Contacts of the strand formed by residues 239 - 246 (chain B) in PDB entry 1UHG
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 MET 239 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B ILE* 5.2 4.9 - - + -
97B TYR* 3.5 37.5 - - + -
99B PHE* 6.3 1.3 - - - -
180B PHE* 3.5 41.3 - - + -
233B PRO* 4.0 0.7 - - - +
234B PHE* 3.0 44.8 + - + +
235B ALA 5.7 0.4 + - - +
237B GLY 3.7 0.6 - - - -
238B THR* 1.3 92.2 + - - +
240B SER* 1.3 63.6 + - - +
368B ILE* 4.5 4.0 - - + -
369B LYS 3.1 9.2 - - - +
370B HIS* 4.7 4.3 - - + -
371B ILE* 4.0 8.2 - - - +
377B LEU* 3.7 29.6 - - + -
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Residues in contact with SER 240 (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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231B GLU* 4.0 27.4 + - - +
232B LEU 3.5 12.8 - - - -
233B PRO* 3.9 8.5 - - - -
234B PHE* 3.7 7.9 - - - -
239B MET* 1.3 78.3 - - - +
241B MET* 1.3 61.4 + - - +
242B LEU* 4.8 0.7 - - - +
367B CYS 3.6 0.5 - - - +
368B ILE* 3.3 3.1 - - - +
369B LYS* 2.9 48.7 + - - +
371B ILE* 4.2 13.6 - - - +
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Residues in contact with MET 241 (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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184B TRP* 4.0 28.9 - - + -
230B LEU 3.5 1.2 - - - +
231B GLU* 3.4 4.2 - - - +
232B LEU* 2.8 36.5 + - + +
234B PHE* 3.9 7.1 - - + -
240B SER* 1.3 75.1 - - - +
242B LEU* 1.3 73.7 + - - +
243B VAL* 4.2 16.9 - - + +
282B LEU* 4.9 7.4 - - - -
285B MET* 5.7 2.9 - - - +
334B ILE* 3.6 35.4 - - + -
364B PHE* 6.2 0.7 - - - -
366B PHE* 4.2 22.0 - - + -
367B CYS 3.3 9.4 - - - +
368B ILE* 3.8 21.8 - - + +
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Residues in contact with LEU 242 (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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229B ILE* 4.4 5.6 - - + -
230B LEU 3.3 2.9 - - - +
231B GLU* 3.8 35.0 - - + +
240B SER* 4.8 0.7 - - - +
241B MET* 1.3 75.3 - - - +
243B VAL* 1.3 61.5 + - - +
244B LEU* 4.0 13.1 - - + +
264B LEU* 4.6 13.5 - - + -
268B THR* 4.2 19.7 - - + +
273B MET* 4.1 13.0 - - + -
366B PHE* 3.1 8.0 - - - +
367B CYS* 2.8 46.7 + - + +
369B LYS* 3.6 40.8 - - + +
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Residues in contact with VAL 243 (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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229B ILE* 3.2 4.9 - - - -
230B LEU* 2.8 45.5 + - + +
232B LEU* 5.2 3.4 - - + -
241B MET* 4.2 22.2 - - + +
242B LEU* 1.3 77.9 - - - +
244B LEU* 1.3 61.0 + - - +
282B LEU* 4.2 23.6 - - + -
358B PHE* 3.6 30.7 - - + -
360B ALA* 4.7 1.3 - - + -
364B PHE* 3.7 34.3 - - + -
365B LEU 3.6 2.7 - - - -
366B PHE* 4.6 3.1 - - + -
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Residues in contact with LEU 244 (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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227B MET* 5.1 2.7 - - + -
228B LYS 3.6 4.7 - - - -
229B ILE* 3.9 14.8 - - + -
242B LEU* 4.0 23.1 - - + +
243B VAL* 1.3 74.2 - - - +
245B LEU* 1.3 58.7 + - - +
246B PRO* 3.7 4.3 - - - +
255B LEU* 4.1 18.3 - - + +
259B ILE* 3.5 31.9 - - + -
264B LEU* 4.1 13.2 - - + -
267B TRP* 3.9 23.8 - - + -
364B PHE* 3.3 5.8 - - - +
365B LEU* 2.9 46.5 + - + +
366B PHE* 4.5 4.5 - - - -
367B CYS* 4.9 3.6 - - + +
379B PHE* 5.7 2.0 - - + -
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Residues in contact with LEU 245 (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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227B MET* 3.3 2.8 - - - +
228B LYS* 2.9 45.8 + - + +
243B VAL 3.8 0.2 + - - -
244B LEU* 1.3 72.9 - - - +
246B PRO* 1.3 69.1 - - + +
247B ASP* 4.5 0.9 - - - +
255B LEU* 5.3 0.2 - - - -
358B PHE* 3.5 33.0 - - + -
359B ARG 3.5 30.1 - - - +
360B ALA* 3.9 13.5 - - + -
362B HIS* 3.6 50.3 - - + +
364B PHE* 3.9 11.0 - - + -
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Residues in contact with PRO 246 (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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226B LYS 3.7 7.6 - - - +
227B MET* 3.9 5.6 - - + -
244B LEU 3.7 7.2 - - - +
245B LEU* 1.3 89.1 - - + +
247B ASP* 1.3 57.2 + - - +
248B GLU 3.6 15.3 - - - +
251B GLY* 3.8 16.4 - - - +
252B LEU* 3.9 23.1 - - + +
255B LEU* 4.1 14.4 - - + -
362B HIS* 2.6 33.1 + - + +
363B PRO 3.3 26.2 - - - +
364B PHE* 4.3 0.4 - - - -
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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