Contacts of the strand formed by residues 251 - 258 (chain D) in PDB entry 3TS8
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 ILE 251 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161D ALA* 4.1 12.1 - - + -
162D ILE 3.3 12.3 - - - +
163D TYR* 3.9 13.2 - - + -
164D LYS* 4.5 2.5 - - - -
173D VAL* 4.4 6.3 - - + -
194D LEU* 3.8 27.4 - - + -
236D PHE* 4.9 2.5 - - + -
240D SER* 5.2 2.0 + - - +
246D MET* 3.5 32.5 - - + -
249D ARG 3.4 11.2 + - - +
250D PRO* 1.3 74.4 - - - +
252D LEU* 1.3 61.2 + - - +
253D VAL* 4.5 6.3 - - + -
271D GLU* 3.2 25.3 - - - +
272D VAL* 3.3 38.3 + - + +
274D VAL* 5.8 1.8 - - + -
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Residues in contact with LEU 252 (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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100D GLN* 3.5 37.5 - - + +
131D ASN* 5.9 1.1 - - - +
160D MET 3.7 1.0 - - - +
161D ALA* 3.4 2.0 - - - -
162D ILE* 2.7 47.1 + - + +
164D LYS* 4.9 19.5 - - + -
251D ILE* 1.3 74.3 - - - +
253D VAL* 1.3 63.1 + - - +
254D ILE* 3.8 21.1 + - + -
269D SER* 4.5 8.1 - - - +
270D PHE* 3.7 26.0 - - - +
271D GLU* 3.8 14.1 - - + +
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Residues in contact with VAL 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D ALA* 4.9 1.6 - - + -
160D MET 3.5 7.9 - - - +
161D ALA* 4.4 0.9 - - + +
195D ILE* 4.2 18.6 - - + -
234D PHE* 5.8 2.5 - - + -
236D PHE* 3.7 22.9 - - + -
251D ILE* 4.5 6.5 - - + -
252D LEU* 1.3 73.5 - - - +
254D ILE* 1.3 62.8 + - - +
255D ILE* 3.9 23.3 - - + -
269D SER* 3.1 20.1 - - - -
270D PHE* 3.0 35.7 + - + +
272D VAL* 3.5 27.4 - - + -
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Residues in contact with ILE 254 (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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98D PRO* 5.7 2.7 - - + -
99D SER 4.1 10.5 - - - +
100D GLN* 3.9 14.8 - - + -
158D ARG 3.6 1.6 - - - +
159D ALA* 3.5 5.2 - - - -
160D MET* 2.7 47.7 + - + +
162D ILE* 4.6 16.8 - - + -
252D LEU* 3.8 26.5 - - + +
253D VAL* 1.3 74.4 - - - +
255D ILE* 1.3 63.1 + - - +
256D THR* 3.9 22.2 + - + +
267D ARG* 3.9 15.0 - - + -
268D ASP 3.8 8.3 - - - +
269D SER* 3.5 20.0 - - - -
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Residues in contact with ILE 255 (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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109D PHE* 3.5 19.8 - - + -
111D LEU* 3.9 30.7 - - + -
143D VAL* 5.5 1.1 - - + -
145D LEU* 5.1 3.8 - - + -
157D VAL* 3.7 26.0 - - + -
158D ARG 3.4 2.0 - - - +
159D ALA* 3.8 24.9 - - + -
234D PHE* 3.9 20.6 - - + -
253D VAL* 3.9 9.6 - - + -
254D ILE* 1.3 80.4 - - - +
256D THR* 1.3 61.6 + - - +
267D ARG* 3.4 1.7 - - - -
268D ASP 3.0 33.7 + - - +
270D PHE* 4.1 11.0 - - + -
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Residues in contact with THR 256 (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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109D PHE* 4.6 2.9 - - - -
156D ARG 4.0 0.2 - - - +
157D VAL* 3.6 6.1 - - - +
158D ARG* 3.1 39.8 + - - +
254D ILE* 3.9 11.4 - - + +
255D ILE* 1.3 79.3 - - - +
257D LEU* 1.3 60.2 + - - +
258D GLU* 3.8 17.0 + - - +
264D LEU* 3.9 13.7 - - + -
266D GLY 3.3 7.2 - - - -
267D ARG* 3.7 31.2 - - + +
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Residues in contact with LEU 257 (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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107D TYR* 4.7 13.7 - - + -
109D PHE* 3.9 39.4 - - + -
147D VAL* 5.1 1.8 - - + -
151D PRO* 4.6 14.4 - - + -
155D THR* 3.6 27.8 - - + -
156D ARG 3.7 7.2 - - - +
157D VAL* 4.1 15.7 - - + -
220D TYR* 4.1 13.0 - - + -
256D THR* 1.3 72.0 - - - +
258D GLU* 1.3 57.0 + - - +
264D LEU* 3.8 2.9 - - - +
265D LEU* 2.7 44.4 + - + -
266D GLY* 2.7 22.0 + - - +
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Residues in contact with GLU 258 (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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155D THR* 3.1 7.4 - - - +
156D ARG* 2.9 51.8 + - + +
158D ARG* 3.1 45.5 + - - -
217D VAL* 4.4 1.9 - - - +
256D THR* 3.8 16.2 + - - +
257D LEU* 1.3 75.2 - - - +
259D ASP* 1.3 64.8 + - - +
262D GLY* 3.6 27.9 - - - +
263D ASN 3.2 16.4 - - - +
264D LEU* 4.7 1.3 - - - +
265D LEU* 3.9 8.1 - - - -
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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