Contacts of the strand formed by residues 181 - 190 (chain A) in PDB entry 5VEB
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 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A ASP* 3.0 23.0 + - - -
150A TYR* 2.8 51.7 + - + +
151A PHE* 3.9 27.8 - + - -
152A PRO 4.4 1.1 - - - -
153A GLU* 3.7 41.3 - - + +
173A ALA* 3.9 15.3 - - + -
174A VAL 3.4 13.5 - - - -
175A LEU* 3.8 35.0 - - + +
176A GLN* 3.8 0.4 - - - -
180A LEU* 1.3 72.6 - - - +
182A SER* 1.3 61.3 + - - +
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Residues in contact with SER 182 (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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146A LEU* 3.9 15.1 - - - +
147A VAL 3.3 10.8 + - - -
148A LYS* 3.7 16.4 - - - +
150A TYR* 4.2 0.4 - - - -
172A PRO 4.6 0.5 - - - +
173A ALA* 3.6 1.7 - - - -
174A VAL* 2.8 42.4 + - - +
176A GLN* 3.7 27.4 - - - -
181A TYR* 1.3 75.9 - - - +
183A LEU* 1.3 61.0 + - - +
179B THR* 5.8 2.6 - - - +
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Residues in contact with LEU 183 (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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146A LEU* 3.8 6.8 - - - +
147A VAL* 2.8 53.1 + - + +
150A TYR* 3.4 12.7 - - - +
153A GLU* 5.0 2.0 - - - +
155A VAL* 3.3 31.2 - - + +
157A VAL* 4.1 15.3 - - + -
170A THR* 4.1 12.3 - - + -
171A PHE* 3.5 22.0 - - - +
172A PRO 4.4 2.0 - - - -
173A ALA* 3.8 13.9 - - + +
182A SER* 1.3 76.5 + - - +
184A SER* 1.3 75.5 + - - +
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Residues in contact with SER 184 (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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129A LEU* 4.3 15.9 - - - -
145A CYS 3.3 9.4 - - - -
146A LEU* 4.5 11.0 - - - -
171A PHE* 3.0 37.3 + - - +
183A LEU* 1.3 80.8 - - - +
185A SER* 1.3 61.0 + - - +
186A VAL* 5.0 2.5 - - - -
134B VAL* 5.0 4.3 - - - -
177B SER* 2.8 32.2 + - - -
179B THR* 5.2 1.7 + - - -
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Residues in contact with SER 185 (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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144A GLY* 3.1 2.9 - - - -
145A CYS* 2.8 37.0 + - - +
147A VAL* 5.7 0.2 - - - -
157A VAL* 3.6 30.9 - - - +
159A TRP* 2.9 28.2 + - - -
168A VAL* 4.2 1.4 - - - +
169A HIS 3.4 5.2 + - - -
170A THR* 3.0 22.7 + - - +
183A LEU* 4.3 0.4 - - - +
184A SER* 1.3 73.5 - - - +
186A VAL* 1.3 61.7 + - - +
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Residues in contact with VAL 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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129A LEU* 4.0 19.7 - - + -
143A LEU 3.3 13.5 - - - +
144A GLY* 4.0 0.2 - - - -
159A TRP* 4.6 2.5 - - - -
167A GLY 3.9 0.4 - - - +
168A VAL* 3.4 5.9 - - - +
169A HIS* 2.9 46.5 + - + +
171A PHE* 3.6 29.6 - - + -
184A SER* 5.0 3.4 - - - -
185A SER* 1.3 78.9 + - - +
187A VAL* 1.3 63.3 + - - +
188A THR* 6.2 0.9 - - + -
119B PHE* 4.9 7.4 - - + -
134B VAL* 5.7 2.5 - - + -
136B LEU* 3.8 33.9 - - + -
138B ASN* 5.1 0.2 - - - +
177B SER* 5.9 0.7 - - - +
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Residues in contact with VAL 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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142A ALA* 3.6 1.7 - - - -
143A LEU* 2.9 58.2 + - + +
159A TRP* 4.0 13.5 - - + -
164A LEU* 3.9 26.9 - - + -
166A SER 3.6 24.7 - - - +
167A GLY 3.5 5.2 - - - -
168A VAL* 3.7 18.2 - - + -
186A VAL* 1.3 78.2 - - - +
188A THR* 1.3 71.5 + - - +
189A VAL* 3.8 8.6 + - + -
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Residues in contact with THR 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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140A THR* 4.1 13.2 - - - +
141A ALA 3.3 6.5 - - - +
142A ALA* 3.9 21.3 - - + -
166A SER 4.6 1.9 - - - +
167A GLY* 3.4 25.7 + - - +
186A VAL* 6.2 0.7 - - + -
187A VAL* 1.3 75.8 - - - +
189A VAL* 1.3 63.8 + - - +
117B PHE* 4.5 11.4 - - + -
136B LEU* 4.8 2.7 - - + -
138B ASN* 3.5 33.5 + - - +
139B ASN* 5.9 0.2 + - - -
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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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140A THR* 3.7 3.5 - - - -
141A ALA* 2.8 35.4 + - + +
143A LEU* 3.7 26.2 - - + -
164A LEU* 4.5 8.5 - - + -
187A VAL* 4.0 21.3 - - + -
188A THR* 1.3 78.6 - - - +
190A PRO* 1.4 70.7 - - + +
193A SER* 4.0 3.6 - - - +
194A LEU* 4.1 7.0 - - + -
199A TYR* 3.4 42.8 - - + +
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Residues in contact with PRO 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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139A GLY 3.3 11.0 - - - +
140A THR* 4.5 1.3 - - - -
189A VAL* 1.4 92.3 - - + +
191A SER* 1.4 60.3 + - - +
192A SER* 3.7 17.0 - - - +
193A SER* 2.7 39.9 + - - +
194A LEU* 3.9 1.4 + - - +
199A TYR* 4.6 0.7 - - - +
157L SER 4.2 0.9 - - - +
158L GLY* 3.6 32.3 - - - +
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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