Contacts of the strand formed by residues 92 - 97 (chain A) in PDB entry 1I73
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 ASN 92 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ARG* 4.4 10.4 - - + +
91A THR* 1.3 78.8 + - - +
93A LEU* 1.3 62.9 + - - +
94A THR* 4.4 3.1 + - - +
127A ILE* 3.2 31.8 + - + +
129A THR* 3.3 29.0 + - - -
137A ASP* 4.3 2.6 - - - +
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Residues in contact with LEU 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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88A TRP* 3.5 44.9 - - + +
90A ARG* 3.6 40.4 - - - +
91A THR 4.4 3.8 - - - +
92A ASN* 1.3 77.8 + - - +
94A THR* 1.3 65.0 + - - +
126A LEU* 4.4 8.3 - - + -
127A ILE 2.9 5.9 + - - -
128A PHE* 3.3 25.3 - - + +
129A THR 2.9 23.0 + - - -
137A ASP* 3.4 16.4 - - + +
138A ILE* 4.5 5.4 - - + -
203A LEU* 4.0 16.2 - - + -
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Residues in contact with THR 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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92A ASN* 5.4 3.6 - - - +
93A LEU* 1.3 78.7 - - - +
95A TYR* 1.3 63.9 + - - +
128A PHE* 5.9 0.9 - - - -
129A THR* 3.0 23.3 - - + +
131A ILE* 4.2 21.7 - - + +
135A GLU 4.6 1.7 + - - -
136A ALA* 3.4 9.3 - - - -
137A ASP* 2.9 29.3 + - - +
138A ILE* 2.9 26.1 + - - +
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Residues in contact with TYR 95 (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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94A THR* 1.3 75.5 - - - +
96A ARG* 1.3 65.6 + - - +
97A ILE* 4.3 9.4 - - + +
110A GLU 5.0 1.0 + - - -
113A ILE* 3.7 16.6 - - + -
114A LYS* 3.9 24.6 + - - +
117A PHE* 3.3 46.0 - + + -
128A PHE* 4.2 18.6 - + + -
129A THR 3.0 15.7 + - - -
130A ARG* 3.5 44.3 - - + +
131A ILE* 2.9 27.2 + - - +
136A ALA* 3.6 4.7 - - - -
138A ILE* 3.1 13.9 - - + +
140A ILE* 3.9 10.1 - - + -
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Residues in contact with ARG 96 (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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95A TYR* 1.3 77.3 - - - +
97A ILE* 1.3 84.2 + - - +
98A ARG* 3.6 48.4 + - - +
130A ARG* 5.4 0.4 - - - -
131A ILE* 3.4 22.7 - - + +
132A SER 4.2 11.4 + - - -
133A GLN* 3.4 27.9 + - - +
134A GLY* 2.7 43.4 + - - +
136A ALA* 3.6 14.6 - - + +
138A ILE 2.9 6.3 + - - -
139A ASN* 3.6 8.1 - - - +
140A ILE* 2.9 28.1 + - - +
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Residues in contact with ILE 97 (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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95A TYR* 4.3 13.0 - - + -
96A ARG* 1.3 79.5 - - - +
98A ARG* 1.3 62.3 + - - +
99A ASN 3.3 21.3 - - - +
100A TYR* 3.8 30.0 + - + +
109A VAL* 4.4 6.7 - - + +
110A GLU* 3.9 30.3 - - + +
113A ILE* 3.9 41.7 - - + -
130A ARG* 4.6 13.6 + - - +
131A ILE 4.7 1.0 + - - -
132A SER 5.3 1.4 - - - +
140A ILE* 3.6 16.4 - - + +
142A PHE* 5.2 0.2 - - + -
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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