Contacts of the helix formed by residues 125 - 141 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77C ASP* 3.2 1.3 + - - -
118C LEU* 4.1 7.0 - - - +
120C VAL* 3.8 21.8 - - - +
122C HIS 4.4 6.2 + - - +
123C SER 3.6 14.6 - - - +
124C SER* 1.3 78.8 - - - +
126C SER* 1.3 66.8 + - - +
127C ILE 3.5 0.9 - - - -
128C SER* 3.4 4.8 + - - -
129C ALA* 3.2 23.8 + - - +
159C MSE 3.7 16.8 - - - -
398C ARG* 4.0 7.2 - - - +
375D THR* 3.8 3.5 - - - +
405D HIS* 4.4 7.8 + - + -
406D ASP* 3.3 35.6 + - - +
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Residues in contact with SER 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ILE* 3.8 27.7 - - - +
77C ASP* 2.8 39.9 + - - +
118C LEU* 5.6 0.4 - - - -
125C THR* 1.3 81.6 + - - +
127C ILE* 1.3 67.3 + - - +
129C ALA* 3.5 2.9 + - - +
130C GLY* 2.7 33.6 + - - -
148C CYS* 3.5 16.1 - - - +
149C VAL 4.5 1.3 - - - -
150C ILE* 3.8 7.6 - - - +
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Residues in contact with ILE 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C SER 4.9 2.1 + - - +
125C THR 3.5 0.6 - - - -
126C SER* 1.3 81.4 + - - +
128C SER* 1.3 66.0 + - - +
130C GLY* 3.5 0.6 - - - +
131C ILE* 2.9 35.5 + - + +
148C CYS* 4.3 8.3 - - + -
150C ILE* 3.8 25.8 - - + -
155C ILE* 4.8 1.6 - - + -
160C ALA* 4.4 12.1 - - + -
163C ALA* 3.8 18.6 - - + -
164C MSE 4.0 31.6 - - + +
174C MSE 4.2 5.2 - - + -
176C VAL* 4.1 40.4 - - + -
248C PHE* 5.0 2.7 - - + -
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Residues in contact with SER 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C SER 4.7 1.5 + - - -
125C THR 3.4 4.3 + - - -
126C SER 3.4 0.4 - - - -
127C ILE* 1.3 80.0 - - - +
129C ALA* 1.3 64.2 + - - +
131C ILE* 3.3 10.4 + - - +
132C GLY 3.3 8.8 + - - -
159C MSE 3.6 20.1 + - - +
163C ALA* 3.5 8.2 - - - +
372D HIS* 2.8 37.4 + - - -
375D THR* 3.5 28.5 - - - -
376D PHE* 3.7 10.2 - - - -
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Residues in contact with ALA 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ILE* 4.8 2.0 - - + -
118C LEU* 3.8 30.7 - - + -
125C THR 3.2 13.6 + - - +
126C SER 3.9 2.2 - - - +
128C SER* 1.3 78.1 - - - +
130C GLY* 1.3 59.7 + - - +
132C GLY 3.2 1.7 + - - -
133C ILE* 2.9 39.7 + - + +
375D THR* 3.6 18.6 + - + +
378D ALA* 5.5 0.2 - - + -
379D GLY* 3.6 12.1 - - - +
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Residues in contact with GLY 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ILE* 3.8 17.2 - - - +
126C SER 2.7 19.6 + - - -
127C ILE 3.1 2.9 + - - -
129C ALA* 1.3 77.6 - - - +
131C ILE* 1.3 55.0 + - - +
133C ILE* 3.3 2.6 + - - +
134C ALA* 2.8 30.8 + - - +
146C THR* 3.6 6.3 - - - +
148C CYS* 3.9 11.2 - - - -
174C MSE 4.0 7.0 - - - -
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Residues in contact with ILE 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C ILE* 2.9 22.6 + - + +
128C SER 3.6 5.6 - - - +
130C GLY* 1.3 72.5 - - - +
132C GLY* 1.3 62.1 + - - +
134C ALA* 3.3 2.6 + - - +
135C VAL* 2.8 35.3 + - + +
163C ALA* 3.1 37.7 - - + +
166C HIS* 4.0 3.8 - - - +
167C ALA* 3.8 13.0 - - + +
170C ILE* 3.8 24.5 - - + -
172C PRO* 4.4 6.1 - - + -
174C MSE 3.7 22.7 - - + -
372D HIS* 3.6 12.6 - - + +
376D PHE* 3.6 17.9 - - + -
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Residues in contact with GLY 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C SER 3.3 4.9 + - - -
129C ALA 3.2 6.5 + - - -
131C ILE* 1.3 78.4 - - - +
133C ILE* 1.3 56.6 + - - +
135C VAL 3.5 0.2 + - - -
136C ALA* 3.1 23.6 + - - +
376D PHE* 3.3 33.7 - - - -
379D GLY 3.7 7.2 - - - +
380D LEU* 3.1 19.1 - - - +
