Contacts of the strand formed by residues 185 - 191 (chain B) in PDB entry 1IVV
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 GLU 185 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B LEU* 4.5 2.0 - - - -
150B ARG* 2.9 22.7 + - - -
179B VAL* 3.5 2.1 - - - +
180B ASP* 2.8 33.3 + - + +
183B SER* 2.9 35.9 + - - +
184B LYS* 1.3 75.3 - - - +
186B VAL* 1.3 64.2 + - - +
187B THR* 3.2 6.0 + - + +
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Residues in contact with VAL 186 (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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111B LEU* 4.0 29.8 - - + +
112B LEU* 3.9 23.8 - - + -
115B ASP* 3.3 20.2 - - + +
117B ARG* 2.7 38.3 + - - +
178B TYR 3.6 5.8 - - - +
179B VAL* 4.3 5.2 - - + -
185B GLU* 1.3 71.1 - - - +
187B THR* 1.3 59.2 + - - +
188B ARG 3.8 7.6 - - - +
189B VAL* 3.7 22.7 - - + -
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Residues in contact with THR 187 (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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117B ARG* 4.1 6.2 + - - -
146B GLU* 4.8 12.3 + - - +
147B GLU* 5.0 1.4 + - - +
150B ARG* 3.5 40.2 - - - +
152B ILE* 4.2 8.3 - - + +
178B TYR* 2.9 29.9 + - - +
180B ASP* 4.0 10.1 - - + +
185B GLU* 3.2 14.1 + - + +
186B VAL* 1.3 72.9 - - - +
188B ARG* 1.3 67.6 + - - +
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Residues in contact with ARG 188 (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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117B ARG* 4.0 5.6 - - - +
144B TYR* 3.4 26.3 - - - -
146B GLU* 2.6 40.1 + - - +
177B ALA* 3.2 4.6 - - - +
178B TYR* 2.8 65.8 + - + +
186B VAL* 3.3 2.7 - - - +
187B THR* 1.3 86.6 + - - +
189B VAL* 1.3 67.5 + - - +
190B ILE* 4.2 12.7 - - + +
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Residues in contact with VAL 189 (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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115B ASP* 3.8 15.3 - - - +
117B ARG* 3.8 43.5 - - + +
118B TRP* 4.1 11.0 - - + +
121B ALA* 5.0 0.7 - - + -
175B LEU* 4.2 20.2 - - + -
176B VAL 3.6 4.0 - - - -
177B ALA* 4.1 10.1 - - + -
186B VAL* 3.7 20.6 - - + -
188B ARG* 1.3 80.9 - - - +
190B ILE* 1.3 63.9 + - - +
191B ASP* 4.1 3.5 + - + +
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Residues in contact with ILE 190 (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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144B TYR* 4.4 5.4 - - + +
174B GLY 3.5 0.4 - - - +
175B LEU* 3.3 9.3 - - - +
176B VAL* 2.8 51.9 + - + +
178B TYR* 3.5 36.8 - - + +
188B ARG* 4.6 14.8 - - + +
189B VAL* 1.3 79.2 - - - +
191B ASP* 1.3 62.2 + - - +
192B THR* 4.1 21.8 - - + -
289B PRO* 5.8 6.7 - - + +
290B ILE* 4.5 2.5 - - + -
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Residues in contact with ASP 191 (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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121B ALA* 3.6 16.0 - - + +
124B ALA* 5.2 2.3 - - - +
125B ARG* 2.8 39.7 + - - -
174B GLY 3.1 2.7 - - - -
175B LEU* 4.4 5.6 - - + -
189B VAL* 4.1 4.1 + - + -
190B ILE* 1.3 75.9 - - - +
192B THR* 1.3 61.4 + - - +
193B GLY* 2.9 26.9 + - - -
194B VAL* 4.3 1.5 + - - +
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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