Contacts of the strand formed by residues 151 - 155 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A ILE* 2.6 39.7 + - - -
103A PRO 3.7 13.4 + - - -
104A PRO* 4.1 0.9 - - - +
105A GLY 4.2 0.4 - - - +
124A GLY* 3.9 1.1 - - - -
125A PHE* 2.9 21.3 + - - +
126A GLY 4.0 0.6 + - - -
149A GLY 4.0 0.7 - - - -
150A ALA* 1.3 72.8 - - - +
152A HIS* 1.3 56.7 + - - +
153A ILE* 3.7 1.4 + - - +
183A PHE* 3.5 23.9 - - - +
184A CYS 2.7 32.8 + - - +
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Residues in contact with HIS 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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105A GLY 3.0 14.1 + - - +
106A ASP* 2.9 26.7 - - - +
107A TYR* 2.8 31.1 + - - +
147A GLN* 3.3 22.2 + - - -
148A PRO* 3.1 34.1 + - + +
149A GLY 3.4 17.7 - - - +
150A ALA 2.8 5.8 + - - +
151A SER* 1.3 68.6 - - - +
153A ILE* 1.3 62.3 + - - +
154A ARG* 3.4 18.3 - - + -
184A CYS* 3.8 9.5 - - - -
186A ASP* 2.9 33.8 - - + +
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Residues in contact with ILE 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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74A ILE* 4.1 24.7 - - + -
102A ILE* 3.8 21.1 - - + -
107A TYR* 3.4 6.7 - - + -
109A LEU* 3.8 30.7 - - + -
151A SER 4.6 2.2 - - - +
152A HIS* 1.3 75.5 + - - +
154A ARG* 1.3 67.1 + - - +
155A VAL* 3.5 2.0 + - + +
165A PHE* 4.2 14.4 - - + -
183A PHE* 3.8 28.5 - - + -
184A CYS 2.7 17.6 + - - +
185A LEU* 3.6 14.8 - - + -
186A ASP* 2.9 26.9 + - - +
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Residues in contact with ARG 154 (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 ASP* 5.6 3.6 - - - -
107A TYR 2.7 19.3 + - - +
108A ASP* 3.2 23.8 + - - +
109A LEU 2.7 31.5 + - - -
132A ARG* 4.2 1.6 - - - +
147A GLN* 3.1 37.2 + - - +
152A HIS* 3.4 26.7 - - + +
153A ILE* 1.3 72.7 - - - +
155A VAL* 1.3 61.5 + - - +
156A LEU* 3.3 18.4 + - + +
186A ASP* 3.4 8.7 - - - +
188A VAL* 3.8 35.2 - - + +
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Residues in contact with VAL 155 (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 LEU* 4.0 5.4 - - - -
153A ILE* 4.1 4.3 - - + +
154A ARG* 1.3 69.1 - - - +
156A LEU* 1.3 61.5 + - - +
157A THR* 3.6 30.1 - - + +
164A ALA* 3.9 18.8 - - + -
185A LEU* 3.8 28.7 - - + -
186A ASP 2.9 20.0 + - - +
187A GLY* 4.3 0.4 - - - +
201A LYS* 2.9 39.3 + - + +
202A THR 4.3 5.4 - - - +
223A LEU* 4.2 18.2 - - + -
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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