Contacts of the strand formed by residues 192 - 204 (chain B) in PDB entry 5D9I
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 HIS 192 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133B GLU 5.6 1.0 + - - -
135B PRO* 4.1 14.6 - - + +
162B TYR* 3.7 30.1 - - + -
163B THR 3.3 9.6 - - - +
164B THR* 4.0 17.3 - - + +
165B LYS 4.4 4.2 + - - +
188B ASN* 3.0 4.5 + - - -
189B SER* 2.8 29.6 + - - +
190B TYR* 6.3 0.2 - - + -
191B ASN* 1.3 92.5 + - + +
193B ASN* 1.3 75.4 + - - +
220B PHE* 3.8 28.6 - + - -
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Residues in contact with ASN 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ILE 3.9 0.3 - - - +
162B TYR* 3.4 5.4 - - - -
163B THR* 3.0 31.4 + - - +
165B LYS* 3.7 27.2 - - - +
168B ALA* 3.3 23.8 - - + +
186B ARG* 2.9 37.4 + - + -
187B HIS 3.2 9.5 + - - +
188B ASN* 3.8 4.4 - - - +
189B SER* 4.3 1.1 - - - +
192B HIS* 1.3 94.9 + - - +
194B ILE* 1.3 64.0 + - - +
195B LEU 4.4 0.2 - - - -
244B ILE* 3.5 19.3 - - - +
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Residues in contact with ILE 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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138B PHE* 4.1 14.6 - - + -
139B PRO* 4.2 6.3 - - + -
142B LEU* 3.6 29.4 - - + -
160B ALA* 4.5 2.9 - - + -
161B ILE 3.1 9.2 - - - +
162B TYR* 3.5 22.7 - - + -
186B ARG* 3.4 2.8 - - - +
187B HIS* 2.7 42.3 + - + +
189B SER* 3.9 21.8 - - - +
193B ASN* 1.3 77.2 - - - +
195B LEU* 1.3 76.5 + - - +
232B MET* 4.6 0.7 - - + -
236B LEU* 3.8 31.2 - - + -
241B PHE* 4.2 0.9 - - + -
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Residues in contact with LEU 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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160B ALA* 3.1 6.4 - - - -
161B ILE* 2.8 45.7 + - + +
163B THR* 5.7 0.2 - - + -
168B ALA* 3.9 20.2 - - + +
171B LEU* 3.6 42.4 - - + +
172B TYR* 4.1 17.5 - - + +
175B ILE* 4.6 9.0 - - + -
184B ILE* 4.7 4.7 - - + -
185B SER 3.3 4.7 - - - +
186B ARG* 3.6 35.4 - - + -
194B ILE* 1.3 78.9 - - - +
196B PHE* 1.3 60.0 + - - +
197B PHE* 4.3 9.7 - - + -
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Residues in contact with PHE 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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158B CYS* 3.5 30.3 - - - -
159B PHE 3.6 6.5 - - - -
160B ALA* 4.6 1.6 - - + +
183B PHE* 4.1 8.3 - + - -
184B ILE* 3.4 0.7 - - - +
185B SER* 2.9 46.4 + - - +
187B HIS* 4.0 0.9 - - - +
195B LEU* 1.3 73.6 - - - +
197B PHE* 1.3 64.2 + - - +
198B LEU* 3.8 28.5 - - + -
226B VAL* 4.8 1.3 - - + -
229B GLU* 3.5 28.0 - - + -
232B MET* 3.9 23.1 - - + -
233B TYR* 3.7 29.4 - + + -
236B LEU* 4.0 15.9 - - + -
252B LEU* 4.6 1.6 - - + -
257B PHE* 4.6 2.7 - + - -
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Residues in contact with PHE 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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158B CYS* 3.3 6.6 - - - -
159B PHE* 3.0 63.1 + + + +
161B ILE* 3.7 25.6 - - + -
175B ILE* 3.7 36.3 - - + -
179B TYR* 5.0 3.1 - + - -
181B VAL* 4.2 10.5 - - + -
183B PHE 3.3 14.1 - - - +
184B ILE* 3.8 18.8 - - + -
195B LEU* 4.3 10.1 - - + -
196B PHE* 1.3 81.2 - - - +
198B LEU* 1.3 63.7 + - - +
199B THR* 4.3 11.2 - - + -
208B ILE* 3.7 26.2 - - + -
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Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ALA* 3.3 13.5 - - + +
158B CYS* 3.8 21.8 - - + -
181B VAL* 3.3 8.7 - - - +
182B THR* 2.9 37.6 + - - +
183B PHE* 3.0 16.6 + - + +
196B PHE* 3.8 23.3 - - + -
197B PHE* 1.3 75.5 - - - +
199B THR* 1.4 62.1 + - - +
229B GLU* 4.7 9.0 - - + -
252B LEU* 3.9 20.2 - - + -
257B PHE* 4.4 10.3 - - + -
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Residues in contact with THR 199 (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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157B ALA* 3.0 32.7 + - - +
159B PHE* 3.9 11.6 - - + -
179B TYR* 4.0 27.4 - - + +
181B VAL* 4.5 1.3 - - + -
182B THR* 3.9 5.7 + - - +
197B PHE* 4.3 13.7 - - + -
198B LEU* 1.4 78.2 - - - +
200B PRO* 1.3 72.2 - - - +
201B HIS 2.8 21.4 + - - -
203B HIS* 3.7 17.6 - - + -
208B ILE* 5.4 0.2 - - + -
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Residues in contact with PRO 200 (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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179B TYR 3.4 13.2 - - - +
180B SER* 3.1 34.8 - - - +
181B VAL* 4.1 0.2 - - - -
182B THR* 3.8 19.5 - - + -
199B THR* 1.3 89.1 - - - +
201B HIS* 1.3 69.6 + - + +
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Residues in contact with HIS 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ALA* 4.2 1.5 - - - +
179B TYR 5.6 2.9 + - - -
199B THR* 2.8 29.0 + - - +
200B PRO* 1.3 88.5 - - + +
202B ARG* 1.3 66.5 + - - +
203B HIS* 3.1 38.9 - + - -
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Residues in contact with ARG 202 (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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154B ARG* 4.8 6.7 - - - +
155B THR* 2.8 56.2 + - - +
156B LEU* 3.1 18.4 - - - +
157B ALA* 4.2 8.1 - - + -
201B HIS* 1.3 82.0 + - - +
203B HIS* 1.3 71.1 + - - +
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Residues in contact with HIS 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B THR* 3.3 8.9 - - - -
156B LEU* 2.9 27.7 + - - +
159B PHE* 3.4 10.4 - + + -
179B TYR* 3.6 31.7 + + - +
199B THR* 3.7 23.0 - - + +
201B HIS* 3.1 55.2 + + - -
202B ARG* 1.3 72.7 + - - +
204B ARG* 1.3 64.4 - - - +
205B VAL 3.7 0.7 + - - -
207B ALA* 4.8 7.0 - - + +
208B ILE* 3.7 27.4 - - + -
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Residues in contact with ARG 204 (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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151B PHE 4.9 4.9 + - - -
152B SER 3.9 16.4 + - - +
153B ASN* 3.6 35.8 + - - +
154B ARG 4.3 6.3 - - - -
155B THR* 3.8 16.8 - - + +
159B PHE* 4.4 1.1 - - - -
203B HIS* 1.3 75.0 - - - +
205B VAL* 1.3 66.7 + - - +
206B SER* 3.6 21.9 + - - +
207B ALA* 3.0 22.9 + - + +
208B ILE* 3.3 11.6 + - - +
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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