Contacts of the strand formed by residues 151 - 155 (chain B) in PDB entry 2INU
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 SER 151 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B ILE* 2.7 42.5 + - - -
103B PRO 3.8 12.3 + - - -
104B PRO 4.2 0.9 - - - -
105B GLY 4.2 0.2 - - - -
124B GLY* 3.9 0.4 - - - -
125B PHE* 2.9 22.1 + - - +
126B GLY 4.0 0.6 + - - -
149B GLY 4.0 0.4 - - - -
150B ALA* 1.3 74.7 - - - +
152B HIS* 1.3 56.3 + - - +
153B ILE* 3.7 1.4 + - - +
183B PHE* 3.6 21.2 - - - +
184B CYS 2.7 32.6 + - - +
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Residues in contact with HIS 152 (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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105B GLY 2.9 14.1 + - - +
106B ASP* 2.9 27.4 - - - +
107B TYR* 2.8 30.9 + - - +
147B GLN* 3.3 21.4 + - + -
148B PRO* 3.1 30.0 + - + +
149B GLY 3.5 19.7 - - - +
150B ALA 2.9 2.4 + - - -
151B SER* 1.3 71.1 - - - +
153B ILE* 1.3 62.1 + - - +
154B ARG* 3.4 18.7 - - + +
184B CYS* 3.9 6.5 - - - -
186B ASP* 2.9 40.6 + - + +
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Residues in contact with ILE 153 (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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74B ILE* 4.2 23.3 - - + -
102B ILE* 3.7 28.5 - - + -
107B TYR* 3.4 8.7 - - + +
109B LEU* 3.8 31.2 - - + -
151B SER 4.5 4.0 - - - +
152B HIS* 1.3 74.9 + - - +
154B ARG* 1.3 65.8 + - - +
155B VAL* 3.5 2.4 + - + -
165B PHE* 4.1 14.6 - - + -
183B PHE* 3.7 21.1 - - + -
184B CYS 2.8 16.5 + - - +
185B LEU* 3.6 14.3 - - + -
186B ASP* 2.9 26.5 + - - +
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Residues in contact with ARG 154 (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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106B ASP* 5.0 6.3 - - - -
107B TYR 2.6 20.6 + - - +
108B ASP* 3.0 23.7 + - - +
109B LEU* 2.7 32.1 + - - -
132B ARG* 3.6 14.1 - - - +
147B GLN* 2.6 39.1 + - - +
152B HIS* 3.4 30.5 - - + +
153B ILE* 1.3 70.5 - - - +
155B VAL* 1.3 61.4 + - - +
156B LEU* 3.3 12.8 + - + +
186B ASP* 3.5 5.6 - - - +
188B VAL* 3.8 29.0 - - + +
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Residues in contact with VAL 155 (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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109B LEU* 4.1 5.2 - - - -
153B ILE* 4.0 4.9 - - + +
154B ARG* 1.3 70.0 - - - +
156B LEU* 1.3 61.2 + - - +
157B THR* 3.6 30.5 - - + +
164B ALA* 3.9 16.6 - - + -
185B LEU* 3.8 29.6 - - + -
186B ASP 2.9 21.0 + - - +
187B GLY 4.2 0.3 - - - +
201B LYS* 2.8 40.0 + - + +
202B THR 4.3 5.6 - - - +
223B LEU* 4.2 17.0 - - + -
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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