Contacts of the strand formed by residues 89 - 94 (chain A) in PDB entry 1RI4
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 89 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ASP 3.3 3.4 + - - -
67A SER* 3.3 25.4 + - - +
68A VAL 2.9 24.2 + - - -
87A ILE* 3.3 11.5 - - - +
88A GLY* 1.3 80.4 - - - +
90A TYR* 1.3 65.3 + - - +
91A TYR* 4.5 0.3 - - - -
114A PHE* 4.2 0.9 - - - -
115A LYS* 3.5 11.0 - - + +
117A PHE* 3.5 30.2 - - + -
132A LYS* 2.8 34.3 + - - +
134A PHE* 4.2 7.0 - - + -
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Residues in contact with TYR 90 (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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68A VAL* 3.6 9.4 - - + -
70A ASP* 2.6 43.9 + - + +
73A CYS* 3.3 12.3 - - - +
76A GLY* 4.5 9.0 - - - -
79A LEU* 3.9 27.4 + - + +
82A TYR* 3.7 34.1 - + + -
87A ILE* 3.8 5.2 - - + -
89A GLU* 1.3 78.2 - - - +
91A TYR* 1.3 61.3 + - - +
92A GLY* 3.6 20.4 - - - -
114A PHE* 3.6 21.1 - - + -
115A LYS 2.8 9.1 + - - +
116A VAL* 3.2 5.0 - - + -
117A PHE* 2.8 26.6 + - - -
118A PHE* 3.8 19.9 - + - -
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Residues in contact with TYR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A VAL 2.8 8.5 + - - -
69A LEU* 3.4 8.3 - - + +
70A ASP* 2.7 32.2 + - - +
89A GLU* 4.9 1.1 - - - +
90A TYR* 1.3 75.2 - - - +
92A GLY* 1.3 57.5 - - - +
93A VAL* 4.0 22.0 - - + -
117A PHE* 3.2 39.7 - + + -
118A PHE 4.3 2.2 + - - -
119A ARG* 3.4 34.6 + - + +
130A LEU* 3.8 23.8 + - + +
132A LYS* 3.7 33.0 - - - -
134A PHE* 3.5 28.5 - + + -
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Residues in contact with GLY 92 (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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70A ASP 3.6 6.7 - - - -
73A CYS* 4.1 10.5 - - - -
90A TYR* 3.6 18.2 - - - -
91A TYR* 1.3 74.9 - - - +
93A VAL* 1.3 63.1 + - - +
100A ILE* 4.0 0.6 - - - +
117A PHE 2.6 12.5 + - - +
118A PHE* 3.1 13.8 - - - +
119A ARG 2.9 24.3 + - - +
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Residues in contact with VAL 93 (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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69A LEU* 4.3 11.2 - - + -
70A ASP 3.1 9.2 + - - +
71A LEU* 4.5 8.3 - - + -
72A GLY 2.8 31.7 + - - -
73A CYS* 3.3 3.0 + - - -
91A TYR* 4.0 22.0 + - + -
92A GLY* 1.3 78.4 - - - +
94A ASP* 1.3 61.3 + - - +
100A ILE* 4.3 0.2 - - - -
119A ARG* 3.1 18.6 - - + +
121A GLN* 3.9 29.8 - - + +
123A SER* 4.0 17.7 - - - +
128A MET* 4.2 12.6 - - - -
130A LEU* 4.6 3.1 - - + -
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Residues in contact with ASP 94 (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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72A GLY* 3.2 12.5 - - - -
73A CYS* 3.9 6.1 - - - -
74A GLY* 3.0 19.5 + - - +
93A VAL* 1.3 75.8 - - - +
95A ILE* 1.3 61.2 + - - +
96A ALA* 2.9 24.0 + - - +
99A SER* 4.2 1.9 - - - -
100A ILE* 3.6 19.7 - - + +
119A ARG 3.1 5.5 + - - -
120A ALA* 2.9 28.1 - - - +
121A GLN 2.9 5.4 + - - -
299A SAM 2.4 51.9 + - - -
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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