Contacts of the helix formed by residues 93 - 98 (chain B) in PDB entry 1RLI
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 ARG 93 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B TYR* 3.2 69.6 + - + +
60B ASP* 5.0 5.5 + - - -
89B LEU 3.2 12.2 + - - +
90B PHE 3.1 8.6 + - - +
91B ILE 3.1 1.2 - - - -
92B ASP* 1.3 71.8 - - - +
94B TRP* 1.3 55.9 + - - +
95B SER 2.9 5.6 - - - -
96B GLN* 2.9 28.9 + - + -
97B THR* 3.2 7.8 + - - -
50C GLY* 3.3 28.0 + - - +
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Residues in contact with TRP 94 (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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59B TYR* 3.4 16.6 - + - -
63B ILE* 4.1 4.7 - - + +
66B ILE* 5.1 2.4 - - + +
74B PHE* 3.8 35.7 - + - -
90B PHE* 3.4 38.1 + + - -
91B ILE* 2.9 34.1 + - + +
93B ARG* 1.3 77.1 - - - +
95B SER* 1.3 57.2 + - - +
97B THR* 3.6 4.9 - - - -
98B LEU* 2.8 33.3 + - - +
106B PHE* 4.0 23.3 - + + -
110B MET* 3.8 19.3 - - + -
139B ILE* 4.0 22.2 - - + -
140B PHE* 5.2 2.0 - + - -
143B MET* 4.0 20.9 - - + -
145B MET* 4.8 4.0 - - - -
80C TRP* 3.7 24.2 - + + -
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Residues in contact with SER 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ASP 3.2 10.8 + - - -
93B ARG 2.9 0.2 - - - -
94B TRP* 1.3 79.7 - - - +
96B GLN* 1.3 62.0 + - - +
98B LEU* 3.7 20.5 + - - +
99B ARG* 4.0 16.8 + - - -
49C GLN* 3.5 32.1 + - - +
80C TRP* 2.9 27.6 + - - -
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Residues in contact with GLN 96 (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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93B ARG* 2.9 19.5 + - + +
95B SER* 1.3 78.8 + - - +
97B THR* 1.3 64.2 + - - +
99B ARG* 3.1 18.4 + - - +
100B ASP* 3.1 13.5 + - - +
48C ALA* 3.5 25.4 - - - +
49C GLN 2.8 22.0 + - - +
50C GLY 3.7 22.7 - - - +
51C GLY* 4.1 10.3 - - - -
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Residues in contact with THR 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B TYR* 2.8 38.8 + - - -
63B ILE* 4.2 6.3 - - + -
93B ARG 3.2 1.8 + - - -
94B TRP* 3.2 8.9 + - - -
96B GLN* 1.3 73.8 - - - +
98B LEU* 1.3 60.0 + - - +
99B ARG 2.9 7.3 + - - -
100B ASP* 3.1 18.9 + - - +
103B PHE* 4.0 36.3 - - + +
106B PHE* 3.6 34.9 - - + +
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Residues in contact with LEU 98 (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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94B TRP 2.8 24.2 + - - +
95B SER* 3.8 10.3 - - - +
96B GLN 3.2 0.6 - - - -
97B THR* 1.3 76.1 - - - +
99B ARG* 1.3 64.5 + - + +
100B ASP 3.7 0.2 - - - -
106B PHE* 4.0 18.6 - - + -
107B LYS* 3.7 41.7 - - + +
142B PHE* 4.4 12.6 - - + -
143B MET* 4.5 3.4 - - + -
80C TRP* 3.9 29.2 - - + -
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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