Contacts of the strand formed by residues 172 - 179 (chain A) in PDB entry 3VPP
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 ASP 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A TYR* 1.3 74.6 - - - +
173A TYR* 1.3 60.8 + - - +
174A TRP 4.2 0.2 - - - -
213A TYR* 3.4 26.8 + - + -
214A VAL 3.6 4.5 - - - -
215A LYS* 2.7 43.1 + - - +
228A LYS* 3.8 25.5 + - + +
229A TYR* 3.0 32.4 + - - +
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Residues in contact with TYR 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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127A VAL* 3.4 19.3 - - + +
128A SER 4.0 4.8 + - - -
164A LEU* 3.7 30.7 - - + -
167A ILE* 3.8 20.1 - - - +
168A LYS 5.0 0.3 + - - -
171A TYR* 3.2 53.0 - - + +
172A ASP* 1.3 71.8 - - - +
174A TRP* 1.3 65.6 + - - +
175A VAL* 3.8 2.1 - - - +
213A TYR* 3.2 4.0 - - - +
214A VAL* 2.8 42.2 + - + +
229A TYR* 3.3 28.4 - + + -
230A PHE* 4.0 5.4 - - - -
231A ILE* 3.7 35.9 - - + -
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Residues in contact with TRP 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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132A SER 2.9 20.9 + - - -
134A TRP* 3.5 30.5 - + + +
137A SER* 3.3 21.8 - - - -
148A LEU* 4.0 9.4 - - + +
172A ASP 4.2 0.4 - - - -
173A TYR* 1.3 75.1 - - - +
175A VAL* 1.3 63.0 + - - +
211A CYS* 3.7 27.8 - - + -
212A GLY 3.4 19.7 - - - -
213A TYR* 4.0 5.1 - - + +
222A SER* 3.8 7.9 - - - -
223A ASN 3.4 21.3 - - - -
224A CYS* 3.7 13.5 - - - -
226A THR* 3.3 29.1 + - - -
228A LYS* 3.6 24.1 - - + +
229A TYR 2.7 24.5 + - - +
230A PHE* 4.0 7.6 - - + -
231A ILE* 3.4 21.5 + - - +
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Residues in contact with VAL 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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134A TRP* 2.8 22.5 + - - -
148A LEU* 3.9 7.4 - - - -
149A LEU* 3.4 32.1 - - + +
151A ILE* 4.5 1.8 - - + -
173A TYR 3.8 2.9 - - - +
174A TRP* 1.3 78.8 - - - +
176A GLY* 1.3 60.3 + - - +
177A LEU* 2.9 14.4 + - + +
188A TRP* 4.1 11.2 - - + -
212A GLY 3.1 25.3 + - - +
213A TYR 4.2 0.2 - - - +
214A VAL* 3.4 28.7 - - + -
219A LEU* 4.0 17.7 - - + -
231A ILE* 5.4 2.0 - - + -
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Residues in contact with GLY 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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134A TRP* 4.2 5.6 - - - -
148A LEU* 3.6 21.9 - - - +
149A LEU 2.7 20.2 + - - -
150A GLN* 4.6 1.7 - - - +
175A VAL* 1.3 68.9 - - - +
177A LEU* 1.3 55.3 + - - +
187A LEU 3.7 0.3 - - - +
188A TRP* 3.2 13.0 - - - -
189A GLN* 3.1 40.6 + - - +
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Residues in contact with LEU 177 (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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134A TRP* 3.7 4.0 + - - +
175A VAL* 2.9 13.5 + - + -
176A GLY* 1.3 73.2 - - - +
178A SER* 1.3 61.6 - - - +
186A TRP* 4.1 9.0 - - + -
187A LEU 3.5 27.1 - - - +
188A TRP* 3.4 41.3 - - + +
194A PRO* 3.9 16.4 - - + -
198A LEU 3.8 12.1 - - - +
200A PRO* 3.7 33.4 - - + -
211A CYS* 3.4 6.2 - - - +
212A GLY* 2.9 26.8 + - - +
219A LEU* 4.5 13.2 - - + -
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Residues in contact with SER 178 (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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134A TRP* 4.2 20.4 - - - -
177A LEU* 1.3 74.6 - - - +
179A GLN* 1.3 62.2 + - - +
180A ASP* 4.0 2.1 + - - +
185A ARG 3.7 1.2 - - - +
186A TRP* 3.5 6.8 - - - -
187A LEU* 3.0 36.8 + - - +
189A GLN* 5.4 2.6 - - - +
209A GLN* 4.1 18.5 + - - -
210A VAL 3.5 9.6 - - - -
211A CYS* 4.2 2.2 - - - -
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Residues in contact with GLN 179 (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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178A SER* 1.3 72.5 - - - +
180A ASP* 1.3 67.2 + - - +
181A GLY* 3.5 2.4 + - - -
184A GLY* 2.9 43.4 + - - +
185A ARG 3.6 2.7 - - - +
186A TRP* 3.3 38.7 - - + +
209A GLN* 4.2 15.2 - - - +
210A VAL* 2.8 45.0 + - + +
221A SER* 4.9 0.3 + - - -
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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