Contacts of the strand formed by residues 112 - 117 (chain D) in PDB entry 4ILW
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 HIS 112 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110D LYS* 3.0 25.4 - - - +
111D THR* 1.3 101.5 + - + +
113D LEU* 1.3 61.4 + - - +
114D THR* 5.6 1.2 - - - +
147D THR* 3.3 29.2 - - - +
149D SER* 5.9 1.6 - - - +
157D ASP* 4.5 0.3 - - - +
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Residues in contact with LEU 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D TRP* 3.6 62.1 - - + +
110D LYS* 3.9 19.3 - - + +
111D THR 4.8 1.1 - - - +
112D HIS* 1.3 76.1 - - - +
114D THR* 1.3 65.7 + - - +
146D LEU* 4.2 15.7 - - + -
147D THR 2.9 6.8 + - - +
148D PHE* 3.2 36.8 - - + -
149D SER* 2.9 27.6 + - - -
157D ASP* 3.6 14.1 - - + +
158D ILE* 4.9 2.9 - - + -
223D LEU* 3.9 8.5 - - + -
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Residues in contact with THR 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D HIS 5.6 1.1 - - - +
113D LEU* 1.3 79.2 - - - +
115D TYR* 1.3 62.9 + - - +
148D PHE* 5.5 0.7 - - - -
149D SER* 3.3 23.3 - - - +
151D LEU* 4.0 22.5 - - + +
155D GLU 4.7 0.3 + - - -
156D ALA* 3.3 12.3 - - - -
157D ASP* 2.8 36.7 + - - +
158D ILE* 2.8 27.0 + - - +
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Residues in contact with TYR 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D THR* 1.3 75.5 - - - +
116D ARG* 1.3 66.1 + - - +
117D ILE* 4.3 9.6 - - + -
133D ILE* 4.2 10.8 - - + -
134D GLU* 3.5 31.2 + - - +
137D LEU* 3.4 34.2 - - + +
148D PHE* 4.0 16.4 - - + -
149D SER* 3.2 13.8 + - - -
150D ARG* 3.5 43.4 - - + +
151D LEU 2.8 25.3 + - - -
156D ALA* 3.3 4.6 - - - +
158D ILE* 3.1 26.9 - - + +
160D ILE* 4.2 16.2 - - + -
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Residues in contact with ARG 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ILE* 2.8 38.0 + - - +
36B TYR* 4.6 6.3 - - - +
115D TYR* 1.3 76.8 - - - +
117D ILE* 1.3 71.3 + - - +
118D VAL* 3.4 31.3 + - + +
150D ARG* 5.2 0.9 - - - -
151D LEU 3.1 25.6 - - - +
152D TYR* 3.7 11.0 + - - -
153D GLU* 3.9 17.6 - - - +
154D GLY 2.8 44.8 + - - +
156D ALA* 3.4 4.4 - - + +
158D ILE 3.0 7.1 + - - +
159D MET* 3.0 20.8 - - + +
160D ILE* 2.9 27.4 + - - +
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Residues in contact with ILE 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D TYR* 4.3 14.6 - - + -
116D ARG* 1.3 78.8 + - - +
118D VAL* 1.3 63.3 + - - +
119D ASN 3.6 14.4 - - - +
120D TYR* 3.5 37.3 + - + +
129D VAL* 4.1 8.5 - - + -
130D ASP* 3.5 25.1 - - - +
133D ILE* 3.6 40.8 - - + -
150D ARG* 4.2 17.9 + - - +
151D LEU 4.7 0.6 + - - -
160D ILE* 3.7 11.4 - - + +
162D PHE* 5.2 2.2 - - + -
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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