Contacts of the strand formed by residues 175 - 181 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A CYS* 3.7 18.8 - - - -
108A LEU* 5.0 3.1 - - + -
120A TYR* 3.4 35.9 - - + -
124A LEU* 3.5 35.0 - - + -
129A TYR* 4.8 6.5 - - + -
130A ILE 3.4 1.5 + - - +
131A GLY* 3.5 0.9 - - - -
132A ALA 3.5 8.1 + - - -
173A ALA* 3.4 9.7 - - - +
174A ASP* 1.3 81.8 - - - +
176A LEU* 1.3 67.1 + - - +
177A ILE* 6.1 0.7 - - + -
197A ILE* 3.6 22.2 - - + -
198A VAL 3.5 4.9 - - - +
199A GLU* 4.5 2.0 - - + -
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Residues in contact with LEU 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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132A ALA* 3.4 18.4 - - + +
133A LEU* 5.7 0.2 - - - -
134A ALA* 5.3 1.3 - - + -
167A ILE* 4.6 2.5 - - + -
170A GLY 4.5 4.3 - - - +
173A ALA* 3.5 30.5 - - + +
174A ASP 4.5 1.8 - - - -
175A VAL* 1.3 84.7 - - - +
177A ILE* 1.3 63.1 + - - +
178A VAL* 3.7 5.5 + - + -
196A PHE 3.4 1.0 - - - +
197A ILE* 3.3 5.9 - - - -
198A VAL* 2.8 60.9 + - + +
200A LYS 4.8 0.9 - - - +
205A PHE* 3.7 22.9 - - + -
224A LEU* 3.5 35.4 - - + -
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Residues in contact with ILE 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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103A LEU 4.3 0.4 - - - +
104A CYS* 3.8 22.7 - - - +
107A GLN* 3.6 22.4 - - + -
108A LEU* 4.1 16.2 - - + -
132A ALA 3.1 11.7 + - - +
133A LEU* 3.5 20.8 - - + +
134A ALA 2.8 28.6 + - - +
175A VAL* 6.1 0.7 - - + -
176A LEU* 1.3 74.5 - - - +
178A VAL* 1.3 60.5 + - - +
179A TYR* 4.2 14.9 - - + +
195A ALA* 4.6 6.3 - - + -
196A PHE 3.3 8.1 - - - +
197A ILE* 5.0 5.8 - - + -
237A LEU* 3.5 35.4 - - + -
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Residues in contact with VAL 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 ALA* 3.4 17.0 - - + +
149A LEU* 4.0 13.2 - - + -
160A LEU* 4.7 7.0 - - + -
164A LYS* 3.7 19.1 - - + -
176A LEU* 4.3 5.8 - - + -
177A ILE* 1.3 77.0 - - - +
179A TYR* 1.3 76.7 + - - +
180A ALA 4.0 0.5 + - - -
194A THR 3.7 0.5 - - - +
195A ALA* 3.3 2.3 - - - -
196A PHE* 2.7 43.2 + - + +
198A VAL* 3.8 32.5 - - + -
224A LEU* 4.4 2.5 - - + -
226A PHE* 3.9 16.2 - - + -
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Residues in contact with TYR 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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107A GLN* 4.2 8.1 + - - +
133A LEU* 3.7 34.7 - - + +
134A ALA 3.1 25.5 + - - +
135A MET* 3.4 16.2 - - + +
147A MET* 3.7 23.8 - - + -
164A LYS* 2.8 30.3 + - - -
177A ILE* 4.2 8.9 - - + +
178A VAL* 1.3 74.5 - - - +
180A ALA* 1.3 60.3 + - - +
193A ILE* 3.8 18.2 - - + -
194A THR 3.3 4.5 - - - -
195A ALA* 3.7 15.5 - - + -
243A GLY 3.7 1.3 - - - -
246A VAL* 3.3 35.0 + - + +
247A LEU* 3.6 36.1 + - + -
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Residues in contact with ALA 180 (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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147A MET* 4.4 4.7 - - - -
149A LEU* 3.3 31.9 - - + +
151A ALA* 3.9 18.4 - - + -
160A LEU* 4.1 11.0 - - + -
178A VAL 4.0 0.2 + - - -
179A TYR* 1.3 75.9 - - - +
181A LYS* 1.3 59.6 + - - +
182A THR 3.3 2.6 + - - -
193A ILE* 3.3 3.0 - - - -
194A THR* 2.7 35.7 + - - +
196A PHE* 4.1 7.2 - - + -
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Residues in contact with LYS 181 (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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145A VAL 3.3 25.4 + - - -
146A SER* 4.5 3.6 - - - +
147A MET* 3.1 39.5 + - + +
148A LYS* 4.8 0.2 - - - -
149A LEU 2.7 15.7 + - - +
151A ALA 3.2 19.8 + - - +
180A ALA* 1.3 69.6 - - - +
182A THR* 1.3 59.9 + - - +
183A ASP 4.7 5.2 - - - +
184A LEU* 3.3 39.8 + - + +
189A ALA* 3.7 28.1 - - - +
192A GLY* 3.0 23.8 - - - +
193A ILE* 4.4 7.0 - - + +
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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