Contacts of the strand formed by residues 127 - 134 (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 LEU 127 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93R PRO* 4.1 1.1 - - + -
115R ASN* 4.0 7.3 - - - +
116R PRO* 4.6 3.6 - - + -
120R ASP* 3.8 12.5 + - - +
125R ASN* 3.0 39.8 + - - +
126R HIS* 1.3 90.9 + - - +
128R THR* 1.4 71.2 + - - +
129R TYR* 3.4 35.7 - - + +
149R TYR* 3.9 6.8 - - - +
152R PRO 4.1 8.4 - - - +
173R ALA* 3.4 26.0 - - + -
174R TRP 3.3 27.1 - - - +
176R GLN* 3.6 4.7 - - - +
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Residues in contact with THR 128 (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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127R LEU* 1.4 76.4 - - - +
129R TYR* 1.3 63.0 + - - +
130R ALA* 4.1 10.8 - - + +
147R VAL* 3.3 34.5 - - + +
148R THR 3.9 0.3 + - - -
149R TYR* 3.2 30.4 + - - +
152R PRO* 4.1 2.1 - - - +
172R ARG 3.4 12.3 - - - +
174R TRP* 3.1 36.3 + - + -
176R GLN* 3.3 21.7 + - - +
182R TRP* 5.6 2.2 - - + -
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Residues in contact with TYR 129 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96R PRO* 3.4 34.9 - - + +
113R TRP* 3.5 31.4 - + + +
115R ASN* 2.8 32.7 + - - -
127R LEU* 3.4 25.6 - - + +
128R THR* 1.3 72.0 + - - +
130R ALA* 1.3 61.4 + - - +
131R VAL* 3.9 15.0 + - + +
146R ASN 3.5 10.2 - - - +
152R PRO* 3.1 37.8 + - + +
153R SER* 3.3 31.9 - - - -
154R LEU 4.0 0.2 - - - -
171R VAL* 3.8 19.5 - - + -
172R ARG 3.7 11.2 - - - -
173R ALA* 4.5 0.9 - - - -
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Residues in contact with ALA 130 (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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128R THR* 3.6 8.1 + - + -
129R TYR* 1.3 70.7 - - - +
131R VAL* 1.3 66.1 + - - +
144R ILE* 6.4 1.8 - - + -
145R TYR 4.7 0.7 - - - +
146R ASN 4.1 2.2 - - - -
147R VAL* 3.5 30.7 - - + -
172R ARG* 3.3 41.3 + - + +
182R TRP* 6.4 1.6 - - + -
185R TRP* 3.5 19.5 - - + -
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Residues in contact with VAL 131 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113R TRP* 3.7 33.9 - - + -
129R TYR* 3.9 17.3 - - + +
130R ALA* 1.3 81.7 - - - +
132R ASN* 1.3 60.5 - - - +
133R ILE* 3.4 37.6 - - + +
144R ILE* 3.6 7.9 - - - +
145R TYR* 3.1 53.7 + - + +
156R ILE* 5.5 4.7 - - + -
170R ARG 4.1 2.9 - - - +
171R VAL* 4.7 6.5 - - + -
185R TRP* 4.5 1.7 - - - -
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Residues in contact with ASN 132 (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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131R VAL* 1.3 70.5 - - - +
133R ILE* 1.3 66.5 + - - +
134R TRP* 4.1 5.1 - - - +
142R PHE* 3.4 32.1 - - - -
143R ARG 3.1 21.2 + - - -
144R ILE* 4.8 6.5 - - + +
168R ARG* 2.7 30.0 + - - +
169R ALA* 3.3 14.3 - - - -
170R ARG* 3.2 40.9 + - + +
185R TRP* 4.5 7.2 - - + -
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Residues in contact with ILE 133 (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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111R LEU* 4.4 20.4 - - + -
113R TRP* 5.1 2.0 - - + -
131R VAL* 3.4 40.4 - - + +
132R ASN* 1.3 80.8 - - - +
134R TRP* 1.3 57.1 + - - +
143R ARG* 2.7 62.1 + - + +
145R TYR* 4.5 11.4 - - + -
156R ILE* 5.8 3.4 - - + -
157R ALA 4.4 17.0 - - - +
158R ALA* 4.7 1.3 - - - -
167R TYR* 2.9 22.2 - - + +
168R ARG 4.3 0.9 - - - -
169R ALA* 4.2 13.2 - - + -
170R ARG 5.4 0.2 - - - +
171R VAL* 5.6 0.2 - - + -
191R TRP* 4.9 2.0 - - + -
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Residues in contact with TRP 134 (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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132R ASN* 4.5 8.3 - - - +
133R ILE* 1.3 78.8 - - - +
135R SER* 1.4 73.4 + - - +
136R GLU* 3.4 25.7 + - + +
137R ASN 3.2 31.2 + - - -
138R ASP* 3.7 10.3 - - + -
140R ALA* 2.7 24.1 + - + -
141R ASP 2.9 22.4 + - - -
142R PHE* 3.6 38.8 - + + -
143R ARG* 4.1 11.2 - - + +
160R THR* 4.5 4.3 - - + -
167R TYR* 3.2 10.4 + - - -
168R ARG* 3.3 51.8 + - - +
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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