Contacts of the strand formed by residues 239 - 246 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90D ILE* 3.5 36.1 - - + -
97D TYR* 3.9 30.1 - - + -
99D PHE* 5.5 2.2 - - + -
180D PHE* 3.9 29.2 - - + -
233D PRO* 3.9 0.3 - - - +
234D PHE* 3.0 39.8 + - + +
235D ALA 5.8 0.2 + - - -
238D THR* 1.3 90.4 + - - +
240D SER* 1.3 62.5 + - - +
368D ILE* 4.5 5.2 - - + -
369D LYS 3.2 10.3 - - - +
370D HIS* 4.8 1.6 - - + -
371D ILE* 3.6 10.2 - - - +
377D LEU* 3.6 26.0 - - + -
378D PHE* 6.3 0.2 - - + -
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Residues in contact with SER 240 (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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231D GLU* 2.9 36.2 + - - +
232D LEU 3.5 12.1 - - - -
233D PRO* 3.9 7.2 - - - -
234D PHE* 3.8 7.2 - - - -
239D MET* 1.3 77.9 - - - +
241D MET* 1.3 60.8 + - - +
242D LEU* 4.8 0.5 - - - +
367D CYS 3.7 0.2 - - - +
368D ILE* 3.3 4.2 - - - +
369D LYS* 3.0 45.6 + - - +
371D ILE* 4.2 9.0 - - - +
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Residues in contact with MET 241 (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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184D TRP* 3.9 22.0 - - + -
230D LEU 3.5 1.4 - - - +
231D GLU* 3.4 4.0 - - - -
232D LEU* 2.8 36.0 + - + +
234D PHE* 3.8 13.1 - - + -
240D SER* 1.3 74.8 - - - +
242D LEU* 1.3 72.3 + - - +
243D VAL* 4.0 19.2 + - + +
282D LEU* 4.9 7.6 - - - -
285D MET* 5.7 2.9 - - - +
334D ILE* 3.4 39.0 - - + -
364D PHE* 6.3 0.2 - - - -
366D PHE* 4.2 20.9 - - + -
367D CYS 3.4 7.0 - - - +
368D ILE* 3.9 20.0 - - + +
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Residues in contact with LEU 242 (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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229D ILE* 4.3 9.4 - - + -
230D LEU 3.4 2.9 - - - +
231D GLU* 3.6 40.2 - - + +
240D SER* 4.8 1.8 - - - +
241D MET* 1.3 74.1 - - - +
243D VAL* 1.3 62.0 + - - +
244D LEU* 3.9 9.9 - - + +
264D LEU* 4.4 15.7 - - + -
268D THR* 4.0 30.5 - - + -
273D MET* 4.8 2.0 - - + -
366D PHE* 3.1 7.1 - - - +
367D CYS* 2.7 50.5 + - + +
369D LYS* 3.8 29.8 - - + -
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Residues in contact with VAL 243 (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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229D ILE* 3.3 5.2 - - - -
230D LEU* 2.9 34.9 + - + +
232D LEU* 4.5 12.1 - - + -
241D MET* 4.0 24.7 - - + +
242D LEU* 1.3 79.3 - - - +
244D LEU* 1.3 62.4 + - - +
282D LEU* 4.3 17.7 - - + -
358D PHE* 3.5 32.1 - - + -
360D ALA* 4.9 1.3 - - + -
364D PHE* 3.8 33.4 - - + -
365D LEU 3.6 2.2 - - - -
366D PHE* 4.6 2.7 - - + -
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Residues in contact with LEU 244 (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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227D MET* 4.3 7.4 - - + -
228D LYS 3.7 5.2 - - - -
229D ILE* 4.3 11.4 - - + -
242D LEU* 3.9 20.2 - - + +
243D VAL* 1.3 74.0 - - - +
245D LEU* 1.3 59.1 + - - +
246D PRO* 3.8 3.6 - - - +
255D LEU* 4.0 18.2 - - + +
259D ILE* 3.5 31.2 - - + -
264D LEU* 4.3 9.0 - - + -
267D TRP* 3.7 27.4 - - + -
364D PHE* 3.3 5.9 - - - +
365D LEU* 2.8 57.0 + - + +
366D PHE* 4.4 2.5 - - - -
367D CYS* 4.7 7.0 - - + +
379D PHE* 5.2 0.7 - - + -
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Residues in contact with LEU 245 (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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227D MET* 3.3 3.6 - - - +
228D LYS* 2.9 40.6 + - + +
243D VAL 3.9 0.4 + - - -
244D LEU* 1.3 72.6 - - - +
246D PRO* 1.3 77.9 - - + +
247D ASP* 3.6 0.9 + - - +
255D LEU* 4.8 0.4 - - - +
358D PHE* 3.6 36.8 - - + -
359D ARG 3.5 32.8 - - - +
360D ALA* 4.0 14.6 - - + -
362D HIS* 3.6 31.2 - - + +
364D PHE* 4.1 14.6 - - + -
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Residues in contact with PRO 246 (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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226D LYS 3.7 7.9 - - - +
227D MET* 4.1 5.6 - - + -
244D LEU 3.8 7.4 - - - +
245D LEU* 1.3 91.3 - - + +
247D ASP* 1.3 56.2 + - - +
248D GLU 3.5 16.2 - - - +
249D VAL* 6.2 0.2 - - - -
251D GLY* 3.8 15.5 - - - +
252D LEU* 3.7 29.6 - - + +
255D LEU* 4.1 9.4 - - + -
362D HIS* 2.7 30.6 + - + -
363D PRO 3.4 24.2 - - - +
364D PHE* 4.3 0.9 - - - -
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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