Contacts of the strand formed by residues 112 - 119 (chain D) in PDB entry 1TYE
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 VAL 112 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D TYR 3.4 10.0 + - - +
111D PRO* 1.3 80.8 - - - +
113D ASP* 1.3 77.5 + - - +
114D ILE* 4.2 10.1 - - + -
142D MET* 3.4 34.1 - - + -
146D THR* 4.4 3.1 - - + -
148D ASN 3.1 6.8 + - - +
149D LEU* 3.5 8.1 - - + +
150D ARG 3.1 24.6 + - - +
239D ARG* 3.4 2.1 + - - +
243D SER* 3.5 11.4 - - - +
245D LEU* 4.5 9.0 - - + -
348D TYR* 3.9 4.9 - - + -
351D ILE* 3.9 24.9 - - + -
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Residues in contact with ASP 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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112D VAL* 1.3 72.7 - - - +
114D ILE* 1.3 66.1 + - - +
150D ARG* 3.3 8.2 - - - +
196D LEU* 3.8 12.1 - - + +
238D TRP* 3.4 27.9 - - + -
239D ARG* 2.7 68.5 + - - +
242D ALA* 4.1 1.6 - - - -
243D SER 2.8 9.4 + - - +
244D HIS* 3.4 12.2 - - + -
245D LEU* 2.9 28.6 + - - +
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Residues in contact with ILE 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 VAL* 4.2 6.7 - - + -
113D ASP* 1.3 79.2 - - - +
115D TYR* 1.3 64.6 + - - +
116D TYR* 4.7 0.7 - - + +
138D LEU* 4.2 21.8 - - + +
142D MET* 3.5 32.1 - - + -
149D LEU* 4.3 6.7 - - + -
150D ARG 2.9 10.2 + - - +
151D ILE* 3.2 21.7 - - + +
152D GLY 3.1 23.0 + - - -
196D LEU* 3.2 6.5 - - - +
245D LEU* 3.7 27.1 - - + +
247D VAL* 4.2 23.1 - - + -
344D ILE* 4.1 9.6 - - + -
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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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113D ASP 4.2 0.2 - - - -
114D ILE* 1.3 76.2 - - - +
116D TYR* 1.3 61.9 + - - +
117D LEU* 3.5 23.3 - - + -
152D GLY* 3.7 12.8 - - - -
153D PHE 3.1 29.7 + - - -
154D GLY* 3.3 6.1 - - - -
190D TYR* 3.0 15.3 + - - -
192D HIS* 2.6 25.6 + + - -
194D LEU 3.8 7.9 - - - -
196D LEU* 4.3 5.4 - - + +
229D ALA* 3.9 11.2 - - + -
236D ILE* 3.5 29.8 - - + -
238D TRP* 3.8 22.8 - - + -
245D LEU 3.2 6.5 + - - -
246D LEU* 3.5 22.1 - - + +
247D VAL* 2.9 27.0 + - - +
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Residues in contact with TYR 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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114D ILE* 4.1 1.7 - - + -
115D TYR* 1.3 74.3 - - - +
117D LEU* 1.3 59.6 + - - +
118D MET* 3.7 30.1 - - + -
131D ILE* 2.7 40.3 + - + +
134D LEU* 3.2 33.6 - - + +
135D GLY* 3.6 19.1 - - - -
138D LEU* 4.1 11.9 - - + -
152D GLY 3.0 9.0 + - - +
153D PHE* 3.0 16.8 - - + +
154D GLY 2.8 31.9 + - - +
203D PHE* 4.5 11.2 - + + -
207D VAL* 4.9 2.9 - - + -
247D VAL* 3.7 22.9 - - + -
249D THR* 3.9 17.2 - - + +
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Residues in contact with LEU 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* 3.5 27.3 + - + -
116D TYR* 1.3 72.5 - - - +
118D MET* 1.3 55.3 + - - +
154D GLY 3.7 9.9 - - - +
155D ALA 4.5 0.2 - - - +
156D PHE* 4.2 8.1 - - + -
190D TYR* 3.7 23.1 - - + -
225D ALA* 3.8 35.2 - - + +
226D ILE* 3.9 18.6 - - + +
229D ALA* 4.2 1.8 - - + -
246D LEU* 4.0 18.2 - - + -
247D VAL 2.7 17.2 + - - +
248D PHE* 4.3 11.2 - - + -
249D THR* 2.8 35.2 + - - +
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Residues in contact with MET 118 (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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116D TYR* 3.7 31.9 - - + -
117D LEU* 1.3 72.3 - - - +
119D ASP* 1.3 60.2 + - - +
120D LEU* 3.3 21.7 + - + -
128D LEU* 4.9 0.9 - - + -
131D ILE* 3.6 30.5 - - + +
132D GLN* 4.4 4.3 - - + -
153D PHE* 3.5 33.2 - - + -
154D GLY 2.8 15.2 + - - +
155D ALA* 3.3 4.8 - - + +
156D PHE* 3.0 31.4 + - - -
207D VAL* 4.0 29.4 - - + +
210D GLN* 4.5 9.2 - - + -
249D THR* 3.5 4.0 - - - +
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Residues in contact with ASP 119 (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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118D MET* 1.3 68.9 - - - +
120D LEU* 1.3 64.0 + - - +
121D SER* 2.8 29.0 + - - -
124D MET* 3.0 38.2 - - + +
131D ILE* 4.1 0.7 - - - +
156D PHE* 3.6 20.8 - - + +
220D GLU* 3.8 12.8 - - - +
249D THR* 3.0 25.9 + - - +
250D THR* 2.7 30.2 + - - -
251D ASP* 3.8 6.8 + - - +
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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