Contacts of the helix formed by residues 157 - 171 (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 ALA 157 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A PHE* 4.2 5.3 - - - -
162A GLU* 4.6 0.7 - - - +
124B SER* 2.9 38.6 - - - +
154B ALA 3.4 1.2 + - - +
155B ILE 3.3 0.6 - - - -
156B THR* 1.3 83.8 + - - +
158B GLY* 1.3 64.9 + - - +
159B MSE 3.2 3.8 - - - +
160B ALA* 3.2 13.0 + - - +
161B PHE 3.5 6.9 + - - -
368B ILE* 3.3 21.5 - - + +
398B ARG* 4.3 12.1 - - - +
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Residues in contact with GLY 158 (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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158A GLY* 3.3 32.2 - - - -
161A PHE* 4.6 0.7 - - - -
162A GLU* 2.8 23.6 + - - +
371A GLN* 4.8 1.1 - - - +
157B ALA* 1.3 74.6 - - - +
159B MSE 1.3 62.5 + - - +
161B PHE* 3.2 5.7 + - - +
162B GLU* 3.1 26.4 + - - +
371B GLN* 4.6 2.9 - - - -
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Residues in contact with MSE 159 (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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371A GLN* 3.6 26.7 - - + +
372A HIS* 4.5 3.9 - - - +
375A THR* 3.2 36.1 - - + +
402A GLN* 3.7 16.8 - - + +
406A ASP* 4.3 2.9 - - - +
123B SER 4.1 0.2 - - - +
124B SER* 3.4 36.3 - - - +
125B THR* 4.3 4.0 - - - -
128B SER* 4.0 12.9 + - - +
157B ALA* 4.3 0.7 - - + -
158B GLY* 1.3 76.7 - - - +
160B ALA* 1.3 59.1 + - - +
162B GLU* 3.8 12.7 - - - +
163B ALA* 3.0 26.7 + - - +
398B ARG* 3.5 38.1 - - - +
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Residues in contact with ALA 160 (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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124B SER* 4.5 9.6 - - - +
127B ILE* 4.5 16.2 - - + -
150B ILE* 4.5 2.7 - - + -
154B ALA 3.7 20.0 - - - +
155B ILE* 4.2 14.1 - - + +
157B ALA 3.2 11.0 + - - +
159B MSE 1.3 78.5 - - - +
161B PHE* 1.3 60.9 + - - +
163B ALA* 3.5 5.5 - - - +
164B MSE 2.9 38.3 + - - +
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Residues in contact with PHE 161 (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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155A ILE 4.2 12.6 - - - -
156A THR* 3.9 17.5 - - - -
157A ALA 3.9 12.6 - - - -
158A GLY* 4.1 3.8 - - - -
161A PHE* 3.2 67.0 - + + -
164A MSE 5.3 4.9 - - + -
242A LEU* 4.5 17.7 - - + -
155B ILE 5.5 0.2 + - - -
157B ALA 3.5 1.6 + - - -
158B GLY 3.2 7.8 + - - +
160B ALA* 1.3 78.8 - - - +
162B GLU* 1.3 63.7 + - - +
164B MSE 3.5 4.6 + - - +
165B ASN* 3.0 54.3 + - - -
246B LEU* 4.3 26.4 - - + +
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Residues in contact with GLU 162 (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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156A THR 4.3 6.5 - - - +
157A ALA* 3.8 2.4 - - - +
158A GLY* 2.8 30.7 + - - +
366A VAL 5.1 2.8 - - - +
368A ILE 4.1 0.3 - - - +
369A ALA* 3.2 37.4 - - + +
370A GLU 4.7 0.5 + - - -
371A GLN* 3.5 16.2 + - - +
372A HIS* 3.0 34.8 + - + +
398A ARG* 5.9 2.9 - - - -
158B GLY 3.1 16.1 + - - +
159B MSE 3.9 6.0 - - - +
161B PHE* 1.3 78.0 - - - +
163B ALA* 1.3 63.4 + - - +
165B ASN* 3.5 5.5 + - - +
166B HIS* 3.1 24.4 + - - +
371B GLN* 5.1 1.7 + - - +
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Residues in contact with ALA 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A HIS* 3.5 25.0 - - + +
127B ILE* 3.6 24.7 - - + -
128B SER* 3.7 12.3 - - - +
131B ILE* 4.3 3.2 - - + +
159B MSE 3.0 19.5 + - - +
160B ALA* 3.5 5.4 - - - +
161B PHE 3.3 0.2 - - - -
162B GLU* 1.3 74.3 - - - +
164B MSE 1.3 65.4 + - - +
166B HIS* 3.2 4.2 + - - +
167B ALA* 3.0 23.6 + - - +
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Residues in contact with MSE 164 (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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127B ILE* 3.9 31.0 - - + -
