Contacts of the strand formed by residues 208 - 215 (chain A) in PDB entry 4BNR
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 TYR 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A ILE* 3.7 8.7 - - - -
122A ALA* 3.2 20.9 - - + +
123A LEU 4.3 5.8 - - - +
124A PRO* 3.5 31.9 - - + -
128A HIS* 3.3 17.3 + + - -
130A ALA* 3.2 16.7 - - + +
200A ALA* 3.4 4.9 - - - -
201A ALA* 3.0 45.8 + - + -
202A SER 4.0 1.3 - - - -
203A ASP* 2.5 30.5 + - - -
204A THR* 3.5 29.8 - - + -
206A SER* 3.6 6.7 - - - +
207A THR* 1.3 75.3 - - - +
209A LEU* 1.3 66.5 + - - +
210A ALA* 3.4 19.0 + - + -
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Residues in contact with LEU 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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45A SER* 3.7 15.9 - - - +
53A ILE* 3.9 34.1 - - + -
121A ILE* 3.7 19.8 - - + +
122A ALA 2.8 16.7 + - - +
123A LEU* 4.5 6.1 - - + -
124A PRO* 3.1 21.7 - - - +
198A PRO* 3.4 34.3 - - + -
199A LEU 4.0 3.6 - - - +
208A TYR* 1.3 69.8 - - - +
210A ALA* 1.3 58.6 + - - +
211A GLY 3.6 13.5 - - - +
212A ILE* 4.7 3.1 - - + -
232A VAL* 3.3 32.2 - - + +
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Residues in contact with ALA 210 (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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124A PRO* 5.1 1.6 - - - -
130A ALA* 3.8 14.5 - - + +
181A ILE* 4.4 4.2 - - + +
199A LEU* 2.9 19.7 + - + -
201A ALA* 3.7 28.9 - - + -
208A TYR* 3.4 14.4 + - + -
209A LEU* 1.3 75.0 - - - +
211A GLY* 1.3 59.8 + - - +
231A GLU* 3.7 11.6 - - - +
232A VAL* 2.9 23.3 + - - -
233A SER 4.5 1.0 + - - +
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Residues in contact with GLY 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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181A ILE* 4.7 1.6 - - - -
198A PRO* 3.7 0.9 - - - +
199A LEU* 2.8 44.2 + - - +
209A LEU* 3.6 12.2 - - - +
210A ALA* 1.3 80.9 - - - +
212A ILE* 1.3 64.6 + - - -
229A TYR* 4.3 7.6 - - - -
230A THR 3.2 9.6 - - - -
232A VAL* 3.9 1.8 - - - -
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Residues in contact with ILE 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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53A ILE* 3.5 29.6 - - + -
54A THR 4.0 1.8 - - - +
55A ALA* 3.9 14.6 - - + +
102A ASP 4.7 2.2 - - - +
103A ILE* 3.7 28.5 - - + -
196A GLY* 3.5 32.5 - - - +
197A GLY 3.4 3.8 - - - +
209A LEU* 4.7 4.0 - - + -
211A GLY* 1.3 76.6 - - - +
213A VAL* 1.3 72.9 - - - +
214A SER* 3.2 2.1 + - - -
229A TYR* 3.2 5.7 - - - +
230A THR* 2.9 40.1 + - + +
232A VAL* 3.8 17.0 - - + -
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Residues in contact with VAL 213 (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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55A ALA* 4.0 4.2 - - - +
138A VAL* 3.9 18.4 - - + -
139A THR 5.0 1.6 - - - +
190A SER* 3.6 23.8 - - - +
194A ASP* 3.3 23.6 - - + +
195A SER* 3.5 23.1 + - - +
196A GLY 2.9 21.6 + - - +
197A GLY* 3.0 20.4 + - - +
198A PRO 4.7 0.7 - - - +
212A ILE* 1.3 74.1 - - - +
214A SER* 1.3 61.5 + - - +
229A TYR* 3.5 25.8 - - + -
15I LYS* 4.0 13.0 - - + -
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Residues in contact with SER 214 (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* 3.1 23.1 - - - -
99A LEU* 4.6 2.8 + - - +
102A ASP* 2.7 28.8 + - - +
180A MET* 5.7 1.1 - - - +
195A SER* 3.3 1.1 + - - -
212A ILE 3.2 8.2 + - - -
213A VAL* 1.3 76.1 - - - +
215A TRP* 1.3 80.4 + - - +
228A VAL 3.3 14.1 + - - -
229A TYR* 4.1 1.1 - - - -
230A THR* 4.0 13.9 + - - -
14I CYS* 3.4 1.0 - - - +
15I LYS* 3.2 18.1 + - - -
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Residues in contact with TRP 215 (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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99A LEU* 3.7 18.5 - - + +
172A TYR* 3.8 23.6 - + - -
175A GLU* 3.7 44.4 - - + -
176A ILE* 3.8 11.9 - - + -
180A MET* 3.7 17.6 - - + +
214A SER* 1.3 105.8 - - - +
216A GLY* 1.3 77.5 - - - +
217A TYR* 5.6 0.2 - - - -
227A GLY 3.8 0.3 - - - -
228A VAL* 2.7 66.3 + - + +
13I PRO* 3.3 33.4 - - + +
14I CYS* 3.8 8.7 - - - +
15I LYS* 3.8 15.9 + - - +
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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