Contacts of the helix formed by residues 290 - 299 (chain A) in PDB entry 1T8U
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 290 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A THR* 5.4 2.0 - - + -
286A ILE* 3.9 10.1 - - + +
287A GLN* 3.1 37.8 + - - +
288A ILE 3.2 0.2 - - - -
289A GLY* 1.3 73.2 - - - +
291A TYR* 1.3 64.9 + - - +
292A ALA 3.3 0.7 - - - +
293A LYS* 3.1 34.8 + - + +
294A HIS* 3.1 16.5 - - - -
386A PHE* 4.0 24.7 - - + -
387A TYR* 4.1 12.1 - - + -
390A PHE* 3.7 42.4 - - + -
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Residues in contact with TYR 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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160A VAL* 3.8 22.0 - - + +
220A PHE* 3.8 17.0 - + + -
242A VAL* 3.9 13.7 - - + -
243A ARG 2.7 37.1 + - - -
245A PRO* 3.8 10.0 - - + +
248A ARG* 3.4 21.6 - - - +
288A ILE 3.3 22.2 - - - -
289A GLY* 2.9 21.3 + - - -
290A ILE* 1.3 70.9 - - - +
292A ALA* 1.3 57.6 + - - +
294A HIS* 3.1 7.8 + - - +
295A LEU* 2.8 29.5 + - - +
390A PHE* 5.8 0.4 - - - +
391A ASN* 5.4 0.9 - - - -
394A PHE* 3.6 25.4 - + + -
404A TRP* 3.6 29.8 - + - -
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Residues in contact with ALA 292 (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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290A ILE 3.3 0.6 + - - -
291A TYR* 1.3 77.1 - - - +
293A LYS* 1.3 62.8 + - - +
295A LEU* 3.3 3.1 + - - +
296A GLU* 3.1 30.5 + - - +
390A PHE* 3.9 30.6 + - + +
393A LYS* 3.9 19.5 - - + +
394A PHE* 3.9 11.7 - - - +
397A MET* 3.8 23.0 - - - +
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Residues in contact with LYS 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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287A GLN* 2.6 32.1 + - - +
290A ILE* 3.1 33.4 + - + +
292A ALA* 1.3 81.5 - - - +
294A HIS* 1.3 70.7 + - + +
296A GLU* 3.5 20.5 + - - +
297A HIS* 3.3 27.2 + - + +
390A PHE* 6.2 0.2 - - + -
393A LYS* 5.5 0.9 - - - +
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Residues in contact with HIS 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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220A PHE* 3.5 32.8 - + + +
221A VAL* 3.7 34.1 - - + +
287A GLN* 2.9 41.6 + - + -
288A ILE 3.7 15.6 + - - -
290A ILE* 3.1 22.0 + - - +
291A TYR 3.1 1.2 + - - +
293A LYS* 1.3 82.1 - - + +
295A LEU* 1.3 67.0 + - - +
297A HIS* 3.1 23.2 + - - +
298A TRP* 3.1 19.0 + - - -
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Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A PHE* 4.0 9.1 - - + -
291A TYR 2.8 16.2 + - - +
292A ALA* 3.3 6.3 + - - +
294A HIS* 1.3 78.0 - - - +
296A GLU* 1.3 63.4 + - - +
298A TRP* 3.1 4.3 + - - +
299A LEU* 2.9 34.5 + - + +
304A ILE* 4.5 3.4 - - + -
307A MET* 3.8 23.3 - - + -
309A PHE* 3.6 25.8 - - + -
394A PHE* 4.1 8.1 - - + -
397A MET* 3.6 29.2 - - + -
398A THR* 3.8 28.9 - - + -
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Residues in contact with GLU 296 (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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292A ALA 3.1 14.9 + - - +
293A LYS* 3.7 16.0 - - - +
294A HIS 3.2 0.4 - - - -
295A LEU* 1.3 76.8 - - - +
297A HIS* 1.3 63.0 + - + +
299A LEU* 3.4 11.7 + - - +
300A ARG* 3.2 30.9 + - - +
393A LYS* 3.0 32.5 + - - -
397A MET* 3.6 16.6 - - + +
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Residues in contact with HIS 297 (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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223A ARG* 5.9 4.9 - - - +
226A PRO* 4.6 9.4 - - + -
293A LYS* 3.3 32.9 + - + +
294A HIS* 3.1 17.9 + - - +
296A GLU* 1.3 77.2 - - + +
298A TRP* 1.3 67.5 + - + +
300A ARG* 3.1 62.6 + - - +
301A HIS* 3.7 10.6 - - - -
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Residues in contact with TRP 298 (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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158A ILE* 3.9 17.5 - - + -
219A TYR 3.3 28.0 - - - -
220A PHE* 2.9 39.4 + + - -
222A THR 5.4 0.2 + - - -
225A ALA* 3.8 8.5 - - + -
226A PRO* 3.5 42.6 - - + +
229A ILE* 3.7 28.7 - - + -
238A LEU* 3.6 30.1 - - + -
294A HIS 3.1 22.8 + - - -
295A LEU* 3.1 7.4 + - - +
297A HIS* 1.3 79.3 - - + +
299A LEU* 1.3 58.1 + - - +
301A HIS* 2.9 20.8 + - - +
302A PHE* 2.9 23.3 + + - +
307A MET* 3.9 20.9 - - + -
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Residues in contact with LEU 299 (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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295A LEU* 2.9 29.4 + - + +
296A GLU* 3.8 8.1 - - - +
297A HIS 3.3 0.2 - - - -
298A TRP* 1.3 75.5 - - - +
300A ARG* 1.3 57.8 + - - +
301A HIS 3.2 1.6 - - - -
302A PHE 3.4 24.0 + - - +
303A PRO* 4.3 0.4 - - + -
304A ILE* 3.8 39.9 - - + +
307A MET* 4.4 4.5 - - - -
397A MET* 4.0 30.5 - - + +
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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