Contacts of the strand formed by residues 156 - 166 (chain A) in PDB entry 4BM9
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 ARG 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A TYR* 3.6 15.4 - - - -
150A CYS* 3.0 29.3 + - - +
153A PRO 5.3 0.2 + - - -
154A CYS* 3.1 35.9 + - + +
155A GLN* 1.3 78.5 - - - +
157A VAL* 1.3 72.6 + - - +
158A GLN* 3.5 27.1 + - + +
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Residues in contact with VAL 157 (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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147A TYR* 4.1 27.4 - - + -
148A VAL 3.3 9.6 - - - +
149A TYR* 3.9 5.5 - - + -
156A ARG* 1.3 79.3 - - - +
158A GLN* 1.3 72.3 + - - +
159A PRO* 4.8 0.3 - - - +
226A LEU* 3.9 16.8 - - + -
229A ILE* 4.2 8.3 - - + -
247A PRO* 5.0 1.3 - - + -
261A LEU* 4.1 24.5 - - + -
306A ILE* 3.8 33.4 - - + -
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Residues in contact with GLN 158 (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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147A TYR* 3.4 6.9 - - - -
148A VAL* 2.8 37.5 + - + +
150A CYS* 4.5 0.7 - - + -
154A CYS* 3.0 31.5 - - + +
156A ARG* 3.5 35.0 + - + +
157A VAL* 1.3 81.2 - - - +
159A PRO* 1.3 78.7 - - + +
212A CYS* 3.6 27.1 - - - -
214A ALA* 3.3 19.7 - - + +
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Residues in contact with PRO 159 (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 ASN* 3.7 33.4 - - - +
146A PHE 3.5 8.5 - - - +
147A TYR* 3.7 20.6 - - + -
157A VAL 4.8 0.2 - - - +
158A GLN* 1.3 100.4 - - + +
160A GLY* 1.3 60.1 + - - +
212A CYS* 4.2 0.7 - - - -
213A GLY* 3.2 23.5 + - - -
214A ALA* 4.7 1.5 + - + +
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Residues in contact with GLY 160 (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 ASN* 4.7 7.3 - - - +
146A PHE* 2.9 28.9 + - - +
147A TYR* 4.2 0.2 - - - +
148A VAL* 4.0 20.0 - - - -
158A GLN 3.4 2.0 + - - -
159A PRO* 1.3 76.0 - - - +
161A LYS* 1.3 69.3 + - - +
211A LYS 3.2 9.6 - - - -
459A GLY 3.8 7.3 - - - +
460A ASP* 4.8 2.4 - - - +
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Residues in contact with LYS 161 (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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160A GLY* 1.3 77.0 - - - +
162A LEU* 1.3 62.5 + - - +
163A ARG* 3.7 42.7 + - - +
210A PHE* 3.2 7.4 - - - -
211A LYS* 2.7 44.2 + - + +
212A CYS 4.9 1.3 - - - +
213A GLY* 4.1 18.8 - - - -
455A ARG 6.1 0.2 - - - -
456A VAL* 4.9 11.5 + - - +
459A GLY* 3.5 5.3 - - - +
460A ASP* 3.0 32.7 + - - +
1474A SO4 4.9 2.5 - - - +
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Residues in contact with LEU 162 (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* 3.6 37.0 - - + -
160A GLY 4.2 0.6 + - - -
161A LYS* 1.3 71.3 - - - +
163A ARG* 1.3 83.6 + - - +
180A PRO* 4.3 1.3 - - + -
186A VAL* 4.1 18.6 - - + -
208A PHE* 3.7 26.7 - - + -
209A PHE 3.8 5.4 - - - +
210A PHE* 3.6 28.9 - - + -
458A MET* 4.1 4.0 - - - +
459A GLY* 2.9 17.3 + - - +
462A TRP* 3.8 34.6 - - + -
463A PHE* 4.3 2.9 - - + -
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Residues in contact with ARG 163 (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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161A LYS* 3.7 36.5 - - - +
162A LEU* 1.3 86.1 + - - +
164A VAL* 1.3 65.5 + - - +
208A PHE* 3.3 11.4 - - - -
209A PHE* 2.7 73.3 + - + +
211A LYS* 4.5 5.4 - - + +
455A ARG* 4.7 6.3 + - - +
459A GLY* 3.8 18.6 - - - +
1474A SO4 2.6 45.5 + - - +
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Residues in contact with VAL 164 (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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163A ARG* 1.3 76.5 - - - +
165A GLN* 1.3 66.4 + - - +
172A ALA* 4.1 16.1 - - - +
174A LEU* 4.8 16.1 - - + +
176A LEU* 4.3 6.5 - - + -
206A ALA* 3.9 16.6 - - + -
207A GLU 3.5 8.3 - - - +
208A PHE* 3.3 32.3 - - + -
209A PHE* 4.6 3.7 - - - -
458A MET* 5.1 3.8 - - + -
462A TRP* 3.3 38.4 - - + -
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Residues in contact with GLN 165 (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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164A VAL* 1.3 76.3 - - - +
166A CYS* 1.3 66.9 + - - +
170A ARG* 3.6 33.4 - - - +
171A GLN 3.4 19.1 - - - +
172A ALA* 4.4 2.7 - - + +
174A LEU* 3.8 8.9 - - - +
206A ALA* 3.7 4.3 - - - -
207A GLU* 2.4 74.3 + - + +
209A PHE* 3.5 24.6 - - + -
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Residues in contact with CYS 166 (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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165A GLN* 1.3 73.5 - - - +
167A SER* 1.3 59.1 + - - +
168A THR* 3.4 22.7 - - - -
169A CYS* 3.6 8.3 - - - -
170A ARG* 2.9 29.5 + - - -
171A GLN 3.0 11.1 + - - +
174A LEU* 3.5 14.8 - - + +
196A CYS* 3.8 11.0 - - + -
203A GLY* 3.8 17.9 - - - -
205A SER 3.7 6.1 - - - -
1469A ZN 2.4 36.8 - - - -
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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