Contacts of the helix formed by residues 125 - 141 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A THR* 3.4 18.6 - - + -
405A HIS* 4.6 3.4 - - - -
406A ASP* 3.0 35.4 + - + +
77B ASP* 2.9 3.0 + - - -
78B VAL 6.4 0.2 - - - -
118B LEU* 4.0 22.2 - - + -
120B VAL* 5.2 4.7 - - - -
122B HIS 4.1 10.3 + - - -
123B SER 3.3 9.5 + - - -
124B SER* 1.3 76.9 - - - +
126B SER* 1.3 67.0 + - - +
128B SER* 3.2 3.4 + - - -
129B ALA* 2.9 25.3 + - + +
159B MSE 4.3 10.6 - - - -
398B ARG* 4.3 2.9 + - - -
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Residues in contact with SER 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ILE* 3.6 28.1 - - - +
76B TRP 5.2 0.6 + - - -
77B ASP* 2.5 45.3 + - - +
118B LEU* 5.5 1.0 - - - +
120B VAL* 5.7 0.6 - - - +
125B THR* 1.3 77.6 - - - +
127B ILE* 1.3 59.4 + - - +
129B ALA* 3.9 0.7 - - - +
130B GLY* 2.7 35.9 + - - -
148B CYS* 3.8 13.9 - - - -
149B VAL 4.3 1.8 - - - -
150B ILE* 3.7 14.0 - - - +
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B SER 4.8 1.7 + - - +
126B SER* 1.3 86.9 + - - +
128B SER* 1.3 58.2 + - - +
130B GLY* 3.6 0.3 - - - -
131B ILE* 2.8 43.3 + - + +
148B CYS* 4.3 11.0 - - + -
150B ILE* 3.9 24.5 - - + -
155B ILE* 4.9 2.0 - - + -
160B ALA* 4.5 11.7 - - + +
163B ALA* 3.6 20.0 - - + -
164B MSE 3.9 37.2 - - + +
174B MSE 4.4 0.8 - - + +
176B VAL* 4.0 37.2 - - + -
248B PHE* 5.0 2.0 - - + -
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Residues in contact with SER 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A HIS* 2.8 36.2 + - - +
375A THR* 3.2 27.1 - - - -
376A PHE* 3.8 10.6 - - - -
124B SER 4.4 3.5 + - - -
125B THR 3.2 9.1 + - - -
126B SER 3.1 0.4 - - - -
127B ILE* 1.3 81.0 - - - +
129B ALA* 1.3 61.6 + - - +
131B ILE* 3.5 5.9 + - - +
132B GLY 3.5 6.1 + - - -
159B MSE 4.0 13.7 - - - +
163B ALA* 3.7 14.2 - - - +
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A THR* 3.5 24.3 - - + +
378A ALA* 5.1 0.9 - - + -
379A GLY* 3.2 17.1 - - - +
75B ILE* 5.1 1.1 - - + -
118B LEU* 4.0 31.6 - - + -
125B THR* 2.9 16.3 + - + +
126B SER 4.1 1.1 - - - +
128B SER* 1.3 74.0 - - - +
130B GLY* 1.3 57.2 + - - +
132B GLY 3.0 2.6 + - - -
133B ILE* 2.8 31.8 + - + +
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Residues in contact with GLY 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ILE* 3.4 21.4 - - - +
126B SER 2.7 23.9 + - - -
127B ILE 3.6 1.6 - - - -
129B ALA* 1.3 70.5 - - - +
131B ILE* 1.3 60.9 + - - +
133B ILE 3.2 1.2 + - - -
134B ALA* 2.8 27.9 + - - +
146B THR* 3.5 6.9 - - - +
148B CYS* 3.8 7.9 - - - -
174B MSE 3.9 5.6 - - - -
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Residues in contact with ILE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A HIS* 3.6 11.7 - - + +
376A PHE* 3.3 13.2 - - + -
127B ILE* 2.8 29.1 + - + +
128B SER* 4.0 2.2 - - - +
129B ALA 3.4 0.2 - - - -
130B GLY* 1.3 74.1 - - - +
132B GLY* 1.3 63.4 + - - +
134B ALA* 3.6 2.1 - - - +
135B VAL* 2.9 35.9 + - - +
163B ALA* 4.3 3.6 - - + +
166B HIS* 2.9 41.1 - - + +
167B ALA* 4.1 17.0 - - + +
170B ILE* 4.0 10.1 - - + -
172B PRO* 4.5 5.4 - - + -
174B MSE 3.8 27.1 - - + -
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Residues in contact with GLY 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A PHE* 3.4 35.2 - - - -
379A GLY 3.7 7.0 - - - -
380A LEU* 3.5 14.6 + - - +
128B SER 3.5 2.4 + - - -
129B ALA 3.0 8.7 + - - -
131B ILE* 1.3 84.7 - - - +
133B ILE* 1.3 55.4 + - - +
136B ALA* 3.2 22.9 + - - +
