Contacts of the strand formed by residues 93 - 98 (chain A) in PDB entry 1INL
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 LYS 93 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LYS* 1.3 84.1 - - + +
94A VAL* 1.3 61.0 + - - +
115A GLU* 5.7 4.3 - - + +
116A LYS* 3.4 22.2 - - + +
118A ILE* 6.1 1.1 - - - -
163A GLU* 3.2 55.5 + - - +
164A PHE* 3.8 15.5 - - + -
165A ASP* 2.8 38.5 + - - +
166A VAL 3.3 5.7 + - - -
196A LYS* 5.0 7.4 - - - +
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Residues in contact with VAL 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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85A MET* 3.9 25.4 - - + -
91A PRO* 4.7 3.4 - - + -
93A LYS* 1.3 82.0 - - - +
95A LEU* 1.3 71.4 + - - +
96A ILE* 4.3 11.2 - - + -
108A VAL* 4.0 29.6 - - + -
114A VAL* 4.3 9.0 - - + -
116A LYS 3.0 10.8 + - - +
117A ALA* 3.3 3.6 - - - -
118A ILE* 2.8 28.4 + - - +
164A PHE* 4.0 4.9 - - - -
166A VAL* 3.4 28.0 - - + +
168A ILE* 4.4 2.0 - - + -
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Residues in contact with LEU 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 VAL* 1.3 74.5 - - - +
96A ILE* 1.3 70.2 + - - +
97A ILE* 4.2 18.2 - - + -
118A ILE* 3.6 29.4 - - + +
120A CYS* 4.2 6.1 - - + -
156A TYR* 4.0 17.3 - - + -
157A VAL* 4.1 29.2 - - + -
164A PHE* 3.8 38.1 - - + -
166A VAL 2.9 6.9 + - - +
167A ILE* 3.3 13.5 - - + +
168A ILE 2.9 25.8 + - - +
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Residues in contact with ILE 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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94A VAL* 4.3 10.5 - - + -
95A LEU* 1.3 77.8 - - - +
97A ILE* 1.3 62.4 + - - +
98A GLY 3.9 5.3 + - - +
99A GLY* 5.2 0.2 - - - -
104A THR* 4.0 24.2 - - + -
105A LEU* 3.5 46.7 - - + +
108A VAL* 3.9 18.6 - - + -
117A ALA* 5.2 1.6 - - + -
118A ILE 2.8 15.0 + - - +
119A LEU* 3.7 19.2 - - + +
120A CYS* 2.8 30.5 + - - +
168A ILE* 3.3 11.9 - - + +
170A ASP* 4.3 10.1 - - + +
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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 LEU* 4.2 20.4 - - + -
96A ILE* 1.3 73.6 - - - +
98A GLY* 1.3 61.6 + - - +
120A CYS* 3.6 7.6 - - + +
153A GLY* 3.9 28.0 - - - +
156A TYR* 5.9 0.7 - - + -
157A VAL* 4.2 13.7 - - + -
167A ILE* 4.7 2.5 - - + -
168A ILE 2.9 9.6 + - - +
169A ILE* 3.7 28.9 - - + -
170A ASP* 2.7 33.3 + - - -
171A SER* 3.5 3.8 + - - +
182A LEU* 3.7 33.4 - - + -
187A PHE* 3.8 15.3 - - + -
191A CYS* 4.7 0.2 - - - -
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Residues in contact with GLY 98 (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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96A ILE* 4.2 0.4 - - - +
97A ILE* 1.3 77.8 - - - +
99A GLY* 1.3 65.1 + - - -
100A GLY* 3.4 2.5 + - - -
119A LEU* 3.2 21.4 - - - +
120A CYS 2.8 18.1 + - - +
121A GLU* 3.7 12.9 - - - +
122A VAL 5.8 0.2 - - - -
170A ASP* 3.5 7.4 - - - -
171A SER* 4.2 8.7 - - - -
182A LEU* 5.9 0.4 - - - -
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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