Contacts of the strand formed by residues 282 - 294 (chain A) in PDB entry 1T2E
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 SER 282 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275A LEU 3.4 7.4 - - - -
276A GLU* 3.5 4.7 - - - -
277A GLY* 2.9 24.0 + - - -
280A GLY 4.3 1.3 + - - -
281A HIS* 1.3 71.4 + - - +
283A ASP* 1.3 84.7 + - - +
285A ILE* 3.2 12.0 + - - +
323A LYS* 4.5 10.6 + - - +
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Residues in contact with ASP 283 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A GLN* 3.2 18.5 + - - +
274A LEU* 4.2 8.7 - - - +
275A LEU 3.3 8.3 + - - -
282A SER* 1.3 85.4 - - - +
285A ILE* 1.3 62.8 + - - +
323A LYS* 5.5 1.6 - - - -
326A LYS* 4.0 11.1 + - - +
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Residues in contact with ILE 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A GLN* 3.6 18.8 - - - +
274A LEU* 3.5 2.7 - - - +
275A LEU* 2.9 41.7 + - + +
281A HIS* 4.2 7.4 - - + +
282A SER 3.7 12.3 - - - +
283A ASP* 1.3 80.8 - - - +
286A PHE* 1.3 75.4 + - - +
319A ILE* 4.0 30.1 - - + -
322A THR* 4.0 21.5 - - + +
323A LYS* 4.1 31.6 - - - -
326A LYS* 4.3 11.0 - - + -
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Residues in contact with PHE 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ASP* 3.8 10.3 + - - +
146A VAL* 3.4 37.0 - - + -
147A GLN* 3.5 27.0 + - + -
150A HIS* 3.6 39.0 - + + -
157A LYS* 5.5 1.1 - - - -
160A ILE* 3.9 18.8 - - + -
193A GLY 4.5 0.2 - - - +
272A SER* 3.4 12.1 - - - +
273A THR* 3.2 25.8 - - - -
274A LEU* 3.5 31.9 - - + -
285A ILE* 1.3 92.0 - - - +
287A GLY* 1.3 59.2 + - - +
319A ILE* 4.0 3.5 - - - +
322A THR* 3.8 14.0 - - - +
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Residues in contact with GLY 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ASP* 4.3 1.3 - - - -
193A GLY* 3.1 13.7 - - - -
271A CYS 3.5 0.2 - - - +
272A SER* 3.8 7.2 - - - -
273A THR* 3.0 28.7 + - - +
275A LEU* 3.9 13.6 - - - +
286A PHE* 1.3 77.4 - - - +
288A GLY* 1.3 64.8 + - - -
289A THR 3.5 1.7 + - - -
315A PHE* 5.2 0.2 - - - -
319A ILE* 3.8 11.0 - - - -
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Residues in contact with GLY 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ASP* 4.2 3.5 + - - -
165A GLY 6.0 1.6 - - - -
192A VAL* 3.2 8.4 - - - +
193A GLY 2.8 39.3 + - - -
194A ALA* 4.8 1.6 - - - -
270A ILE* 4.1 11.0 - - - -
271A CYS 3.3 13.2 - - - -
272A SER* 4.0 2.4 - - - +
287A GLY* 1.3 70.1 - - - -
289A THR* 1.3 63.6 - - - -
315A PHE* 3.7 4.9 - - - -
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Residues in contact with THR 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A VAL* 4.2 1.6 - - - -
270A ILE* 3.7 8.7 - - - +
271A CYS 3.0 24.2 + - - +
273A THR* 3.6 28.5 - - + -
275A LEU* 4.2 9.4 - - + -
279A TYR* 2.7 27.4 + - + -
287A GLY 4.5 0.2 - - - -
288A GLY* 1.3 76.4 - - - -
290A PRO* 1.3 72.5 - - - +
291A VAL* 3.2 2.1 + - - +
302A VAL* 3.7 18.6 - - + -
303A ILE 2.6 23.9 + - - -
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Residues in contact with PRO 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A HIS* 3.9 17.5 - - + +
192A VAL* 4.1 12.6 - - + -
268A VAL* 3.7 22.9 - - + -
269A LEU 3.6 7.0 - - - +
270A ILE* 3.8 18.1 - - + -
289A THR* 1.3 91.7 - - - +
291A VAL* 1.3 58.3 + - - +
303A ILE* 2.7 52.0 + - + +
305A LEU* 4.0 19.7 - - + -
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Residues in contact with VAL 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ILE* 5.0 0.2 - - + -
267A LYS 3.4 0.7 - - - +
268A VAL* 3.1 4.9 - - - -
269A LEU 2.8 44.2 + - - +
271A CYS* 4.0 15.9 - - + +
273A THR* 3.7 31.9 - - + -
289A THR 3.6 7.6 - - - +
290A PRO* 1.3 81.4 - - - +
292A VAL* 1.3 63.5 + - - +
293A LEU* 3.6 27.6 - - + -
298A VAL* 4.1 11.7 - - + -
301A GLN 3.3 15.9 - - - +
302A VAL* 4.0 5.2 - - - -
303A ILE* 4.4 0.9 - - - +
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Residues in contact with VAL 292 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A LYS* 3.4 37.7 - - + +
267A LYS 3.3 3.1 - - - -
268A VAL* 4.0 12.1 - - + -
291A VAL* 1.3 76.2 - - - +
293A LEU* 1.3 60.6 + - - +
297A GLY 3.4 0.3 - - - +
298A VAL* 3.6 3.3 - - - -
299A GLU* 2.8 38.3 + - + +
301A GLN* 3.0 50.4 + - + +
303A ILE* 4.0 15.9 - - + -
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Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A PHE* 4.3 8.7 - - + -
161A ILE* 3.5 30.3 - - + -
257A MET* 3.7 33.2 - - + +
260A SER* 2.6 36.9 + - - +
261A TYR* 4.4 6.1 - - + +
266A LYS* 3.1 12.1 + - - -
267A LYS 3.1 8.8 + - - +
269A LEU* 3.9 12.8 - - + -
271A CYS* 4.2 3.1 - - - -
291A VAL* 3.6 27.1 - - + -
292A VAL* 1.3 71.9 - - - +
294A GLY* 1.3 58.3 + - - +
297A GLY 3.3 5.2 - - - +
298A VAL* 3.8 22.2 - - + -
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Residues in contact with GLY 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A SER 3.7 6.7 - - - -
261A TYR* 3.1 19.6 - - - -
264A ASP* 3.4 11.0 - - - -
266A LYS 4.2 2.9 - - - -
293A LEU* 1.3 75.6 - - - +
295A ALA* 1.3 57.1 + - - -
296A ASN 3.2 3.1 - - - -
297A GLY 2.7 29.7 + - - -
299A GLU* 3.4 13.2 - - - +
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Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A LYS* 5.9 0.2 - - - -
261A TYR* 3.4 28.6 + - - -
264A ASP* 2.6 34.6 + - + +
266A LYS* 5.0 0.4 - - - +
294A GLY* 1.3 70.9 - - - -
296A ASN* 1.3 66.0 + - - +
297A GLY 3.3 3.1 + - - -
299A GLU* 3.2 1.5 + - - +
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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