Contacts of the strand formed by residues 169 - 181 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A LYS* 3.4 19.7 + - - +
141A PHE 3.8 5.8 - - - +
142A ASP 5.3 0.2 - - - +
144A ILE* 3.6 27.6 - - + +
165A ILE* 3.4 26.9 - - + +
166A LEU* 3.8 32.2 - - + +
167A SER 3.3 1.2 - - - -
168A LEU* 1.3 79.3 - - - +
170A ARG* 1.3 66.6 + - - +
173A PHE* 3.7 50.3 - - + -
174A GLN 5.2 1.8 - - - +
175A TYR* 4.7 8.3 - - + -
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Residues in contact with ARG 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ARG* 3.5 30.7 - - - +
140A LYS* 3.1 40.0 + - + +
141A PHE* 2.9 19.4 + - - +
142A ASP* 3.1 40.5 + - - -
169A LEU* 1.3 76.7 - - - +
171A LYS* 1.3 90.2 + - + +
172A GLU 3.3 10.9 + - - +
173A PHE* 3.1 20.8 - - - -
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Residues in contact with LYS 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LYS* 4.4 13.9 - - - +
170A ARG* 1.3 97.5 - - + +
172A GLU* 1.3 65.1 + - + +
173A PHE* 3.7 4.6 - - - -
239A GLU* 3.3 24.8 - - - +
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Residues in contact with GLU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLN* 5.7 2.9 + - - -
142A ASP* 4.2 9.7 - - - +
143A ARG* 5.6 1.6 - - - -
170A ARG* 3.5 15.6 - - - +
171A LYS* 1.3 84.5 - - + +
173A PHE* 1.3 64.7 + - - +
239A GLU* 3.7 20.5 - - + +
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Residues in contact with PHE 173 (chain A).
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 4.4 1.3 - - - +
142A ASP 3.2 14.8 - - - +
143A ARG* 4.5 4.0 - - - +
166A LEU* 5.7 0.4 - - + -
169A LEU* 3.7 43.1 - - + -
170A ARG 3.1 21.8 - - - +
171A LYS 3.7 8.3 - - - -
172A GLU* 1.3 75.0 - - - +
174A GLN* 1.3 66.1 + - - +
175A TYR* 4.0 8.1 - - + -
206A LYS 4.4 4.7 - - - -
207A CYS* 3.7 22.2 - - - -
237A LEU 3.6 22.0 - - - -
238A THR* 3.5 31.2 - - - +
239A GLU* 3.2 32.7 + - + +
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Residues in contact with GLN 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A THR 4.5 3.4 + - - -
51A PHE* 3.6 20.0 + - + -
142A ASP 3.1 6.3 + - - +
143A ARG* 3.3 45.8 - - - +
144A ILE 3.2 21.1 + - - -
169A LEU* 5.2 0.2 - - - +
173A PHE* 1.3 80.2 - - - +
175A TYR* 1.3 61.2 + - - +
236A LEU* 3.9 4.7 - - + +
237A LEU 3.6 3.4 - - - -
238A THR* 4.0 12.1 - - + +
302A PM6 2.5 43.7 + - - -
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Residues in contact with TYR 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ILE* 3.6 31.9 - - + +
146A ASP* 2.7 42.1 + - + -
150A LEU* 4.8 0.5 - - - +
161A TYR* 4.3 1.2 - - - -
165A ILE* 3.8 26.1 - - + +
169A LEU* 4.7 9.4 - - + -
173A PHE* 4.0 12.3 - + + -
174A GLN* 1.3 72.5 - - - +
176A LEU* 1.3 63.4 + - - +
177A VAL* 3.8 14.3 + - + +
203A PHE* 3.5 34.6 - + - -
207A CYS* 5.1 1.1 - - - -
235A TYR 3.5 3.1 - - - +
236A LEU* 3.5 1.6 - - - +
237A LEU* 2.7 71.1 + - + +
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Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU* 4.1 9.0 - - + -
47A HIS* 4.9 5.2 - - + -
51A PHE* 3.4 40.1 - - + -
144A ILE 3.0 11.4 + - - +
145A TRP* 3.5 30.9 - - + -
146A ASP* 2.9 28.0 + - - +
174A GLN 4.1 0.4 - - - -
175A TYR* 1.3 72.4 - - - +
177A VAL* 1.3 59.7 + - - +
212A LEU* 3.8 28.5 - - + -
234A LEU* 4.2 11.4 - - + -
235A TYR 3.4 10.8 - - - +
236A LEU* 4.0 11.0 - - + -
302A PM6 4.1 11.9 - - - -
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Residues in contact with VAL 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ASP* 3.3 25.1 - - + +
150A LEU* 3.7 29.8 - - + -
175A TYR* 4.0 13.5 - - + +
176A LEU* 1.3 74.1 - - - +
178A ALA* 1.3 63.5 + - - +
179A VAL* 4.1 11.3 + - + +
199A LEU* 4.0 18.6 - - + -
233A LYS 3.8 1.0 - - - +
234A LEU* 3.6 4.4 - - - +
235A TYR* 3.0 46.2 + - + +
237A LEU* 4.6 9.2 - - + -
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Residues in contact with ALA 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A HIS* 4.4 4.0 - - + +
145A TRP* 4.6 1.6 - - + -
146A ASP* 2.8 19.1 + - - +
147A ARG* 4.0 22.7 - - + +
148A GLY 4.6 2.8 + - - -
150A LEU* 5.9 0.2 - - - +
151A VAL* 3.6 14.4 - - - +
177A VAL* 1.3 74.2 - - - +
179A VAL* 1.3 63.3 + - - +
180A LEU* 5.6 1.0 - - - +
232A GLU* 4.0 21.3 - - + +
233A LYS 3.3 7.9 - - - +
234A LEU* 4.2 14.1 - - + +
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Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LEU* 4.3 3.4 - - + -
151A VAL* 3.7 10.1 - - + -
177A VAL* 4.1 17.7 - - + +
178A ALA* 1.3 77.7 - - - +
180A LEU* 1.3 67.2 + - - +
181A SER* 6.4 0.2 - - - -
194A VAL* 3.6 42.0 - - + +
195A PRO 5.6 1.8 - - - -
199A LEU* 4.6 9.2 - - + -
231A PHE 3.8 0.2 - - - +
232A GLU* 3.5 5.4 - - - +
233A LYS* 2.9 51.1 + - + +
235A TYR* 3.9 24.0 - - + -
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Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A VAL* 4.1 10.3 - - + +
178A ALA 5.6 0.4 - - - +
179A VAL* 1.3 84.4 - - - +
181A SER* 1.3 60.5 + - - +
182A TYR* 4.1 9.4 - - + -
191A PRO* 3.8 22.4 - - + -
192A PHE 4.5 3.9 - - - +
193A TYR* 3.5 19.6 - - - -
194A VAL 3.9 11.1 + - - +
217A ALA* 4.7 4.0 - - + -
225A TRP* 6.2 0.2 - - + -
230A LEU* 4.1 29.2 - - + -
231A PHE 3.5 2.5 - - - +
232A GLU* 3.9 31.2 - - + +
301A PM6 3.7 31.0 - - + +
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Residues in contact with SER 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU* 1.3 71.9 - - - +
182A TYR* 1.3 64.4 + - - +
193A TYR* 3.8 18.6 - - - -
194A VAL 5.8 1.1 - - - -
195A PRO* 6.0 1.3 - - - -
229A TYR* 3.9 7.5 - - - -
230A LEU* 3.4 4.0 - - - -
231A PHE* 2.9 60.1 + - - +
233A LYS* 4.6 16.2 - - - +
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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