Contacts of the strand formed by residues 147 - 153 (chain A) in PDB entry 1IJI
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 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A ALA* 3.2 10.3 - - + +
103A ILE 4.3 4.5 - - - +
104A LEU* 4.0 17.9 - - + -
125A ARG* 3.8 14.4 - - - +
143A LYS 3.6 24.0 - - - +
144A LEU* 2.9 24.2 + - + +
146A GLY* 1.3 79.9 + - - +
148A LYS* 1.3 64.3 + - - +
149A VAL 3.7 20.6 - - - +
150A VAL* 3.7 20.9 - - + -
178A LYS* 3.6 15.6 + - - +
179A ALA* 3.6 5.3 - - + +
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Residues in contact with LYS 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PHE* 2.9 42.3 + - + +
96A CYS* 3.8 13.5 - - - -
100A LYS* 5.4 5.4 - - - +
101A ASP* 3.3 34.3 + - + +
102A ALA 2.9 6.2 + - - +
146A GLY 4.5 0.7 - - - +
147A VAL* 1.3 74.4 - - - +
149A VAL* 1.3 65.2 + - + +
178A LYS 4.1 13.2 - - - +
179A ALA* 3.2 9.1 - - - +
180A ILE* 2.8 26.9 + - - +
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Residues in contact with VAL 149 (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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91A LEU* 4.1 14.6 - - + +
92A ILE* 4.8 0.4 - - - -
95A PHE* 4.1 16.2 - - + -
96A CYS* 3.7 24.0 - - - -
102A ALA 3.7 2.4 + - - -
103A ILE* 3.2 8.1 - - + +
104A LEU 3.0 23.0 + - - -
147A VAL* 3.7 2.1 - - - +
148A LYS* 1.3 86.0 - - - +
150A VAL* 1.3 66.2 + - - +
151A TYR* 3.5 32.0 + - + +
180A ILE* 3.4 9.4 - - + +
182A VAL* 3.7 25.1 - - + -
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Residues in contact with VAL 150 (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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104A LEU* 3.5 24.0 - - + +
140A ILE* 5.6 2.5 - - + -
144A LEU* 4.2 8.1 - - + -
147A VAL* 3.7 20.2 - - + -
149A VAL* 1.3 78.5 - - - +
151A TYR* 1.3 65.4 + - - +
152A VAL* 4.0 13.4 + - + -
171A LEU* 4.3 17.3 - - + -
175A THR* 4.1 22.4 - - + -
179A ALA* 4.5 1.6 - - + -
180A ILE 2.8 14.2 + - - +
181A VAL* 3.6 7.8 - - + +
182A VAL* 2.7 33.1 + - - +
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Residues in contact with TYR 151 (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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88A ILE* 2.8 44.2 + - + -
91A LEU* 3.5 14.3 - - + +
92A ILE* 3.2 20.1 - - + +
103A ILE* 4.3 17.7 - - + -
104A LEU 3.0 18.9 + - - +
105A TYR* 3.8 12.9 - - + +
106A CYS* 4.5 3.1 + - - -
113A TYR* 3.6 50.6 - + + -
149A VAL* 3.5 24.7 - - + +
150A VAL* 1.3 71.3 - - - +
152A VAL* 1.3 70.5 + - - +
153A CYS 4.3 0.2 - - - -
182A VAL* 3.5 32.1 - - + -
184A ASP* 6.0 0.7 - - + -
209A LEU* 4.5 1.3 - - + -
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Residues in contact with VAL 152 (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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106A CYS* 5.1 5.8 - - - -
113A TYR* 4.8 0.7 - - - -
135A LEU* 4.3 21.8 - - + -
140A ILE* 5.8 0.4 - - + -
150A VAL* 4.1 8.7 - - + +
151A TYR* 1.3 80.3 - - - +
153A CYS* 1.3 61.4 + - - +
154A SER 3.7 0.7 + - - -
163A ILE* 3.9 20.9 - - + -
168A PHE* 3.4 30.8 - - + -
171A LEU* 3.7 26.9 - - + -
181A VAL* 5.3 0.9 - - + -
182A VAL 2.9 8.8 + - - +
183A ALA* 3.3 7.6 - - - +
184A ASP* 3.0 22.6 + - - -
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Residues in contact with CYS 153 (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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109A THR* 3.7 7.4 + - - +
113A TYR* 3.4 16.0 + - - +
152A VAL* 1.3 70.6 - - - +
154A SER* 1.3 64.1 + - - +
155A PRO 3.3 21.5 - - - -
156A ASN* 3.3 35.2 + - - +
157A ASN* 3.7 13.5 - - - -
163A ILE* 3.9 8.5 - - - +
184A ASP* 3.7 13.7 - - - -
187A TYR* 5.1 3.1 - - - -
500A PLP 3.4 32.1 - - - -
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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