Contacts of the strand formed by residues 188 - 197 (chain B) in PDB entry 3O4O
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 GLY 188 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B MET* 5.5 4.0 - - - -
187B ASN* 1.3 77.5 - - - +
189B ASN* 1.3 66.9 + - - -
190B TYR* 2.9 21.8 - - - -
210B THR* 4.3 1.8 - - - -
211B VAL 3.1 20.7 + - - -
1E NAG 4.8 14.1 - - - -
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Residues in contact with ASN 189 (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 LEU* 4.1 13.7 - - + +
159B MET* 2.8 28.1 - - - +
160B GLY* 4.7 0.7 - - - -
188B GLY* 1.3 73.5 - - - -
190B TYR* 1.3 60.6 + - - +
191B THR* 5.5 0.9 - - + -
208B THR* 4.5 3.8 - - - +
209B LEU 3.8 4.9 - - - +
210B THR* 3.5 17.8 - - + +
1E NAG 1.5 64.8 + - - +
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Residues in contact with TYR 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ILE* 6.0 0.2 - - + -
157B TRP* 5.0 5.8 - - + -
158B TYR 3.4 7.4 - - - +
159B MET* 2.9 36.0 - - + +
164B ILE* 4.2 11.9 - - + -
170B VAL* 4.6 3.6 - - + +
177B LEU* 3.5 26.5 - - + -
179B PHE* 3.4 27.3 - + - -
186B ASN* 2.5 33.8 + - - +
188B GLY* 2.9 32.1 - - - -
189B ASN* 1.3 76.5 - - - +
191B THR* 1.3 63.2 + - - +
208B THR* 3.2 8.1 + - - -
209B LEU* 2.8 39.5 + - + +
211B VAL* 3.4 22.9 - - + -
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Residues in contact with THR 191 (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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118B PHE* 3.5 50.0 - - + -
157B TRP* 4.0 4.8 - - - -
158B TYR* 2.9 51.0 + - + +
159B MET 4.1 6.5 - - - +
160B GLY 4.5 0.2 - - - +
189B ASN* 5.2 0.9 - - + +
190B TYR* 1.3 79.9 - - - +
192B CYS* 1.3 64.6 + - - +
206B THR* 4.1 2.3 + - - -
207B ARG 3.6 10.7 + - - -
208B THR* 3.4 17.7 - - - +
209B LEU* 5.5 0.4 - - - -
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Residues in contact with CYS 192 (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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140B CYS* 2.1 51.1 - - - -
141B PRO* 3.7 8.5 - - - -
155B ILE* 4.4 2.2 - - + -
156B THR 3.5 6.1 - - - +
157B TRP* 3.5 33.1 - - + -
191B THR* 1.3 71.1 + - - +
193B VAL* 1.3 67.5 + - - +
205B LEU 3.9 0.3 - - - +
206B THR* 3.5 0.3 - - - -
207B ARG* 3.1 47.3 + - - +
209B LEU* 5.3 0.2 - - - -
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Residues in contact with VAL 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B PHE* 3.5 32.5 - - + -
154B THR* 4.1 0.5 - - - +
155B ILE* 3.5 3.0 - - - -
156B THR* 2.9 33.0 + - - +
158B TYR* 3.5 22.4 - - + +
191B THR* 4.1 2.2 - - - +
192B CYS* 1.3 80.7 - - - +
194B VAL* 1.3 61.6 + - - +
195B THR* 3.8 5.6 + - - +
204B HIS* 4.5 22.4 - - + -
205B LEU 3.4 4.9 - - - +
206B THR* 4.1 16.8 - - + -
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Residues in contact with VAL 194 (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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140B CYS* 4.2 9.6 - - - -
143B VAL* 3.5 25.6 - - + -
147B PHE* 4.3 19.5 - - + -
153B PRO* 4.0 17.7 - - + -
154B THR 3.5 4.9 - - - +
155B ILE* 4.0 15.7 - - + -
175B MET* 4.8 2.9 - - + -
193B VAL* 1.3 73.1 - - - +
195B THR* 1.3 72.9 + - - +
196B TYR* 4.7 1.7 - - + -
203B PHE 4.0 0.7 - - - +
204B HIS 3.7 0.7 - - - -
205B LEU* 2.8 58.9 + - + +
207B ARG* 5.5 0.7 - - - -
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Residues in contact with THR 195 (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 PRO* 3.2 19.4 - - - +
154B THR* 2.8 29.6 + - - +
193B VAL* 4.2 7.1 + - - +
194B VAL* 1.3 75.8 - - - +
196B TYR* 1.3 69.7 + - - +
202B THR* 4.0 24.2 - - + -
203B PHE 3.4 12.6 - - - +
204B HIS* 4.2 25.8 + - + +
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Residues in contact with TYR 196 (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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22B PRO* 3.4 23.9 - - - +
80B TRP* 4.3 3.6 - - - -
146B TYR* 3.7 21.0 + - + +
147B PHE* 3.6 38.6 - + + -
151B VAL* 4.9 2.9 - - + -
153B PRO* 4.5 10.5 - - + -
194B VAL* 4.7 3.6 - - + -
195B THR* 1.3 83.2 - - - +
197B PRO* 1.3 78.7 - - + +
198B GLU* 3.5 27.2 + - + -
201B ARG 3.5 0.5 - - - +
202B THR* 3.3 6.0 - - - -
203B PHE* 2.8 50.4 + + + +
205B LEU* 3.4 28.2 - - + +
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Residues in contact with PRO 197 (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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148B PRO* 6.1 0.3 - - - +
151B VAL* 4.4 30.3 - - + +
152B LYS 4.9 10.3 - - - +
153B PRO* 5.5 0.2 - - + -
196B TYR* 1.3 93.4 - - + +
198B GLU* 1.3 64.2 + - - +
200B GLY* 5.8 1.8 - - - +
201B ARG 2.9 12.6 - - - +
202B THR* 4.3 8.7 - - + -
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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