
138A GLU* 1.3 87.4 + - - +
140A GLU* 1.3 64.6 + - - +
141A GLY* 3.5 0.5 + - - -
340B MSE 4.0 27.8 - - + +
361B ASP* 3.0 39.6 + - - +
364B PHE* 4.3 6.4 - - - -
380B LEU* 6.1 0.4 - - + -
385B TYR* 3.2 27.0 + - + +
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Residues in contact with GLU 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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71A PHE* 4.7 2.1 - - - -
136A ALA 2.9 13.5 + - - +
137A ALA* 3.3 10.6 - - - +
139A LYS* 1.3 78.7 - - - +
141A GLY* 1.3 61.2 + - - +
142A LYS* 3.7 32.2 - - + +
144A ARG* 3.1 46.8 + - - +
385B TYR* 3.9 6.3 + - + +
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Residues in contact with GLY 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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137A ALA 3.1 8.9 + - - -
138A GLU* 3.5 9.3 + - - -
139A LYS 3.3 3.3 - - - -
140A GLU* 1.3 77.7 - - - +
142A LYS* 1.3 66.5 + - - +
143A ASN 3.4 3.5 + - - -
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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