Contacts of the strand formed by residues 185 - 195 (chain B) in PDB entry 3Q3G
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 LEU 185 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ALA* 4.3 10.3 - - + -
128B THR* 3.7 31.9 - - + +
155B GLY* 3.8 25.6 - - - +
156B TYR 3.6 7.0 - - - +
157B PHE* 3.8 20.2 - - + -
181B LEU* 3.5 8.3 - - - -
182B GLN* 2.8 33.9 + - - +
183B SER* 4.6 11.7 - - - +
184B ASP* 1.3 81.3 - - + +
186B TYR* 1.3 59.8 + - - +
187B THR* 5.2 0.2 - - - -
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Residues in contact with TYR 186 (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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121B THR* 3.9 22.9 + - - +
155B GLY 2.9 23.0 + - - -
156B TYR* 2.8 52.8 + + + +
157B PHE* 3.6 26.9 - + - -
158B PRO* 4.4 1.6 - - + -
159B GLU* 3.3 48.8 - - + +
179B ALA* 4.1 11.9 - - + -
180B VAL 3.4 10.5 - - - -
181B LEU* 3.6 25.9 - - + +
185B LEU* 1.3 71.9 - - - +
187B THR* 1.3 61.7 + - - +
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Residues in contact with THR 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A THR* 5.5 7.0 - - + +
152B LEU* 3.8 20.9 - - + -
153B VAL 3.3 6.5 - - - +
154B LYS* 3.4 32.8 - - + +
155B GLY* 3.7 1.7 + - - -
156B TYR* 4.4 0.4 - - - -
178B PRO 4.5 0.5 - - - +
179B ALA* 3.4 1.9 - - - -
180B VAL* 3.0 44.0 + - + +
182B GLN* 4.2 27.2 + - - +
185B LEU 4.8 0.3 + - - -
186B TYR* 1.3 77.0 + - - +
188B LEU* 1.3 63.6 + - - +
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Residues in contact with LEU 188 (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 LEU* 3.5 6.9 - - - +
153B VAL* 2.8 45.3 + - + +
156B TYR* 3.6 24.0 - - + +
159B GLU* 4.8 2.0 - - - +
161B VAL* 3.9 14.8 - - + +
163B VAL* 3.8 28.0 - - + -
176B THR* 4.0 15.7 - - + -
177B PHE 3.5 20.6 - - - +
178B PRO* 4.9 1.8 - - + -
179B ALA* 4.2 13.2 - - + +
187B THR* 1.3 75.7 - - - +
189B SER* 1.3 69.3 + - - +
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Residues in contact with SER 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A VAL* 4.9 2.9 - - - -
141A PHE* 3.6 16.3 - - - -
182A SER* 2.8 29.4 + - - -
184A THR* 4.9 2.3 + - - -
135B LEU* 4.8 2.9 - - - -
151B CYS 3.2 12.1 - - - -
152B LEU* 4.3 12.3 - - - -
176B THR* 3.8 2.3 - - - +
177B PHE* 2.9 34.3 + - - +
188B LEU* 1.3 80.1 - - - +
190B SER* 1.3 61.4 + - - +
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Residues in contact with SER 190 (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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141A PHE* 3.5 5.2 - - - -
150B GLY* 3.1 6.4 - - - -
151B CYS* 3.0 32.2 + - - -
163B VAL* 3.7 20.8 - - - +
165B TRP* 2.9 32.2 + - - -
174B VAL* 4.0 1.0 - - - +
175B HIS 3.2 6.9 + - - -
176B THR* 2.8 26.3 + - - -
188B LEU* 4.7 0.2 - - - +
189B SER* 1.3 74.7 - - - +
191B SER* 1.3 60.5 + - - +
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Residues in contact with SER 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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141A PHE* 3.5 21.1 - - - -
143A ASN* 2.9 28.2 + - - -
148B THR* 3.8 8.3 - - - +
149B LEU 3.5 5.6 - - - -
165B TRP* 4.4 1.3 - - - -
173B GLY 4.1 1.1 + - - -
174B VAL* 3.1 10.2 - - - +
175B HIS* 2.7 41.7 + - - -
177B PHE* 3.9 9.4 - - - -
190B SER* 1.3 72.3 - - - +
192B VAL* 1.4 63.0 + - - +
193B THR* 4.6 0.3 + - - -
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Residues in contact with VAL 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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147B VAL 3.7 1.0 - - - +
148B THR* 3.3 2.9 - - - -
149B LEU* 2.8 50.4 + - + +
165B TRP* 3.6 37.7 - - + -
170B LEU* 3.9 26.9 - - + -
172B SER 5.0 0.9 - - - +
173B GLY 3.4 4.0 - - - -
174B VAL* 3.7 20.9 - - + -
191B SER* 1.4 74.1 + - - +
193B THR* 1.3 66.8 + - - +
194B VAL* 4.2 8.1 - - + -
204B VAL* 3.8 12.6 - - + -
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Residues in contact with THR 193 (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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120A THR* 6.1 0.2 - - - +
143A ASN* 4.8 4.9 + - - -
146B MET* 3.7 41.5 - - + +
147B VAL 3.4 6.7 - - - +
148B THR* 2.8 27.1 + - - +
170B LEU* 5.4 1.2 - - - +
172B SER 4.3 5.2 - - - +
173B GLY* 3.0 29.6 + - - -
175B HIS* 5.9 0.5 - - - -
191B SER* 4.6 2.8 + - - -
192B VAL* 1.3 72.8 - - - +
194B VAL* 1.4 65.8 + - - +
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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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146B MET* 3.5 7.1 - - - -
147B VAL* 2.7 50.7 + - + +
149B LEU* 4.4 4.7 - - + -
170B LEU* 3.9 37.9 - - + -
192B VAL* 4.2 8.0 - - + -
193B THR* 1.4 78.6 - - - +
195B PRO* 1.4 78.5 - - + +
198B PRO* 4.4 6.3 - - + -
199B ARG* 3.9 15.9 - - + -
204B VAL* 4.2 15.9 - - + -
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Residues in contact with PRO 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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145B SER 3.4 10.8 - - - +
146B MET* 4.0 13.0 - - + -
147B VAL* 3.7 2.3 - - - +
194B VAL* 1.4 97.4 - - + +
196B SER* 1.3 61.6 + - - +
197B SER* 3.1 10.1 - - - +
198B PRO* 3.0 41.1 - - + +
199B ARG 3.9 1.0 + - - -
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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