Contacts of the strand formed by residues 189 - 197 (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 PHE 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A THR* 4.1 18.4 - - + -
155A GLU* 4.8 7.0 - - - -
160A LEU* 4.5 6.3 - - + -
166A LEU* 3.8 22.0 - - + -
182A HIS* 3.9 21.8 - + - -
183A VAL* 3.4 29.4 - - + +
186A SER* 3.4 21.0 + - - +
187A SER 3.3 2.3 - - - +
188A CYS* 1.3 87.6 - - + +
190A GLU* 1.3 58.9 + - - +
191A CYS* 4.0 4.5 - - - -
210A ALA* 4.0 17.5 - - + -
211A ILE 3.2 4.3 - - - -
212A TYR* 3.7 39.5 - + + -
213A LYS* 3.7 8.7 + - - +
303A K 2.6 26.7 - - - -
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Residues in contact with GLU 190 (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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189A PHE* 1.3 70.9 - - - +
191A CYS* 1.3 70.5 + - - +
192A THR* 5.1 3.4 + - - +
209A LYS* 3.6 2.6 - - - +
211A ILE* 2.8 52.0 + - + +
213A LYS* 3.7 26.6 + - + +
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Residues in contact with CYS 191 (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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183A VAL* 3.3 54.3 - - - -
184A ARG* 3.8 12.3 - - + -
189A PHE* 4.0 3.3 + - - -
190A GLU* 1.3 84.8 - - - +
192A THR* 1.3 66.2 + - - +
208A GLU* 3.5 16.8 - - - +
209A LYS 3.1 5.2 - - - +
210A ALA* 4.0 9.0 - - - -
303A K 4.6 0.2 - - - -
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Residues in contact with THR 192 (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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190A GLU* 4.2 4.2 + - - +
191A CYS* 1.3 75.8 + - - +
193A HIS* 1.3 69.0 + - - +
194A TYR* 3.9 27.2 + - + +
208A GLU* 3.7 5.9 - - - -
209A LYS* 2.8 58.5 + - - +
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Residues in contact with HIS 193 (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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171A VAL* 3.5 23.3 - - + -
172A ILE* 3.4 31.6 - - + +
180A LEU* 5.7 0.2 - - + -
184A ARG* 3.3 17.8 + - - +
192A THR* 1.3 79.5 - - - +
194A TYR* 1.3 66.3 + - - +
195A GLN* 3.6 25.7 + - + +
206A GLY* 4.0 3.8 - - - -
207A LEU 3.5 7.1 + - - -
208A GLU* 2.8 26.1 + - - +
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Residues in contact with TYR 194 (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 ILE* 3.8 37.5 - - + -
53A VAL* 4.5 13.1 - - + +
56A GLU* 4.8 2.9 + - - -
167A LEU* 4.9 4.7 - - + -
192A THR* 3.9 23.2 - - + +
193A HIS* 1.3 77.1 - - - +
195A GLN* 1.3 63.2 + - - +
196A SER* 3.7 0.3 + - - -
206A GLY* 3.1 4.2 - - - -
207A LEU* 3.0 43.6 + - - +
209A LYS* 2.7 54.3 + - + -
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Residues in contact with GLN 195 (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 ILE* 4.3 5.4 - - - +
172A ILE* 5.0 5.1 - - + +
193A HIS* 3.6 18.4 + - + +
194A TYR* 1.3 73.9 - - - +
196A SER* 1.3 69.9 + - - +
197A PHE* 6.2 1.4 - - - -
204A VAL* 4.0 29.5 - - + +
205A ASP 3.7 11.2 - - - +
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Residues in contact with SER 196 (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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45A LYS* 4.1 10.0 - - - +
46A LYS* 3.6 31.2 + - - +
49A ILE* 3.8 19.9 - - - +
194A TYR 3.7 2.9 + - - -
195A GLN* 1.3 79.1 + - - +
197A PHE* 1.3 84.4 + - - +
204A VAL* 3.7 10.2 - - - +
205A ASP 2.8 23.9 + - - +
207A LEU* 4.9 0.9 - - - -
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Residues in contact with PHE 197 (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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45A LYS* 3.7 41.6 - - + +
46A LYS* 3.3 23.6 + - - +
195A GLN* 6.2 1.8 - - - -
196A SER* 1.3 93.4 + - - +
198A LEU* 1.3 65.8 + - - +
199A GLU* 3.4 0.7 + - - -
201A ARG 3.6 14.8 - - - +
202A GLU* 3.4 35.4 - - + -
203A VAL 3.4 5.4 - - - -
204A VAL* 4.1 14.4 - - + -
205A ASP* 3.8 6.7 - - - +
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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