Contacts of the strand formed by residues 185 - 193 (chain A) in PDB entry 3VS5
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 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A LEU* 3.6 27.2 - - + +
150A PHE* 3.8 21.5 - + - -
175A ILE* 4.1 13.9 - - + -
176A ARG 3.2 11.0 - - - +
177A ASP* 3.8 17.3 - - - -
178A SER* 4.3 1.8 - - - -
183A GLY 4.6 14.2 + - - -
184A SER* 1.3 83.2 - - - +
186A SER* 1.3 64.4 + - - +
204A LYS* 4.3 0.5 - - - +
205A ILE* 2.9 38.9 + - + +
213A PHE* 3.7 38.4 - + - -
224A LEU* 4.0 13.0 - - + -
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Residues in contact with SER 186 (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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175A ILE* 3.3 2.6 - - - -
176A ARG* 2.7 73.1 + - - +
178A SER* 4.1 4.7 + - - +
185A TYR* 1.3 74.3 + - - +
187A LEU* 1.3 60.0 + - - +
203A TYR 3.3 12.7 + - - -
204A LYS* 4.1 4.9 - - - +
205A ILE* 3.8 5.8 - - - -
527A PTR 2.9 29.4 + - - -
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Residues in contact with LEU 187 (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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173A PHE* 4.1 17.0 - - + -
174A MET 3.4 13.5 - - - +
175A ILE* 3.9 17.7 - - + +
186A SER* 1.3 73.6 - - - +
188A SER* 1.3 62.0 + - - +
189A VAL* 3.8 24.9 - - + -
202A HIS* 3.3 3.5 - - - +
203A TYR* 2.7 42.3 + - + +
205A ILE* 3.8 14.8 - - + +
215A ILE* 3.6 26.7 - - + -
227A LEU* 4.7 7.2 - - + -
238A LEU* 4.2 22.2 - - + -
242A LEU* 4.4 9.4 - - + -
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Residues in contact with SER 188 (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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159A ALA* 3.7 3.8 - - - +
163A LEU* 3.4 19.8 - - - +
173A PHE* 3.2 5.0 - - - -
174A MET* 2.9 41.9 + - - -
176A ARG* 2.9 25.8 + - - -
186A SER 4.1 0.4 + - - -
187A LEU* 1.3 69.4 - - - +
189A VAL* 1.3 61.7 + - - +
200A VAL* 4.1 4.3 - - - -
201A LYS 3.4 4.7 - - - -
202A HIS* 2.7 28.2 + - - -
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Residues in contact with VAL 189 (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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163A LEU* 4.6 0.2 - - - -
171A GLY* 3.9 20.2 - - - +
172A SER 3.5 3.8 - - - +
173A PHE* 3.9 2.7 - - + -
187A LEU* 3.8 17.9 - - + -
188A SER* 1.3 79.5 - - - +
190A ARG* 1.3 74.9 + - - +
191A ASP* 3.4 1.9 + - - +
200A VAL* 3.5 4.1 - - - +
201A LYS* 2.9 34.7 + - - +
203A TYR* 4.7 7.9 - - + -
238A LEU* 5.0 2.9 - - + -
239A CYS* 4.5 10.5 - - - -
240A GLN* 4.0 17.9 - - + +
242A LEU* 3.6 29.2 - - + -
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Residues in contact with ARG 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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163A LEU* 2.7 39.9 + - + +
164A LEU* 3.9 20.6 + - + +
165A ALA 3.9 8.9 + - - -
166A PRO* 5.6 0.8 - - - +
168A ASN* 3.2 30.6 + - - +
169A MET* 3.1 33.8 - - - +
170A LEU* 3.9 7.0 - - + +
171A GLY 3.1 20.4 + - - -
172A SER* 2.8 18.8 + - - +
189A VAL* 1.3 74.4 - - - +
191A ASP* 1.3 65.3 + - - +
198A ASP* 3.5 33.1 + - - +
199A THR 3.4 12.1 - - - +
200A VAL* 4.4 4.0 - - + -
240A GLN* 4.1 2.3 - - - +
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Residues in contact with ASP 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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170A LEU* 3.8 6.1 - - - +
189A VAL 3.4 0.8 + - - -
190A ARG* 1.3 76.6 - - - +
192A TYR* 1.3 87.4 + - - +
193A ASP* 4.9 0.9 - - - +
198A ASP* 3.4 8.8 - - - +
199A THR* 2.8 38.3 + - - +
201A LYS* 3.1 31.0 + - + -
239A CYS* 3.1 38.7 - - - +
240A GLN* 3.3 18.7 - - - +
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Residues in contact with TYR 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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170A LEU* 3.7 25.6 - - + +
191A ASP* 1.3 92.5 + - - +
193A ASP* 1.3 63.8 + - - +
194A PRO* 3.6 38.8 + - + +
197A GLY* 3.5 31.4 - - - -
198A ASP* 3.7 16.6 - - - +
240A GLN* 5.2 1.0 - - - +
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Residues in contact with ASP 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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191A ASP* 5.7 0.9 - - - +
192A TYR* 1.3 78.7 - - - +
194A PRO* 1.3 62.9 - - + +
195A ARG* 2.8 26.3 + - + +
196A GLN* 3.0 44.4 + - - +
197A GLY 2.7 36.7 + - - +
199A THR* 3.6 16.1 + - - -
201A LYS* 4.0 13.2 + - - -
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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