Contacts of the strand formed by residues 190 - 197 (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 TYR 190 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115D TYR* 3.0 23.8 + - - -
117D LEU* 3.7 24.5 - - + -
155D ALA 3.4 9.6 - - - -
188D PHE* 4.3 0.9 - - - -
189D GLY* 1.3 75.5 + - - +
191D LYS* 1.3 76.1 + - - +
192D HIS* 3.6 15.7 - - + +
224D ASP* 5.7 0.7 - - + -
225D ALA* 3.4 34.5 - - + +
228D GLN* 3.8 21.3 - - + -
229D ALA* 4.2 6.9 - - + +
236D ILE* 3.3 18.6 - - + +
275D VAL* 3.7 27.1 - - + -
280D HIS* 3.5 6.1 - - - +
281D TYR* 3.0 45.8 + - + +
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Residues in contact with LYS 191 (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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120D LEU* 5.8 1.0 - - - +
154D GLY* 3.3 2.3 - - - -
155D ALA* 2.7 46.6 + - - +
185D LEU* 5.0 12.3 - - - +
188D PHE* 3.6 43.7 - - + -
190D TYR* 1.3 78.3 - - - +
192D HIS* 1.3 69.4 + - - +
193D VAL* 3.6 11.1 + - + +
210D GLN* 5.1 8.2 + - - -
279D ASN* 3.5 7.6 - - + +
280D HIS* 3.7 29.6 - - + +
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Residues in contact with HIS 192 (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* 2.6 27.8 + + - -
190D TYR* 3.6 18.0 - - + +
191D LYS* 1.3 73.7 - - - +
193D VAL* 1.3 59.6 + - - +
194D LEU 3.5 28.9 + - - -
195D THR* 3.2 20.5 + - - -
235D LYS* 3.1 34.9 + - + -
236D ILE* 3.5 13.9 - - + +
275D VAL* 4.4 5.8 - - + -
279D ASN* 2.9 57.9 + - + +
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Residues in contact with VAL 193 (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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153D PHE* 3.2 54.5 + - + +
154D GLY* 3.7 11.0 - - - -
155D ALA* 4.1 8.5 - - + +
191D LYS* 4.0 15.9 - - + +
192D HIS* 1.3 77.0 + - - +
194D LEU* 1.3 63.9 + - + +
195D THR 4.3 0.6 + - - -
206D GLU* 4.3 13.1 - - + +
210D GLN* 4.3 11.2 - - - +
279D ASN* 4.9 5.1 + - - +
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Residues in contact with LEU 194 (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* 3.8 1.0 - - - -
152D GLY* 3.3 2.2 - - - -
153D PHE* 2.9 51.8 + - + +
192D HIS* 3.5 8.4 - - - -
193D VAL* 1.3 80.1 - - + +
195D THR* 1.3 75.9 + - - +
197D THR* 4.2 8.1 - - + -
202D ARG* 3.5 43.7 - - - +
203D PHE* 3.5 51.1 - - + +
206D GLU* 4.7 8.5 - - + +
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Residues in contact with THR 195 (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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151D ILE 3.2 5.9 - - - +
152D GLY* 4.2 0.2 - - - -
192D HIS* 3.2 21.9 + - - -
193D VAL 4.4 0.4 + - - -
194D LEU* 1.3 89.5 - - - +
196D LEU* 1.3 81.7 + - - +
197D THR* 3.0 8.6 + - - +
234D GLU 5.1 2.2 - - - +
235D LYS 3.5 11.4 + - - +
236D ILE 3.1 16.8 - - - +
237D GLY* 4.3 6.5 - - - -
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Residues in contact with LEU 196 (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* 3.8 11.9 - - - +
114D ILE 3.2 34.8 - - - +
115D TYR* 4.3 6.5 - - + +
150D ARG* 3.5 40.2 + - + +
151D ILE 3.3 1.6 - - - -
152D GLY* 3.6 8.7 - - - +
195D THR* 1.3 81.3 - - - +
197D THR* 1.3 59.3 + - - +
236D ILE* 3.1 19.9 + - + +
237D GLY* 3.6 32.4 - - - +
238D TRP* 3.7 24.2 - - + +
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Residues in contact with THR 197 (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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150D ARG* 3.4 8.9 - - - +
151D ILE* 2.7 48.5 + - - +
194D LEU* 4.2 15.7 - - + -
195D THR* 3.7 9.0 - - - +
196D LEU* 1.3 73.2 - - - +
198D ASP* 1.3 70.1 + - - +
199D GLN* 3.1 41.9 + - + +
202D ARG* 4.0 19.5 - - - +
203D PHE* 5.2 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