Contacts of the strand formed by residues 206 - 212 (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 ALA 206 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A VAL* 3.9 4.9 - - + -
165A GLN 3.7 4.7 - - - -
167A SER* 4.6 2.5 - - - -
174A LEU* 3.8 8.5 - - + +
176A LEU* 3.7 28.0 - - + -
190A ASN* 4.3 18.0 + - - +
191A ARG 5.3 0.7 + - - -
192A MET* 3.0 20.7 + - + +
204A THR 4.1 0.8 + - - -
205A SER* 1.3 74.5 - - - +
207A GLU* 1.3 59.0 + - - +
208A PHE* 3.9 20.9 - - + -
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Residues in contact with GLU 207 (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 4.1 0.2 - - - +
164A VAL* 3.5 1.8 - - - +
165A GLN* 2.4 77.3 + - + +
167A SER* 4.0 26.9 - - - +
170A ARG* 5.3 1.4 - - - +
206A ALA* 1.3 73.0 - - - +
208A PHE* 1.3 68.4 + - - +
209A PHE* 4.4 3.2 - - + -
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Residues in contact with PHE 208 (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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162A LEU* 3.7 17.5 - - + -
163A ARG 3.3 11.9 - - - -
164A VAL* 3.3 24.2 - - + -
176A LEU* 3.4 16.8 - - + -
180A PRO* 4.2 9.9 - - + -
185A ASP 3.6 25.8 - - - -
186A VAL* 3.6 38.6 + - + +
192A MET* 3.3 31.6 - - + -
206A ALA* 3.9 17.7 - - + -
207A GLU* 1.3 83.2 - - - +
209A PHE* 1.3 65.3 + - - +
210A PHE* 5.4 1.1 - - + -
462A TRP* 4.2 4.7 - + - -
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Residues in contact with PHE 209 (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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162A LEU* 3.7 1.9 - - - +
163A ARG* 2.7 68.8 + - + +
164A VAL 4.6 1.3 - - - -
165A GLN* 3.5 37.5 - - + -
207A GLU* 4.4 7.0 - - + -
208A PHE* 1.3 79.7 - - - +
210A PHE* 1.3 66.5 + - - +
211A LYS* 3.8 23.6 - - + -
219A ASP 4.8 9.0 - - - -
222A THR* 3.7 30.5 - - + -
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Residues in contact with PHE 210 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A PHE* 3.7 38.1 - + + -
148A VAL* 3.7 15.0 - - + -
161A LYS 3.2 7.0 - - - +
162A LEU* 3.6 38.8 - - + -
183A TRP* 3.5 24.7 - + - -
186A VAL* 4.0 12.6 - - + -
187A LEU* 4.3 13.0 - - + -
208A PHE 5.6 0.2 - - - -
209A PHE* 1.3 80.2 - - - +
211A LYS* 1.3 70.6 + - - +
222A THR* 3.4 6.3 - - - -
223A SER* 3.0 35.7 + - - +
225A ALA* 3.6 26.2 - - + -
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Residues in contact with LYS 211 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A VAL* 4.6 3.6 - - - -
160A GLY* 3.2 4.3 - - - -
161A LYS* 2.7 45.2 + - + +
163A ARG* 4.5 4.3 - - + -
209A PHE* 3.8 26.9 - - + -
210A PHE* 1.3 81.7 - - - +
212A CYS* 1.3 64.0 + - - +
217A THR* 3.0 27.0 + - - +
218A SER 2.8 26.2 + - - +
219A ASP* 3.9 9.8 + - - +
221A GLU 3.3 27.4 - - - +
222A THR* 4.8 0.2 - - + -
223A SER 4.4 1.8 - - - +
1474A SO4 3.2 35.4 + - - +
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Residues in contact with CYS 212 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A VAL* 4.0 10.1 - - + +
150A CYS* 3.7 15.5 - - + -
154A CYS* 3.9 0.9 - - - -
158A GLN* 3.6 25.6 - - - -
161A LYS* 4.9 1.0 - - - +
211A LYS* 1.3 76.1 - - - +
213A GLY* 1.3 62.7 + - - +
214A ALA 3.5 12.7 + - - -
215A HIS* 3.6 12.1 - - + +
217A THR* 3.8 20.2 + - + +
221A GLU 5.0 0.6 + - - -
223A SER* 4.0 12.6 + - - +
1466A ZN 2.3 36.1 - - - -
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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