Contacts of the strand formed by residues 177 - 186 (chain A) in PDB entry 2BZG
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 LYS 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A ASP* 4.2 13.3 - - - +
175A GLY* 3.9 8.4 - - - -
176A LYS* 1.3 81.9 - - + +
178A PHE* 1.3 64.4 + - - +
244A GLU* 3.5 29.4 + - + +
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Residues in contact with PHE 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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146A PHE 4.5 1.1 - - - +
147A ASP 3.2 13.9 - - - +
171A PHE* 4.9 1.1 - + - -
174A LEU* 3.6 42.6 - - + -
175A GLY 3.3 20.4 - - - +
176A LYS 4.2 3.8 - - - -
177A LYS* 1.3 75.8 - - - +
179A GLN* 1.3 65.5 + - - +
180A TYR* 3.9 9.6 - - + -
211A ILE* 4.6 13.9 - - + -
212A CYS* 3.8 24.0 - - - -
242A LEU 3.6 19.1 - - - -
243A THR* 3.5 21.4 - - - +
244A GLU* 3.1 45.6 + - + +
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Residues in contact with GLN 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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56A PHE* 3.1 38.1 + - - +
60A LYS* 3.9 22.4 - - - +
63A LEU* 5.3 0.4 - - - +
147A ASP 3.0 8.1 + - - +
148A MSE 3.1 32.4 - - + +
149A ILE 3.1 21.7 + - - -
174A LEU* 5.4 0.4 - - - +
178A PHE* 1.3 79.2 - - - +
180A TYR* 1.3 60.6 + - - +
181A LEU* 3.9 2.2 - - + -
241A LEU* 3.9 28.1 - - + +
242A LEU 3.6 3.8 - - - -
243A THR* 4.2 6.8 - - + +
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Residues in contact with TYR 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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149A ILE* 3.8 26.0 - - + +
151A ASP* 2.6 43.7 + - + -
166A TYR* 3.8 1.4 - - - -
170A MSE 3.7 28.7 - - + +
171A PHE* 5.8 0.4 - + - -
174A LEU* 4.2 12.1 - - + -
178A PHE* 3.9 11.4 - + + -
179A GLN* 1.3 70.4 - - - +
181A LEU* 1.3 68.3 + - - +
182A LEU* 4.1 11.6 - - + +
208A PHE* 3.5 42.3 - + - -
212A CYS* 5.4 1.6 - - - -
240A TYR 3.7 0.7 - - - +
241A LEU* 3.6 1.7 - - - -
242A LEU* 2.8 61.8 + - + +
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Residues in contact with LEU 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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49A LEU* 4.1 6.1 - - + -
56A PHE* 3.5 47.8 - - + -
79A PHE* 5.0 2.5 - - + -
148A MSE 4.3 19.7 - - + -
149A ILE 2.9 16.1 + - - +
150A TRP* 3.6 29.4 - - + -
151A ASP* 2.9 31.8 + - - +
179A GLN* 4.5 9.0 - - + +
180A TYR* 1.3 73.3 - - - +
182A LEU* 1.3 59.3 + - - +
239A LEU* 4.6 2.5 - - + -
240A TYR 3.5 6.3 - - - +
241A LEU* 3.6 27.8 - - + -
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Residues in contact with LEU 182 (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 ASP* 3.5 31.2 - - - +
155A LEU* 3.8 32.1 - - + -
180A TYR* 4.1 12.6 - - + +
181A LEU* 1.3 75.1 - - - +
183A CYS* 1.3 74.4 + - - +
184A VAL* 4.0 6.5 - - + -
204A ILE* 4.2 23.1 - - + -
208A PHE* 4.2 16.4 - - + -
238A LYS 3.5 1.6 - - - +
239A LEU* 3.5 2.8 - - - +
240A TYR* 2.8 48.7 + - + +
242A LEU* 4.3 12.3 - - + -
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Residues in contact with CYS 183 (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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46A HIS* 3.5 22.0 - - - -
150A TRP* 3.4 36.3 - - - -
151A ASP* 2.9 13.0 + - - +
152A ARG* 3.8 19.0 - - + -
153A GLY 4.8 1.9 + - - -
156A VAL* 3.9 9.9 + - - +
182A LEU* 1.3 78.2 - - - +
184A VAL* 1.3 66.9 + - - +
237A GLU* 3.4 15.9 - - - +
238A LYS 3.3 6.3 - - - +
239A LEU* 3.9 13.9 - - - -
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Residues in contact with VAL 184 (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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155A LEU* 4.4 1.1 - - + -
156A VAL* 3.9 11.7 - - + -
182A LEU* 4.0 22.0 - - + -
183A CYS* 1.3 80.2 - - - +
185A LEU* 1.3 65.2 + - - +
186A SER* 4.3 0.4 + - - -
199A VAL* 3.7 42.4 - - + +
200A PRO 6.0 0.2 - - - -
204A ILE* 4.0 7.0 - - + -
237A GLU* 3.4 6.8 - - - +
238A LYS* 2.9 43.7 + - + +
240A TYR* 3.9 26.2 - - + -
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Residues in contact with LEU 185 (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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152A ARG* 6.4 0.7 - - - +
156A VAL* 4.1 11.5 - - + +
183A CYS 6.0 0.2 - - - -
184A VAL* 1.3 83.5 - - - +
186A SER* 1.3 60.6 + - - +
187A TYR* 4.0 9.6 + - + -
196A PRO* 3.5 35.7 - - + -
197A PHE 4.7 4.2 - - - +
198A TYR* 3.5 20.3 - - - -
199A VAL 4.2 9.5 + - - +
222A ALA* 4.8 2.5 - - + -
227A HIS* 5.8 0.4 - - - +
230A TRP* 4.3 11.2 - - + -
235A LEU* 4.0 25.4 - - + -
236A PHE 3.4 7.6 - - - +
237A GLU* 3.9 25.8 - - + +
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Residues in contact with SER 186 (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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185A LEU* 1.3 72.8 - - - +
187A TYR* 1.3 64.8 + - - +
198A TYR* 4.0 15.0 + - - -
219A LYS* 5.4 4.1 + - - -
234A CYS 4.2 0.5 - - - +
235A LEU* 3.5 4.7 - - - +
236A PHE* 2.8 47.9 + - - +
238A LYS* 4.8 21.9 + - - -
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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