155B ILE* 5.3 6.5 - - - -
160B ALA* 2.9 20.9 + - - +
161B PHE* 4.1 1.3 - - - +
163B ALA* 1.3 75.7 - - - +
165B ASN* 1.3 57.8 + - - +
167B ALA* 3.2 1.6 + - - -
168B GLY* 2.8 27.0 + - - -
176B VAL* 5.5 0.2 - - + -
243B PHE* 3.3 47.1 - - + -
246B LEU* 3.6 31.1 - - + +
248B PHE* 3.5 34.2 - - + -
277B PHE* 3.9 15.9 - - + -
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Residues in contact with ASN 165 (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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156A THR* 5.0 3.8 + - - +
242A LEU* 6.0 1.2 - - - +
161B PHE* 3.0 61.0 + - - +
162B GLU* 3.7 6.8 - - - +
164B MSE 1.3 76.6 - - - +
166B HIS* 1.3 63.2 + - - +
168B GLY* 3.2 11.1 + - - -
169B ASP* 3.2 12.5 + - - +
246B LEU* 4.1 23.8 - - - +
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Residues in contact with HIS 166 (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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364A PHE* 4.0 19.0 - + - +
365A ASP 4.0 16.7 + - - -
366A VAL* 3.8 31.0 - - + +
372A HIS* 3.0 26.2 - + + +
376A PHE* 4.0 7.6 - + - -
131B ILE* 2.9 20.2 - - + +
162B GLU 3.1 9.8 + - - +
163B ALA 3.6 0.4 - - - +
165B ASN* 1.3 79.8 - - - +
167B ALA* 1.3 60.7 + - - +
169B ASP* 3.0 19.2 + - + +
170B ILE* 3.0 50.5 + - + +
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Residues in contact with ALA 167 (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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131B ILE* 4.1 20.4 - - + +
163B ALA 3.0 16.1 + - - +
164B MSE 3.6 4.0 - - - +
166B HIS* 1.3 70.4 - - - +
168B GLY* 1.3 56.7 + - - +
169B ASP 2.9 5.2 - - - -
170B ILE* 4.3 2.5 - - - -
171B ARG* 2.7 34.8 + - - -
172B PRO* 3.5 17.3 - - + +
174B MSE 4.5 2.9 - - - -
248B PHE* 3.8 22.7 - - + -
275B PRO* 4.0 4.5 - - + +
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Residues in contact with GLY 168 (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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164B MSE 2.8 11.8 + - - -
165B ASN 3.2 2.8 + - - -
167B ALA* 1.3 76.4 - - - +
169B ASP* 1.3 59.3 + - - +
171B ARG* 3.7 17.0 - - - -
246B LEU 3.6 22.2 - - - -
247B GLY* 3.8 22.1 - - - -
248B PHE* 4.3 0.8 - - - -
275B PRO* 4.5 3.1 - - - -
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Residues in contact with ASP 169 (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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365A ASP 5.4 2.4 - - - +
165B ASN 3.2 9.2 + - - +
166B HIS* 3.0 15.3 + - + +
167B ALA 2.9 1.8 - - - -
168B GLY* 1.3 77.6 - - - +
170B ILE* 1.3 74.3 + - + +
171B ARG* 3.2 11.7 - - - +
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Residues in contact with ILE 170 (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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363A TYR 6.1 0.2 - - - +
364A PHE* 4.1 17.9 - - + -
131B ILE* 4.0 7.0 - - + -
135B VAL* 3.8 28.9 - - + -
138B GLU* 5.2 2.3 - - - +
166B HIS* 3.4 49.1 - - + +
167B ALA* 4.3 0.9 - - - -
169B ASP* 1.3 83.3 - - - +
171B ARG* 1.3 72.5 + - - +
172B PRO* 3.6 11.0 - - + +
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Residues in contact with ARG 171 (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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138B GLU* 4.6 3.1 - - - +
167B ALA 2.7 14.7 + - - -
168B GLY 3.7 16.2 - - - +
169B ASP 3.2 16.8 - - - +
170B ILE* 1.3 81.0 - - - +
172B PRO* 1.3 68.2 - - - +
173B ASP* 3.9 1.9 + - - +
247B GLY 3.8 10.9 + - - -
249B ASN* 6.0 1.4 - - - +
273B LYS* 4.7 5.7 + - - +
274B GLY* 3.9 22.2 - - - +
275B PRO* 3.6 28.3 + - + +
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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