Contacts of the strand formed by residues 169 - 181 (chain B) in PDB entry 3BGD
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 169 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B LYS* 3.6 16.2 + - - +
141B PHE 3.9 4.5 - - - +
143B ARG 5.3 0.4 - - - -
144B ILE* 3.3 34.3 - - + +
165B ILE* 3.7 23.8 - - + +
166B LEU* 3.4 31.7 + - + +
167B SER 3.3 1.4 - - - -
168B LEU* 1.3 78.0 - - - +
170B ARG* 1.3 68.5 + - - +
173B PHE* 3.8 50.3 - - + -
175B TYR* 4.6 9.9 - - + -
207B CYS* 5.0 0.4 - - - -
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Residues in contact with ARG 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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59B ARG* 4.0 19.2 - - - +
139B GLY* 5.6 0.8 - - - -
140B LYS* 3.2 47.7 + - + +
141B PHE 2.9 22.0 + - - +
142B ASP* 3.5 32.6 + - - +
168B LEU 3.9 0.2 + - - -
169B LEU* 1.3 78.9 - - - +
171B LYS* 1.3 68.4 + - - +
172B GLU 3.3 12.1 - - - +
173B PHE* 3.2 17.0 - - - +
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Residues in contact with LYS 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ARG* 1.3 76.0 - - - +
172B GLU* 1.3 95.2 + - - +
173B PHE* 3.8 4.0 - - - -
239B GLU* 3.6 23.4 - - + +
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Residues in contact with GLU 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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142B ASP* 4.3 9.9 - - - +
143B ARG* 5.3 1.2 + - - -
170B ARG* 3.9 14.5 - - - +
171B LYS* 1.3 108.9 + - - +
173B PHE* 1.3 64.0 + - - +
239B GLU* 3.2 26.0 - - + +
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Residues in contact with PHE 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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141B PHE 4.4 1.3 - - - +
142B ASP 3.1 15.5 - - - +
143B ARG* 4.5 2.9 - - - +
166B LEU* 5.9 0.2 - - + -
169B LEU* 3.8 45.5 - - + -
170B ARG 3.2 20.6 - - - +
171B LYS 3.8 5.4 - - - -
172B GLU* 1.3 76.0 - - - +
174B GLN* 1.3 73.1 + - - +
175B TYR* 4.0 5.4 - - + -
206B LYS 4.8 2.5 - - - -
207B CYS* 3.8 20.6 - - - -
237B LEU 3.7 9.9 - - - -
238B THR* 3.4 39.6 - - - -
239B GLU* 3.3 35.2 + - + +
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Residues in contact with GLN 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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50B THR 4.5 1.7 - - - +
51B PHE* 3.6 31.1 - - + +
142B ASP 3.0 6.3 + - - -
143B ARG* 3.3 33.8 - - - +
144B ILE* 3.1 21.5 + - - +
173B PHE* 1.3 80.2 - - - +
175B TYR* 1.3 60.7 + - - +
236B LEU* 3.8 17.0 - - + +
237B LEU 3.4 5.2 - - - -
238B THR* 3.6 18.2 - - + +
302B PM6 3.3 25.9 + - - -
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Residues in contact with TYR 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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144B ILE* 3.6 28.5 - - + -
146B ASP* 2.6 36.2 + - + -
150B LEU* 4.6 0.3 - - - +
161B TYR* 4.1 3.3 - - - -
165B ILE* 3.6 27.1 - - + +
169B LEU* 4.6 9.6 - - + -
173B PHE* 4.0 11.2 - - + -
174B GLN* 1.3 73.2 - - - +
176B LEU* 1.3 60.7 + - - +
177B VAL* 3.0 28.1 + - + +
203B PHE* 3.4 35.5 - + - -
