Contacts of the helix formed by residues 290 - 299 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B THR* 5.0 6.7 - - - -
286B ILE 3.8 9.4 - - - +
287B GLN* 3.1 38.9 + - - +
288B ILE 3.2 0.2 - - - -
289B GLY* 1.3 72.8 - - - +
291B TYR* 1.3 63.5 + - - +
292B ALA 3.3 0.9 - - - -
293B LYS* 3.2 32.7 + - + +
294B HIS* 3.2 18.5 + - - +
386B PHE* 4.1 24.9 - - + -
387B TYR* 4.1 12.6 - - + -
390B PHE* 3.8 37.5 - - + -
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Residues in contact with TYR 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B VAL* 3.8 29.5 - - + +
220B PHE* 3.7 14.7 - + + -
242B VAL* 3.8 14.4 - - + -
243B ARG 2.6 37.6 + - - -
245B PRO* 3.8 9.7 - - + +
248B ARG* 3.4 21.1 - - - +
288B ILE 3.4 21.8 - - - -
289B GLY* 2.9 18.7 + - - -
290B ILE* 1.3 74.1 - - - +
292B ALA* 1.3 57.5 + - - +
294B HIS 3.2 1.6 + - - -
295B LEU* 2.8 31.0 + - - +
390B PHE* 5.7 0.6 - - - +
391B ASN* 5.3 1.6 - - - -
394B PHE* 3.6 25.6 - + + -
404B TRP* 3.6 28.9 - + - -
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ILE 3.3 0.8 - - - -
291B TYR* 1.3 77.9 - - - +
293B LYS* 1.3 63.5 + - + +
295B LEU* 3.3 4.9 + - - +
296B GLU* 3.1 29.0 + - - +
390B PHE* 3.8 32.4 + - + +
393B LYS* 4.2 10.1 - - + -
394B PHE* 4.0 11.1 - - - +
397B MET* 3.7 24.9 - - - +
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Residues in contact with LYS 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B GLN* 6.2 0.4 - - - +
290B ILE* 3.2 31.5 + - + +
292B ALA* 1.3 76.7 - - + +
294B HIS* 1.3 69.4 + - + +
296B GLU* 3.5 28.1 + - - +
297B HIS* 3.8 17.9 + - + -
390B PHE* 4.6 17.3 - - + -
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Residues in contact with HIS 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B PHE* 3.5 29.5 + + + +
221B VAL* 3.7 36.2 - - + +
287B GLN* 2.9 49.0 + - + -
288B ILE 3.7 12.8 - - - -
290B ILE* 3.2 23.5 + - - +
291B TYR 3.2 2.0 + - - +
293B LYS* 1.3 78.7 - - + +
295B LEU* 1.3 63.6 + - - +
297B HIS* 3.0 30.3 + + - +
298B TRP* 3.2 16.7 - - - -
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B PHE* 3.9 10.7 - - + -
291B TYR 2.8 17.5 + - - +
292B ALA* 3.5 6.5 - - - +
293B LYS 3.2 0.2 - - - -
294B HIS* 1.3 79.1 - - - +
296B GLU* 1.3 63.2 + - - +
298B TRP* 3.0 3.9 + - - -
299B LEU* 3.0 33.8 + - + +
304B ILE* 4.6 2.5 - - + -
307B MET* 3.9 23.3 - - + -
309B PHE* 3.6 30.5 - - + -
394B PHE* 4.0 20.4 - - + -
397B MET* 3.7 37.9 - - + -
398B THR* 4.1 3.4 - - + -
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Residues in contact with GLU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B ALA 3.1 18.7 + - - +
293B LYS* 3.7 20.6 + - - +
294B HIS 3.2 0.6 - - - -
295B LEU* 1.3 75.9 - - - +
297B HIS* 1.3 65.4 + - + +
299B LEU* 3.4 14.1 + - - +
300B ARG* 3.4 24.4 + - - +
397B MET* 3.8 20.1 - - + +
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Residues in contact with HIS 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B ARG* 5.8 7.5 + - - +
226B PRO* 3.9 12.8 - - + +
293B LYS* 3.9 17.1 + - + +
294B HIS* 3.0 21.7 + + - +
296B GLU* 1.3 80.9 - - + +
298B TRP* 1.3 61.7 + - + +
300B ARG* 3.5 45.3 + - - +
301B HIS* 3.7 18.7 - - - -
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Residues in contact with TRP 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B ILE* 3.7 23.3 - - + -
219B TYR 3.2 24.9 - - - -
220B PHE* 2.9 37.7 + + - -
225B ALA* 3.7 17.7 - - + -
226B PRO* 3.4 39.6 - - + +
229B ILE* 3.7 22.7 - - + -
238B LEU* 3.6 30.3 - - + -
294B HIS 3.2 22.7 - - - -
295B LEU 3.0 7.2 + - - +
297B HIS* 1.3 75.5 - - + +
299B LEU* 1.3 56.8 + - - +
300B ARG 3.1 4.9 - - - -
301B HIS* 3.0 5.7 + - - -
302B PHE* 2.9 37.8 + + - +
307B MET* 3.8 20.9 - - + -
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Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B LEU* 3.0 22.4 + - + +
296B GLU* 4.0 6.7 - - - +
297B HIS 3.4 0.4 - - - -
298B TRP* 1.3 76.0 - - - +
300B ARG* 1.3 58.6 + - - +
301B HIS 3.1 2.2 + - - -
302B PHE 3.3 23.4 + - - +
304B ILE* 3.6 43.3 - - + +
307B MET* 4.1 10.3 - - - -
397B MET* 3.9 30.7 - - + +
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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