Contacts of the strand formed by residues 108 - 114 (chain R) in PDB entry 1ILL
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 THR 108 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102R HIS 3.4 4.2 - - - +
104R ASN* 3.2 36.1 + - - +
106R SER* 2.6 32.4 + - - +
107R ASP* 1.3 70.8 - - - +
109R LEU* 1.3 62.2 + - - +
110R LEU* 3.8 20.4 - - + +
159R SER* 5.8 0.7 - - - +
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Residues in contact with LEU 109 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101R VAL* 3.8 28.5 - - + -
102R HIS 3.4 5.4 - - - +
103R THR* 4.4 10.8 - - + -
104R ASN 4.6 2.5 - - - +
107R ASP* 3.5 13.1 + - - +
108R THR* 1.3 80.0 - - - +
110R LEU* 1.3 64.8 + - - +
111R LEU 3.5 0.4 + - - -
157R ALA* 3.2 9.6 - - - +
158R ALA* 2.9 51.0 + - + +
159R SER* 5.1 1.2 - - - +
161R LEU* 3.4 50.0 - - + +
167R TYR* 4.6 5.4 - - + -
191R TRP* 3.9 9.4 - - + -
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Residues in contact with LEU 110 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100R THR 4.2 0.2 - - - +
101R VAL* 3.5 3.6 - - - -
102R HIS* 3.3 56.1 + - + +
104R ASN* 5.5 0.7 - - + -
108R THR* 3.8 28.5 - - + +
109R LEU* 1.3 72.2 - - - +
111R LEU* 1.3 60.3 + - - +
112R THR* 3.9 5.1 + - - +
156R ILE 4.2 5.2 - - - +
157R ALA* 5.0 7.9 - - + -
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Residues in contact with LEU 111 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100R THR 3.8 2.5 - - - +
101R VAL* 3.6 16.8 - - + -
109R LEU 3.5 0.2 + - - -
110R LEU* 1.3 69.0 - - - +
112R THR* 1.3 82.5 + - - +
113R TRP* 3.5 44.8 - - + +
133R ILE* 4.4 10.5 - - + -
154R LEU 3.9 0.2 - - - +
155R ARG* 3.5 6.8 + - - -
156R ILE* 3.0 46.5 + - + +
157R ALA* 3.6 26.9 - - - +
158R ALA* 3.7 14.4 - - + +
191R TRP* 3.7 20.6 - - + -
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Residues in contact with THR 112 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98R ASN* 2.9 14.5 - - + +
100R THR* 3.0 44.0 + - + +
101R VAL* 5.2 0.4 - - - -
102R HIS 5.6 1.1 - - - +
110R LEU 4.5 5.8 - - - +
111R LEU* 1.3 79.8 - - - +
113R TRP* 1.3 64.2 + - - +
154R LEU 3.4 4.9 - - - -
155R ARG* 2.7 36.6 + - - -
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Residues in contact with TRP 113 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96R PRO* 4.6 2.2 - - + -
97R GLY 3.6 5.4 - - - +
98R ASN 3.3 4.5 - - - -
99R LEU* 4.0 27.8 - - + -
111R LEU* 3.5 27.4 - - + +
112R THR* 1.3 80.1 - - - +
114R SER* 1.4 63.4 + - - +
115R ASN* 3.2 6.2 + - - +
129R TYR* 3.5 39.5 - + + +
131R VAL* 3.7 33.0 - - + -
133R ILE* 5.1 1.6 - - + -
153R SER 3.2 27.4 - - - -
154R LEU* 3.3 12.5 + - - +
155R ARG* 3.2 19.1 + - - -
156R ILE* 3.4 31.4 - - + -
171R VAL* 3.4 33.6 - - + +
191R TRP* 4.8 3.6 - - - -
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Residues in contact with SER 114 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96R PRO* 3.6 1.9 - - - +
97R GLY* 2.7 39.7 + - - +
98R ASN* 3.4 29.8 + - - +
113R TRP* 1.4 71.5 - - - +
115R ASN* 1.3 78.8 + - - +
116R PRO* 5.0 0.7 - - - +
118R PRO* 4.8 6.9 - - - +
129R TYR* 4.2 0.3 + - - -
155R ARG* 5.3 0.7 - - - +
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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