207B CYS* 5.3 1.3 - - - -
235B TYR 3.6 1.0 - - - +
236B LEU* 3.6 2.7 - - - -
237B LEU* 2.7 66.9 + - + +
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Residues in contact with LEU 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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44B LEU* 3.9 24.0 - - + -
47B HIS* 4.7 5.2 - - + -
51B PHE* 3.5 37.4 - - + -
144B ILE 3.0 8.2 + - - +
145B TRP* 3.7 21.0 - - + -
146B ASP* 2.9 29.0 + - - +
174B GLN 4.0 0.6 - - - -
175B TYR* 1.3 71.2 - - - +
177B VAL* 1.3 60.0 + - - +
212B LEU* 3.8 27.8 - - + -
234B LEU* 4.1 10.5 - - + -
235B TYR 3.3 13.0 - - - +
236B LEU* 3.9 8.5 - - + -
302B PM6 3.9 12.3 - - - -
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Residues in contact with VAL 177 (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 ASP* 3.3 22.7 - - - +
150B LEU* 3.8 24.5 - - + -
175B TYR* 3.0 48.9 - - + +
176B LEU* 1.3 72.3 - - - +
178B ALA* 1.3 69.8 + - - +
179B VAL* 4.0 4.7 + - + +
199B LEU* 4.8 12.3 - - + -
203B PHE* 5.4 1.3 - - + -
233B LYS 3.7 1.6 - - - +
234B LEU* 3.6 5.5 - - - +
235B TYR* 2.9 36.6 + - + +
237B LEU* 4.8 7.2 - - + -
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Residues in contact with ALA 178 (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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41B HIS* 4.3 4.3 - - + +
145B TRP* 4.6 0.9 - - + -
146B ASP* 2.8 13.2 + - - +
147B ARG* 3.7 26.1 - - + +
148B GLY 4.8 0.3 + - - -
150B LEU* 5.4 0.3 - - - +
151B VAL* 4.0 16.1 + - - +
177B VAL* 1.3 74.6 - - - +
179B VAL* 1.3 64.1 + - - +
180B LEU* 5.7 0.9 - - - -
232B GLU* 3.3 25.4 - - - +
233B LYS 3.5 7.0 - - - +
234B LEU* 4.4 12.7 - - + +
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Residues in contact with VAL 179 (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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150B LEU* 4.3 14.8 - - + -
151B VAL* 3.9 10.5 - - + -
177B VAL* 4.0 5.8 + - + +
178B ALA* 1.3 76.6 - - - +
180B LEU* 1.3 67.0 + - - +
194B VAL* 3.6 42.8 - - + +
195B PRO 5.6 2.9 - - - -
196B SER* 5.6 0.7 - - - +
199B LEU* 5.0 8.7 - - + -
232B GLU* 3.4 5.9 - - - +
233B LYS* 2.9 55.1 + - + +
235B TYR* 4.1 16.2 - - + -
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Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B VAL* 4.2 10.6 - - + +
178B ALA 5.6 0.7 - - - +
179B VAL* 1.3 80.9 - - - +
181B SER* 1.3 60.4 + - - +
182B TYR* 3.8 9.4 + - + -
191B PRO* 3.7 36.1 - - + -
192B PHE 4.8 1.1 - - - +
193B TYR* 3.5 18.0 - - - -
194B VAL 4.0 10.2 + - - +
217B ALA* 5.3 2.2 - - + -
225B TRP* 6.1 0.4 - - + -
230B LEU* 4.1 26.9 - - + -
231B PHE 3.2 4.0 - - - +
232B GLU* 3.7 38.1 - - + +
301B PM6 4.0 20.6 - - + +
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Residues in contact with SER 181 (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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180B LEU* 1.3 72.3 - - - +
182B TYR* 1.3 61.1 + - - +
193B TYR* 3.8 18.3 + - - -
214B GLU* 5.9 0.2 - - - -
229B TYR* 3.8 13.6 + - - -
230B LEU* 3.2 7.5 - - - +
231B PHE* 2.6 52.4 + - - -
233B LYS* 5.6 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