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Residues in contact with ILE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A GLY* 3.6 19.1 - - - +
382A ILE* 4.0 16.8 - - + -
383A GLY* 4.8 6.2 - - - +
73B GLN* 3.6 30.5 - - + +
75B ILE* 3.4 27.4 - - + -
117B VAL* 3.4 23.6 - - + -
118B LEU* 5.3 1.1 - - + -
129B ALA* 2.8 18.2 + - + +
130B GLY* 3.6 7.0 - - - +
131B ILE 3.2 0.2 - - - -
132B GLY* 1.3 75.6 - - - +
134B ALA* 1.3 58.8 + - - +
136B ALA* 3.4 4.6 + - - +
137B ALA* 2.9 27.9 + - + +
144B ARG* 5.6 1.1 - - - -
146B THR* 3.8 10.1 - - + +
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Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B GLY 2.8 17.8 + - - +
131B ILE* 3.6 8.5 - - - +
133B ILE* 1.3 76.0 - - - +
135B VAL* 1.3 59.4 + - - +
137B ALA* 3.4 3.6 + - - +
138B GLU* 2.9 29.8 + - - +
146B THR* 3.5 14.1 + - - +
172B PRO* 4.1 10.8 - - + -
173B ASP 3.6 23.7 - - - +
174B MSE 3.9 12.1 - - + -
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Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A PHE* 3.8 25.8 - - + -
376A PHE* 4.1 7.0 - - + -
380A LEU* 4.0 13.0 - - + -
131B ILE 2.9 21.0 + - - +
132B GLY 3.8 4.7 - - - +
134B ALA* 1.3 73.0 - - - +
136B ALA* 1.3 67.7 + - - +
138B GLU* 3.2 11.8 + - + +
139B LYS* 3.1 36.5 + - + +
170B ILE* 3.8 28.3 - - + -
172B PRO* 4.1 11.9 - - + -
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A LEU* 4.4 5.6 - - + +
383A GLY* 3.6 32.3 - - - +
385A TYR* 3.7 27.8 - - + -
132B GLY 3.2 12.8 + - - +
133B ILE 3.6 7.6 - - - +
135B VAL* 1.3 80.8 - - - +
137B ALA* 1.3 52.2 + - - +
139B LYS* 3.1 4.0 + - - -
140B GLU* 2.8 35.8 + - - +
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Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ILE* 2.9 18.3 + - + +
134B ALA* 3.7 8.1 - - - +
136B ALA* 1.3 76.7 - - - +
138B GLU* 1.3 63.5 + - - +
140B GLU* 3.7 12.5 - - - +
141B GLY* 3.4 15.9 + - - -
142B LYS 4.4 2.8 + - - -
143B ASN* 5.0 1.6 + - - -
144B ARG* 3.5 45.0 + - + +
146B THR* 4.4 5.2 - - - +
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Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ALA 2.9 12.3 + - - +
135B VAL* 3.2 15.9 - - + +
137B ALA* 1.3 79.5 - - - +
139B LYS* 1.3 63.2 + - + +
141B GLY* 3.5 10.0 + - - -
170B ILE 5.2 1.9 - - - +
171B ARG 4.6 2.8 - - - +
172B PRO* 3.7 21.2 - - - +
173B ASP* 3.1 40.1 + - - +
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Residues in contact with LYS 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A MSE 3.8 30.6 - - + +
361A ASP* 2.7 42.8 + - - +
362A ARG* 5.0 1.4 - - - +
364A PHE* 4.6 4.0 - - - -
380A LEU* 6.1 0.2 - - + -
385A TYR* 3.3 25.5 + - + +
135B VAL* 3.1 30.0 + - + +
136B ALA* 3.7 4.0 - - - +
138B GLU* 1.3 74.6 - - + +
140B GLU* 1.3 65.7 + - - +
141B GLY* 3.1 3.6 + - - -
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Residues in contact with GLU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A GLY 5.9 1.3 - - - +
385A TYR* 3.5 9.6 + - + +
136B ALA 2.8 20.1 + - - +
137B ALA* 3.7 7.3 - - - +
138B GLU 3.3 0.4 - - - -
139B LYS* 1.3 73.9 - - - +
141B GLY* 1.3 61.1 + - - +
142B LYS* 3.3 50.4 + - + +
144B ARG* 3.1 50.5 + - - +
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Residues in contact with GLY 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ALA 3.4 7.7 + - - -
138B GLU 3.5 8.5 + - - -
139B LYS 3.1 5.0 - - - -
140B GLU* 1.3 78.4 - - - +
142B LYS* 1.3 58.8 + - - +
143B ASN 3.4 6.1 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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