Contacts of the strand formed by residues 169 - 176 (chain A) in PDB entry 3BFR
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 LEU 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A VAL* 4.2 15.5 - - + -
146A LYS 3.7 1.1 - - - -
147A ASN* 3.6 38.8 - - + +
155A ASP* 6.2 0.9 - - + -
157A VAL* 4.5 19.1 - - + -
165A VAL* 3.9 35.8 - - + +
166A THR 3.4 15.7 + - - +
167A GLY 3.3 5.1 - - - +
168A PRO* 1.3 80.3 - - + +
170A VAL* 1.3 63.3 + - - +
171A PRO* 3.6 8.4 - - - +
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Residues in contact with VAL 170 (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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145A VAL* 3.1 6.5 - - - -
146A LYS* 2.8 45.4 + - + +
148A LEU* 3.7 35.9 - - + -
167A GLY 5.0 2.9 - - - +
168A PRO 4.1 0.9 - - - +
169A LEU* 1.3 73.1 - - - +
171A PRO* 1.3 79.2 - - + +
172A LEU* 3.4 6.0 + - + +
209A ARG* 4.0 18.6 - - + +
213A GLY* 3.8 29.4 - - - +
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Residues in contact with PRO 171 (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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91A LEU* 3.8 38.1 - - + -
143A PHE* 4.2 9.6 - - + -
144A ILE 4.0 4.5 - - - +
145A VAL* 4.3 2.2 - - + -
165A VAL* 3.6 28.9 - - + +
169A LEU 3.6 8.5 - - - +
170A VAL* 1.3 94.5 - - + +
172A LEU* 1.3 60.3 + - - +
173A VAL 5.3 1.6 - - - +
174A ALA* 5.7 0.4 - - + -
209A ARG* 3.5 19.6 + - - +
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Residues in contact with LEU 172 (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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95A ASN* 4.3 0.9 - - - +
111A LEU* 3.9 10.8 - - + -
144A ILE* 2.8 25.2 + - + +
145A VAL 3.8 8.7 - - - -
146A LYS* 3.8 9.4 - - + +
154A LEU* 3.5 32.5 - - + -
170A VAL* 3.7 15.9 - - + +
171A PRO* 1.3 76.8 - - - +
173A VAL* 1.3 62.8 + - + +
203A TRP* 6.3 0.7 - - + -
206A ALA* 3.6 20.5 - - + +
209A ARG* 2.7 35.6 + - - +
210A PHE* 3.6 42.4 - - + +
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Residues in contact with VAL 173 (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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95A ASN* 3.8 13.7 - - + +
142A ALA 3.8 0.9 - - - +
143A PHE* 3.3 7.4 - - - -
144A ILE* 2.9 39.9 + - + +
171A PRO* 5.4 0.4 - - - -
172A LEU* 1.3 87.4 - - + +
174A ALA* 1.3 61.6 + - - +
175A ILE* 3.7 29.0 + - + +
198A TRP* 4.2 7.4 - - + -
201A VAL* 4.2 17.0 - - + -
203A TRP* 3.9 25.1 - - + -
206A ALA* 3.7 19.3 - - + -
209A ARG* 4.6 0.2 - - - -
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Residues in contact with ALA 174 (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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88A ASN 4.4 0.4 - - - +
91A LEU* 4.1 17.5 - - + -
92A PHE* 3.2 14.0 - - - +
95A ASN* 2.9 34.0 - - - +
141A TRP* 4.1 13.5 - - + -
142A ALA 3.7 4.0 - - - -
143A PHE* 3.6 27.8 - - + -
171A PRO* 5.7 0.9 - - + +
173A VAL* 1.3 72.6 - - - +
175A ILE* 1.3 65.3 + - - +
209A ARG* 4.3 0.6 - - - +
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Residues in contact with ILE 175 (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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92A PHE* 4.0 1.3 - - + -
95A ASN* 4.8 1.8 - - - +
96A LEU* 5.6 0.2 - - + -
129A THR* 4.7 4.0 - - + -
133A LEU* 3.6 34.0 - - + +
141A TRP* 3.4 8.8 - - - -
142A ALA 3.0 34.1 + - - +
144A ILE* 6.2 0.2 - - + -
173A VAL* 3.7 23.1 - - + +
174A ALA* 1.3 80.7 - - - +
176A ASP* 1.3 69.3 + - - +
177A ALA 3.5 0.3 + - - -
193A TYR* 4.5 1.3 - - - +
194A PHE* 4.8 3.8 - - + -
197A ILE* 4.2 33.0 - - + -
198A TRP* 4.1 22.4 - - + -
201A VAL* 4.1 15.9 - - + -
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Residues in contact with ASP 176 (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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34A HIS* 2.7 11.4 + - - -
89A HIS* 3.4 1.2 + - - -
92A PHE* 3.5 23.6 - - + -
141A TRP* 3.5 26.8 - - + -
175A ILE* 1.3 74.3 - - - +
177A ALA* 1.3 67.3 + - - +
178A TRP* 3.1 26.6 + - - -
180A HIS* 3.6 0.3 + - - -
181A ALA* 3.8 12.1 - - + +
193A TYR* 2.9 30.0 + - - -
194A PHE* 4.5 0.2 - - - -
216A MN3 2.0 33.5 + - - -
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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