Contacts of the strand formed by residues 163 - 176 (chain B) in PDB entry 1O9S
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 GLU 163 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159B PHE* 3.0 6.1 - - - -
160B ILE* 2.8 40.6 + - + +
161B ASP 3.2 2.6 - - - +
162B GLY* 1.3 79.1 - - - +
164B MET* 1.3 65.4 + - - +
165B ILE* 3.3 18.3 + - + +
193B PHE* 3.6 44.1 - - + +
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Residues in contact with MET 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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155B LEU* 3.6 43.7 - - + -
158B LYS 4.0 0.2 - - - -
159B PHE* 3.6 34.0 - - + -
162B GLY 3.9 0.8 + - - -
163B GLU* 1.3 71.1 - - - +
165B ILE* 1.3 64.3 + - - +
167B GLY* 3.7 11.7 - - - +
191B TYR* 3.6 36.8 - - + +
192B HIS* 3.7 8.0 - - - +
193B PHE* 2.9 31.8 + - - +
311B PRO* 3.6 37.9 + - + +
312B ARG* 4.0 3.4 - - + +
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Residues in contact with ILE 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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158B LYS* 2.9 35.1 + - + +
159B PHE 4.3 0.2 - - - -
160B ILE* 3.7 37.2 - - + +
163B GLU* 3.7 31.0 - - + +
164B MET* 1.3 79.0 - - - +
166B GLU* 1.3 63.7 + - + +
192B HIS* 3.3 20.4 - - - +
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Residues in contact with GLU 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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142B GLU* 5.2 2.6 - - - +
156B TYR 3.8 0.3 - - - +
157B GLY* 3.3 6.2 - - - -
158B LYS* 3.0 44.8 + - + +
159B PHE* 5.4 0.2 - - - -
164B MET* 4.3 0.4 - - - -
165B ILE* 1.3 83.8 - - + +
167B GLY* 1.3 58.9 + - - +
168B LYS* 3.7 28.2 + - - +
190B VAL* 3.7 28.2 - - + +
191B TYR 3.7 3.6 - - - -
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Residues in contact with GLY 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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155B LEU* 4.4 2.7 - - - -
156B TYR 3.6 11.7 - - - -
157B GLY 4.6 0.4 - - - -
159B PHE* 5.0 0.7 - - - -
164B MET* 3.7 19.3 - - - +
166B GLU* 1.3 74.7 - - - +
168B LYS* 1.3 61.4 + - - -
190B VAL* 3.3 7.1 - - - -
191B TYR* 2.8 46.0 + - - -
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Residues in contact with LYS 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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155B LEU* 3.5 3.2 - - - -
156B TYR 2.8 35.9 + - - +
157B GLY* 5.8 0.4 - - - -
166B GLU* 3.7 29.8 + - - +
167B GLY* 1.3 78.0 - - - +
169B LEU* 1.3 67.5 + - - +
170B ALA* 3.3 1.0 + - - +
184B LEU* 3.4 38.0 - - + +
189B SER 4.3 8.3 - - - +
190B VAL* 4.3 14.4 - - + -
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Residues in contact with LEU 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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153B THR* 3.8 19.7 - - + -
154B ALA 3.5 10.8 - - - +
155B LEU* 4.2 3.8 - - + -
168B LYS* 1.3 74.1 - - - +
170B ALA* 1.3 64.8 + - - +
184B LEU* 3.4 6.6 - - - +
185B MET* 2.9 53.4 + - + +
186B PRO 5.8 1.8 - - - +
189B SER* 4.8 3.0 + - - +
191B TYR* 4.2 19.7 - - + +
210B PRO* 3.6 37.0 - - + -
214B GLU* 5.8 3.8 - - - +
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Residues in contact with ALA 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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153B THR* 3.8 4.2 - - - +
154B ALA* 2.9 33.1 + - + +
156B TYR* 4.0 14.8 - - + -
168B LYS 3.8 7.2 - - - +
169B LEU* 1.3 81.0 - - - +
171B THR* 1.3 66.7 + - - +
182B PHE* 4.2 12.8 - - + -
183B GLU 3.3 16.4 - - - +
184B LEU* 3.9 12.6 - - + +
185B MET* 4.1 4.7 - - - +
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Residues in contact with THR 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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152B ARG* 3.3 48.0 + - + +
153B THR* 5.5 0.6 - - - -
170B ALA* 1.3 77.8 + - - +
172B LEU* 1.3 70.5 + - - +
173B MET* 3.3 20.8 + - + +
182B PHE* 3.3 6.7 - - - -
183B GLU* 2.9 32.9 + - - -
185B MET* 3.6 21.2 - - - +
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Residues in contact with LEU 172 (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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120B TRP* 4.1 21.8 - - + -
147B VAL* 5.3 4.5 - - + -
151B GLU* 3.5 26.1 - - + +
152B ARG* 2.9 20.8 + - - +
171B THR* 1.3 77.3 - - - +
173B MET* 1.3 60.8 + - - +
174B SER* 3.4 27.6 - - - +
175B THR* 4.2 8.5 - - - +
180B PRO* 3.6 25.8 - - + -
181B HIS 3.9 5.4 - - - +
182B PHE* 3.8 22.3 - - + -
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Residues in contact with MET 173 (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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152B ARG* 5.8 3.6 - - - +
171B THR* 3.5 31.4 - - + +
172B LEU* 1.3 73.8 - - - +
174B SER* 1.3 66.2 + - - +
181B HIS* 2.9 29.2 + - + +
183B GLU* 3.7 48.7 - - + +
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Residues in contact with SER 174 (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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172B LEU* 3.4 8.6 - - - +
173B MET* 1.3 80.5 - - - +
175B THR* 1.3 69.9 + - - +
176B GLU* 6.0 1.2 - - - +
181B HIS* 3.0 41.8 + - - +
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Residues in contact with THR 175 (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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120B TRP* 4.1 11.6 - - + -
172B LEU* 4.2 16.3 - - - +
174B SER* 1.3 82.7 + - - +
176B GLU* 1.3 75.6 + - - +
177B GLU 4.2 0.6 + - - -
178B GLY* 3.5 35.4 - - - +
179B ARG 3.5 7.9 - - - +
180B PRO* 4.0 1.5 - - - +
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Residues in contact with GLU 176 (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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174B SER* 6.0 1.3 - - - +
175B THR* 1.3 81.1 - - - +
177B GLU* 1.3 72.0 + - + +
178B GLY 3.1 0.2 - - - -
179B ARG* 2.8 50.4 + - + +
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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