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Residues in contact with ILE 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C GLN* 3.7 27.1 - - + +
75C ILE* 3.6 23.8 - - + -
117C VAL* 3.7 21.3 - - + -
129C ALA* 2.9 23.8 + - + +
130C GLY* 3.6 3.8 - - - +
132C GLY* 1.3 74.5 - - - +
134C ALA* 1.3 60.8 + - - +
136C ALA* 3.2 5.5 + - - +
137C ALA* 2.8 27.9 + - + +
144C ARG* 5.5 1.1 - - - -
146C THR* 3.7 17.0 - - + +
379D GLY* 3.4 18.4 - - - +
382D ILE* 4.0 21.1 - - + -
383D GLY* 4.7 5.1 - - - +
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Residues in contact with ALA 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C GLY 2.8 22.1 + - - +
131C ILE* 3.8 4.0 - - - +
133C ILE* 1.3 71.5 - - - +
135C VAL* 1.3 60.6 + - - +
137C ALA* 3.2 5.1 + - - +
138C GLU* 2.9 29.5 + - - +
146C THR* 3.6 15.9 + - - +
172C PRO* 4.0 17.6 - - + +
173C ASP 3.6 26.1 + - - +
174C MSE 4.2 4.9 - - + -
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Residues in contact with VAL 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C ILE* 2.8 24.2 + - + +
132C GLY 3.6 4.5 - - - +
134C ALA* 1.3 77.1 - - - +
136C ALA* 1.3 61.7 + - - +
138C GLU* 3.2 9.1 + - - +
139C LYS* 3.2 44.2 + - - +
170C ILE* 4.0 27.1 - - + -
172C PRO* 4.7 7.9 - - + -
364D PHE* 4.0 15.9 - - + -
376D PHE* 4.0 9.4 - - + -
380D LEU* 4.0 16.6 - - + -
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Residues in contact with ALA 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C GLY 3.1 18.3 + - - +
133C ILE 3.2 4.9 + - - +
135C VAL* 1.3 79.2 - - - +
137C ALA* 1.3 57.1 + - - +
139C LYS* 3.3 4.9 + - - +
140C GLU* 2.9 28.1 + - - +
380D LEU* 4.7 4.5 - - + +
383D GLY* 3.7 23.9 - - - +
385D TYR* 3.6 35.2 - - + -
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Residues in contact with ALA 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C ILE 2.8 16.8 + - - +
134C ALA* 3.5 10.8 - - - +
136C ALA* 1.3 76.8 - - - +
138C GLU* 1.3 61.4 + - - +
140C GLU* 3.2 21.2 + - - +
141C GLY* 3.3 10.4 + - - -
142C LYS 4.4 3.1 + - - -
143C ASN* 5.0 1.2 + - - -
144C ARG* 3.5 44.7 + - + +
146C THR* 4.5 4.3 - - - +
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Residues in contact with GLU 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C ALA 2.9 17.2 + - - +
135C VAL* 3.2 9.2 + - - +
137C ALA* 1.3 77.7 - - - +
139C LYS* 1.3 81.3 + - - +
141C GLY* 3.6 9.9 + - - -
172C PRO* 6.4 2.2 - - + -
173C ASP* 5.8 9.0 - - + +
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Residues in contact with LYS 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C VAL* 3.2 31.2 + - + +
136C ALA 3.7 3.8 - - - +
137C ALA 3.2 0.2 - - - -
138C GLU* 1.3 90.2 + - - +
140C GLU* 1.3 65.3 + - - +
141C GLY* 3.2 1.3 + - - -
340D MSE 3.9 23.1 - - + -
361D ASP* 3.2 36.6 + - - +
364D PHE* 4.4 4.8 - - - -
385D TYR* 3.1 35.2 + - + +
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Residues in contact with GLU 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C PHE* 4.4 1.0 - - - -
136C ALA 2.9 17.2 + - - +
137C ALA* 3.4 7.3 - - - +
139C LYS* 1.3 78.7 - - - +
141C GLY* 1.3 59.8 + - - +
142C LYS* 3.3 44.2 + - + +
144C ARG* 2.6 59.9 + - - +
383D GLY 6.2 0.4 - - - -
385D TYR* 4.1 4.7 + - + +
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Residues in contact with GLY 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C ALA 3.3 7.0 + - - -
138C GLU 3.6 8.9 + - - -
139C LYS 3.2 3.9 - - - -
140C GLU* 1.3 77.7 - - - +
142C LYS* 1.3 60.4 - - - +
143C ASN 3.4 6.8 + - - -
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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