Contacts of the strand formed by residues 239 - 246 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A ILE* 3.6 35.0 - - + -
97A TYR* 3.6 33.9 - - + +
99A PHE* 5.3 2.0 - - + -
180A PHE* 3.8 30.5 - - + -
233A PRO* 4.1 0.9 - - - +
234A PHE* 3.0 41.6 + - + +
237A GLY* 3.7 0.4 - - - -
238A THR* 1.3 91.1 + - - +
240A SER* 1.3 63.5 + - - +
368A ILE* 4.6 4.9 - - + -
369A LYS 3.2 14.1 - - - +
370A HIS* 4.7 2.5 - - + -
371A ILE* 3.9 8.0 - - - +
377A LEU* 3.7 22.2 - - + -
378A PHE* 6.5 0.2 - - - -
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Residues in contact with SER 240 (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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231A GLU* 3.0 34.3 + - - +
232A LEU 3.5 10.8 - - - -
233A PRO* 4.2 5.4 - - - -
234A PHE* 3.9 7.0 - - - -
239A MET* 1.3 77.3 - - - +
241A MET* 1.3 61.3 + - - +
242A LEU 4.2 0.2 - - - -
367A CYS 3.8 0.2 - - - +
368A ILE* 3.3 4.3 - - - +
369A LYS* 2.9 50.4 + - - +
371A ILE* 4.1 10.4 - - - +
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Residues in contact with MET 241 (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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184A TRP* 3.8 22.7 - - + -
230A LEU 3.5 1.6 - - - +
231A GLU* 3.4 4.0 - - - -
232A LEU* 2.8 39.6 + - + +
234A PHE* 3.9 12.8 - - + -
240A SER* 1.3 75.1 - - - +
242A LEU* 1.3 72.0 + - - +
243A VAL* 4.3 15.2 - - + +
282A LEU* 5.0 4.5 - - - -
285A MET* 5.3 4.5 - - + +
334A ILE* 3.5 36.3 - - + -
364A PHE* 6.4 0.4 - - - -
366A PHE* 3.5 30.3 - - + -
367A CYS 3.3 9.6 - - - +
368A ILE* 3.7 17.0 - - + +
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Residues in contact with LEU 242 (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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229A ILE* 4.4 5.6 - - + -
230A LEU 3.3 2.9 - - - +
231A GLU* 3.9 36.3 - - + +
241A MET* 1.3 73.3 - - - +
243A VAL* 1.3 60.8 + - - +
244A LEU* 4.0 8.0 - - + +
264A LEU* 4.4 23.6 - - + -
268A THR* 4.0 19.7 - - + +
273A MET* 4.0 17.7 - - + -
366A PHE* 3.1 8.1 - - - +
367A CYS* 2.8 49.4 + - + +
369A LYS* 4.0 29.2 - - + +
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Residues in contact with VAL 243 (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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229A ILE* 3.3 5.8 - - - -
230A LEU* 2.9 41.4 + - + +
232A LEU* 5.1 5.2 - - + -
241A MET* 4.3 20.6 - - + +
242A LEU* 1.3 77.9 - - - +
244A LEU* 1.3 61.2 + - - +
245A LEU* 4.9 0.2 - - + -
282A LEU* 4.1 22.7 - - + -
358A PHE* 3.5 31.0 - - + -
360A ALA* 4.7 1.8 - - + -
364A PHE* 3.6 33.9 - - + -
365A LEU 3.6 2.5 - - - -
366A PHE* 4.4 2.9 - - + -
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Residues in contact with LEU 244 (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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227A MET* 3.6 17.0 - - + -
228A LYS 3.8 4.7 - - - -
229A ILE* 4.0 27.1 - - + -
242A LEU* 4.0 21.5 - - + +
243A VAL* 1.3 74.2 - - - +
245A LEU* 1.3 59.2 + - - +
246A PRO* 3.6 4.7 - - - +
255A LEU* 4.0 12.2 - - + +
259A ILE* 3.7 29.4 - - + -
264A LEU* 4.2 12.6 - - + -
267A TRP* 4.3 5.6 - - + -
364A PHE* 3.3 5.0 - - - +
365A LEU* 2.8 50.6 + - + +
366A PHE* 4.3 3.1 - - - -
367A CYS* 4.7 5.2 - - + +
379A PHE* 5.5 2.2 - - + -
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Residues in contact with LEU 245 (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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227A MET* 3.4 3.1 - - - +
228A LYS* 2.9 46.8 + - + +
243A VAL* 3.7 0.6 + - + -
244A LEU* 1.3 74.2 - - - +
246A PRO* 1.3 73.9 - - + +
247A ASP* 4.5 1.2 - - - +
358A PHE* 3.6 34.1 - - + -
359A ARG 3.4 33.4 - - - +
360A ALA* 3.9 11.4 - - + -
362A HIS* 3.6 43.1 - - + +
364A PHE* 3.9 12.6 - - + -
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Residues in contact with PRO 246 (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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226A LYS 3.7 8.5 - - - +
227A MET* 4.0 4.7 - - + -
244A LEU 3.6 8.3 - - - +
245A LEU* 1.3 88.8 - - + +
247A ASP* 1.3 58.6 + - - +
248A GLU 3.3 9.9 - - - +
251A GLY* 3.8 21.3 - - - +
252A LEU* 3.9 32.5 - - + +
255A LEU* 4.1 11.2 - - + -
362A HIS* 2.7 29.8 + - + +
363A PRO 3.5 21.3 - - - +
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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