Contacts of the strand formed by residues 204 - 212 (chain A) in PDB entry 3BWM
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 VAL 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A ILE* 4.1 20.3 - - + +
173A CYS* 3.7 9.4 - - - +
195A GLN* 4.0 30.7 - - + +
196A SER 3.7 10.3 - - - +
197A PHE* 4.1 17.7 - - + +
202A GLU 3.3 3.0 + - - +
203A VAL* 1.3 86.2 - - - +
205A ASP* 1.3 73.4 + - - +
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Residues in contact with ASP 205 (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 LYS* 2.9 27.4 + - + +
170A ASN* 3.0 23.0 + - - -
172A ILE* 3.3 19.8 + - - +
173A CYS 2.7 32.8 + - - +
195A GLN* 3.7 0.7 - - - -
196A SER* 2.8 29.5 + - - +
197A PHE* 3.8 4.7 - - - +
198A LEU* 3.6 22.1 - - + +
203A VAL 3.6 1.0 + - - -
204A VAL* 1.3 80.8 - - - +
206A GLY* 1.3 69.3 + - - +
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Residues in contact with GLY 206 (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 LYS* 5.1 0.7 - - - -
170A ASN 3.3 9.2 + - - -
171A VAL* 3.1 28.0 + - - -
172A ILE* 3.8 3.4 - - - +
193A HIS* 4.0 12.3 - - - -
194A TYR 3.1 13.7 - - - -
196A SER* 4.2 2.2 - - - -
205A ASP* 1.3 82.9 + - - +
207A LEU* 1.3 66.9 + - - -
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Residues in contact with LEU 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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42A VAL* 4.8 1.3 - - + -
46A LYS* 3.9 32.1 - - + -
49A ILE* 4.2 26.7 - - + -
50A VAL* 4.0 25.8 - - + -
139A PHE* 4.1 10.8 - - + -
167A LEU* 4.1 19.7 - - + -
168A ALA 3.1 14.1 - - - +
169A ASP* 3.9 20.2 - - + +
171A VAL* 4.0 3.1 - - - -
192A THR 4.1 0.2 - - - +
193A HIS* 3.5 6.6 + - - -
194A TYR* 3.0 38.3 + - + +
196A SER* 4.9 0.2 - - - -
206A GLY* 1.3 76.7 - - - -
208A GLU* 1.3 61.9 + - - +
209A LYS 4.2 0.2 - - - -
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Residues in contact with GLU 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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166A LEU 3.4 1.9 - - - +
167A LEU* 3.3 8.2 - - - +
168A ALA* 2.9 32.0 + - - +
171A VAL* 3.9 10.0 - - + +
179A PHE* 4.3 8.4 - - + -
180A LEU* 3.4 30.1 - - + +
183A VAL* 4.5 14.6 - - + -
184A ARG* 2.9 24.9 + - - -
191A CYS* 3.5 18.5 - - + +
192A THR 3.7 13.4 - - - +
193A HIS* 2.8 33.7 + - - +
207A LEU* 1.3 72.8 - - - +
209A LYS* 1.3 64.8 + - - +
210A ALA* 3.9 1.0 + - + +
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Residues in contact with LYS 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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53A VAL* 4.3 17.4 - - + +
56A GLU* 4.0 23.6 + - - -
57A HIS* 4.4 7.1 + - - +
165A VAL* 3.8 26.9 - - + -
166A LEU 3.3 3.1 - - - +
167A LEU* 4.0 8.4 - - + +
190A GLU 3.6 1.5 - - - +
191A CYS* 3.1 5.5 - - - +
192A THR* 2.8 58.0 + - - +
194A TYR* 2.7 36.2 + - + +
207A LEU 4.2 0.4 + - - -
208A GLU* 1.3 72.1 - - - +
210A ALA* 1.3 61.7 + - - +
211A ILE* 4.0 22.6 - - + +
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Residues in contact with ALA 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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164A THR 3.7 0.2 - - - +
165A VAL* 4.8 0.2 - - - -
166A LEU* 2.8 47.7 + - + +
179A PHE* 4.8 4.7 - - + -
183A VAL* 3.9 34.1 - - + -
189A PHE* 4.0 10.6 - - + -
190A GLU 3.6 4.0 - - - -
191A CYS* 4.0 8.3 - - - -
208A GLU* 3.9 2.4 + - + -
209A LYS* 1.3 72.7 - - - +
211A ILE* 1.3 63.6 + - - +
212A TYR 3.6 2.3 + - - -
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Residues in contact with ILE 211 (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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57A HIS* 4.0 22.4 - - + +
163A GLY* 3.7 30.7 - - - +
164A THR 3.4 5.4 - - - +
165A VAL* 4.3 11.9 - - + -
189A PHE* 3.2 3.5 - - - -
190A GLU* 2.8 56.0 + - + +
209A LYS* 4.2 24.9 - - + -
210A ALA* 1.3 72.3 - - - +
212A TYR* 1.3 67.5 - - - +
213A LYS* 3.4 4.0 + - + +
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Residues in contact with TYR 212 (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 GLU* 2.8 44.0 + - + +
160A LEU* 3.6 32.1 - - + -
161A ARG* 3.4 25.4 - - - +
162A LYS* 3.5 0.9 - - - +
163A GLY* 2.8 30.3 + - - -
164A THR* 2.9 19.8 + - - +
166A LEU* 6.0 0.9 - - + -
188A CYS* 3.3 27.4 - - + -
189A PHE* 3.7 24.0 - + + -
210A ALA 3.6 2.6 + - - -
211A ILE* 1.3 72.3 - - - +
213A LYS* 1.3 58.5 + - - +
214A GLY* 3.4 25.6 - - - -
215A PRO* 3.4 25.2 - - + +
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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