Contacts of the strand formed by residues 175 - 181 (chain B) in PDB entry 1IVH
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 VAL 175 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B CYS* 4.2 17.2 - - - -
108B LEU* 4.4 10.1 - - + -
120B TYR* 3.5 30.7 - - + -
124B LEU* 4.0 15.5 - - + -
129B TYR* 3.9 24.0 - - + -
130B ILE 3.5 2.3 + - - +
131B GLY* 3.5 5.2 - - - -
132B ALA 3.4 19.2 + - - -
173B ALA* 3.6 0.3 - - - +
174B ASP* 1.3 82.8 - - - +
176B LEU* 1.3 69.3 + - - +
177B ILE* 5.4 0.2 - - + -
197B ILE* 3.8 20.4 - - + -
198B VAL 3.5 5.4 - - - +
199B GLU* 5.1 1.3 - - + -
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Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ALA* 3.5 17.9 - - + +
134B ALA* 5.4 1.1 - - + +
167B ILE* 4.9 2.2 - - + -
170B GLY 4.4 4.9 - - - +
173B ALA* 3.6 34.8 - - + +
174B ASP 4.4 1.8 - - - -
175B VAL* 1.3 84.9 - - - +
177B ILE* 1.3 65.1 + - - +
178B VAL* 3.8 5.4 - - + -
196B PHE 3.4 0.5 - - - +
197B ILE* 3.2 6.1 - - - +
198B VAL* 2.7 62.1 + - + +
200B LYS 4.7 0.9 - - - +
205B PHE* 3.7 22.4 - - + -
224B LEU* 3.8 33.4 - - + -
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Residues in contact with ILE 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LEU 4.2 0.9 - - - +
104B CYS* 3.6 38.6 - - - +
107B GLN* 3.7 12.8 - - + -
108B LEU* 4.1 13.2 - - + -
132B ALA 3.1 8.1 + - - +
133B LEU* 3.6 21.1 - - + +
134B ALA 2.8 31.9 + - - +
175B VAL* 5.4 0.2 - - + -
176B LEU* 1.3 73.8 - - - +
178B VAL* 1.3 57.5 + - - +
179B TYR* 4.3 14.1 - - + +
195B ALA* 4.5 5.8 - - + -
196B PHE 3.5 5.6 - - - +
197B ILE* 4.9 8.7 - - + -
237B LEU* 3.7 34.8 - - + -
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Residues in contact with VAL 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ALA* 3.4 17.0 - - + +
149B LEU* 3.7 29.8 - - + -
160B LEU* 4.6 8.3 - - + -
164B LYS* 3.9 11.2 - - + -
176B LEU* 4.4 3.6 - - + -
177B ILE* 1.3 75.8 - - - +
179B TYR* 1.3 67.0 + - - +
194B THR 3.7 1.0 - - - +
195B ALA* 3.3 1.0 - - - -
196B PHE* 2.7 42.5 + - + +
198B VAL* 3.7 33.4 - - + -
224B LEU* 4.2 4.9 - - + -
226B PHE* 3.8 17.9 - - + -
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Residues in contact with TYR 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B GLN* 3.1 30.1 + - - +
133B LEU* 3.8 27.3 - - + +
134B ALA 3.1 25.0 + - - +
135B MET* 3.4 21.1 - - + +
147B MET* 3.3 11.0 - - + +
164B LYS* 2.9 31.2 + - - -
177B ILE* 4.3 6.1 - - + -
178B VAL* 1.3 74.5 - - - +
180B ALA* 1.3 58.6 + - - +
193B ILE* 3.6 28.0 - - + -
194B THR 3.4 2.5 - - - -
195B ALA* 3.5 17.9 - - + -
243B GLY 4.3 1.6 - - - -
246B VAL* 3.2 26.6 - - + +
247B LEU* 3.3 27.9 + - + -
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Residues in contact with ALA 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B MET* 4.3 2.5 - - - -
149B LEU* 3.3 28.5 - - + +
151B ALA* 3.8 20.6 - - + -
160B LEU* 4.4 6.5 - - + -
178B VAL* 3.8 1.1 + - + +
179B TYR* 1.3 74.6 - - - +
181B LYS* 1.3 62.2 + - - +
182B THR 3.4 2.1 + - - -
193B ILE* 3.2 4.9 - - - -
194B THR* 2.8 35.7 + - - +
196B PHE* 3.9 12.8 - - + -
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Residues in contact with LYS 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B VAL* 3.2 27.3 + - - +
146B SER* 4.8 2.2 - - - +
147B MET* 3.0 38.1 + - + +
148B LYS* 4.6 1.1 - - - -
149B LEU 2.7 15.1 + - - +
150B LYS* 3.9 0.3 - - - +
151B ALA* 3.3 17.9 + - - +
180B ALA* 1.3 68.2 - - - +
182B THR* 1.3 63.2 + - - +
183B ASP 3.4 5.2 + - - +
184B LEU* 3.8 36.9 - - + +
189B ALA* 3.5 31.8 + - - +
192B GLY* 3.0 20.6 - - - +
193B ILE* 4.2 8.7 - - + +
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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