Contacts of the strand formed by residues 149 - 156 (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 LEU 149 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112D VAL* 3.5 17.5 - - + +
114D ILE* 4.3 15.3 - - + -
139D ALA* 4.0 28.5 - - + +
142D MET* 3.8 36.1 - - + -
143D ARG* 4.0 26.9 + - - +
146D THR* 4.8 7.2 - - + +
147D SER 3.2 4.7 + - - +
148D ASN* 1.3 79.2 - - - +
150D ARG* 1.3 84.7 + - - +
151D ILE* 4.7 6.3 - - + -
197D THR 4.8 0.2 - - - -
198D ASP* 3.8 17.4 - - - +
200D VAL* 4.8 6.3 - - + -
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Residues in contact with ARG 150 (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 3.1 4.7 + - - +
113D ASP* 3.3 15.6 - - - +
114D ILE 2.9 24.8 + - - -
148D ASN* 5.6 0.2 + - - -
149D LEU* 1.3 83.0 - - - +
151D ILE* 1.3 61.7 + - - +
196D LEU* 3.5 31.2 + - + +
197D THR* 3.4 19.5 - - - +
198D ASP* 4.0 13.4 + - - +
237D GLY 4.7 7.1 + - - -
239D ARG* 3.3 47.9 - - - +
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Residues in contact with ILE 151 (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* 3.2 32.3 - - + +
116D TYR* 5.9 0.2 - - + -
138D LEU* 4.6 5.8 - - + -
139D ALA* 3.8 26.5 - - + +
149D LEU* 4.7 9.2 - - + -
150D ARG* 1.3 74.6 - - - +
152D GLY* 1.3 65.4 + - - +
195D THR 3.2 1.9 - - - +
196D LEU* 3.6 5.2 - - - -
197D THR* 2.7 49.8 + - + +
200D VAL* 4.5 18.4 - - + -
203D PHE* 3.6 53.7 - - + -
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Residues in contact with GLY 152 (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 3.1 6.6 + - - +
115D TYR* 3.5 8.7 - - - -
116D TYR* 3.0 19.9 + - - +
151D ILE* 1.3 77.3 - - - +
153D PHE* 1.3 63.4 + - - +
194D LEU* 3.3 16.2 - - - -
195D THR 3.7 5.2 - - - -
196D LEU* 3.6 3.2 - - - +
203D PHE* 3.4 17.1 - - - -
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Residues in contact with PHE 153 (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* 3.1 17.1 + - - -
116D TYR* 3.0 27.6 - - + +
118D MET* 3.5 31.6 - - - -
152D GLY* 1.3 74.6 - - - +
154D GLY* 1.3 63.3 + - - +
155D ALA* 5.5 1.1 - - + -
193D VAL* 3.2 36.9 + - + +
194D LEU* 2.9 42.8 + - + +
203D PHE* 3.8 16.4 - + + -
206D GLU* 3.6 35.7 - - + -
207D VAL* 3.6 12.6 - - + -
210D GLN* 3.8 17.7 - - + -
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Residues in contact with GLY 154 (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* 3.3 13.4 + - - -
116D TYR 2.8 9.9 + - - +
117D LEU* 3.3 11.0 - - - -
118D MET* 2.8 26.7 + - - +
153D PHE* 1.3 77.3 - - - +
155D ALA* 1.3 61.7 + - - +
190D TYR* 4.3 0.4 - - - -
191D LYS 3.3 11.9 - - - -
192D HIS* 4.3 0.2 - - - -
193D VAL* 3.7 7.2 - - - -
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Residues in contact with ALA 155 (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* 3.3 9.2 - - + +
120D LEU* 3.5 32.5 - - + -
153D PHE* 5.5 1.6 - - + -
154D GLY* 1.3 75.2 - - - +
156D PHE* 1.3 61.5 + - - +
188D PHE* 3.4 13.0 - - + -
190D TYR* 3.4 5.4 - - - -
191D LYS* 2.7 47.0 + - - +
193D VAL* 4.1 8.9 - - + +
210D GLN* 5.0 1.1 - - - +
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Residues in contact with PHE 156 (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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117D LEU* 4.2 10.1 - - + -
118D MET 3.0 24.5 + - - -
119D ASP* 3.6 19.5 - - + +
120D LEU 3.1 23.7 + - - -
155D ALA* 1.3 76.8 - - - +
157D VAL* 1.3 72.9 + - - +
188D PHE* 3.6 2.7 - - - -
189D GLY 3.2 15.9 - - - +
190D TYR* 4.3 0.2 - - - -
220D GLU* 4.1 10.8 - - + -
221D GLY 3.9 3.1 - - - +
222D GLY* 3.4 26.2 - - - -
225D ALA* 3.9 25.8 - - + -
248D PHE* 3.6 32.5 - + - -
249D THR 3.5 20.0 - - - -
250D THR* 4.6 2.0 - - - -
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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