Contacts of the helix formed by residues 338 - 350 (chain A) in PDB entry 1UPB
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 ASP 338 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A LYS* 2.8 35.8 + - - -
194A PRO 5.0 4.0 - - - +
196A GLY* 5.9 4.9 - - - -
198A VAL* 4.3 8.6 - - + +
230A SER* 2.6 21.5 + - - -
320A PRO* 4.4 11.6 - - + +
337A THR* 1.3 84.9 + - - +
339A VAL* 1.3 59.0 + - - +
340A LEU* 3.4 0.7 + - - +
341A ALA* 3.3 27.6 + - + +
342A PHE 2.9 24.3 + - - -
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Residues in contact with VAL 339 (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 ALA 4.2 6.1 - - - +
227A ALA* 3.9 15.7 - - + -
230A SER* 3.5 10.7 + - - +
232A ALA* 3.8 17.7 - - + -
236A ILE* 4.4 1.6 - - + -
294A VAL* 3.6 27.6 - - + -
295A GLY* 3.9 26.9 - - - +
318A ILE* 4.5 9.2 - - + -
320A PRO* 4.3 17.4 - - + +
338A ASP* 1.3 75.4 + - - +
340A LEU* 1.3 63.9 + - - +
342A PHE* 3.1 7.8 + - - +
343A VAL* 3.0 23.2 + - + +
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Residues in contact with LEU 340 (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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193A LYS* 3.8 16.8 - - - +
230A SER* 3.3 14.3 + - - +
231A GLY* 4.2 9.2 - - - +
232A ALA* 4.0 15.6 - - + +
235A ALA* 3.9 28.9 - - + -
338A ASP* 3.5 9.6 - - - +
339A VAL* 1.3 77.9 - - - +
341A ALA* 1.3 61.9 + - - +
343A VAL* 3.2 2.6 + - + +
344A GLU* 3.0 48.4 + - + +
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Residues in contact with ALA 341 (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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202A TRP* 3.5 26.2 - - + -
337A THR* 4.2 5.2 - - - +
338A ASP* 3.3 25.2 + - + +
340A LEU* 1.3 78.8 - - - +
342A PHE* 1.3 62.4 + - - +
344A GLU* 4.1 9.1 - - - +
345A HIS* 3.2 17.0 + - - +
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Residues in contact with PHE 342 (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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202A TRP* 3.9 9.0 - - - -
206A ALA* 4.1 25.1 - - + -
209A ALA* 4.7 3.6 - - + -
221A LEU* 6.2 1.3 - - + -
239A LEU* 5.6 2.2 - - + -
292A LEU* 4.6 5.4 - - + -
294A VAL* 5.0 9.4 - - + -
318A ILE* 3.7 49.1 - - + -
335A VAL* 4.1 9.9 - - + -
337A THR* 3.7 12.7 - - + +
338A ASP 2.9 12.9 + - - +
339A VAL 3.4 7.0 - - - +
341A ALA* 1.3 76.8 - - - +
343A VAL* 1.3 76.5 + - + +
345A HIS* 3.3 2.6 + - - +
346A PHE* 2.9 75.6 + + + +
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Residues in contact with VAL 343 (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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232A ALA* 4.8 1.6 - - + -
235A ALA* 3.7 41.1 - - + +
236A ILE* 3.8 24.9 - - + +
239A LEU* 4.6 13.2 - - + -
294A VAL* 4.8 2.2 - - + -
339A VAL* 3.0 26.6 + - + +
340A LEU* 3.2 8.0 + - - +
342A PHE* 1.3 92.5 - - + +
344A GLU* 1.3 56.4 + - - +
346A PHE* 3.7 5.2 - - - +
347A GLU* 3.0 33.3 + - + +
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Residues in contact with GLU 344 (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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235A ALA* 5.5 2.9 - - + -
340A LEU* 3.0 50.4 + - + +
341A ALA* 4.1 7.9 - - - +
343A VAL* 1.3 76.8 - - + +
345A HIS* 1.3 62.0 + - - +
347A GLU* 3.6 9.3 - - + +
348A THR* 3.4 22.3 + - - -
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Residues in contact with HIS 345 (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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202A TRP* 4.0 13.3 - + + -
203A GLN* 3.5 39.3 + - + +
206A ALA* 4.0 15.0 - - + -
207A ASP* 2.8 30.2 + - - -
341A ALA 3.2 15.1 + - - +
342A PHE 3.7 3.4 - - - +
344A GLU* 1.3 77.9 - - - +
346A PHE* 1.3 59.5 + - - +
348A THR* 3.2 8.7 + - - -
349A ALA* 2.9 28.6 + - + +
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Residues in contact with PHE 346 (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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206A ALA* 3.9 11.4 - - + -
209A ALA* 3.9 5.2 - - + -
210A ALA* 3.6 30.7 - - + -
213A LEU* 3.5 35.0 - - + -
221A LEU* 5.8 1.8 - - + -
239A LEU* 3.7 33.4 - - + -
245A ILE* 5.7 0.9 - - + -
292A LEU* 4.1 19.3 - - + -
342A PHE* 2.9 47.5 + + + +
343A VAL* 3.7 5.6 - - - +
345A HIS* 1.3 75.0 - - - +
347A GLU* 1.3 58.9 + - - +
349A ALA* 3.4 4.2 + - - +
350A THR* 2.6 44.2 + - + +
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Residues in contact with GLU 347 (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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235A ALA* 4.1 4.1 - - + +
238A ALA* 4.0 7.3 - - - +
239A LEU* 3.4 34.0 + - + +
242A ARG* 2.8 36.4 + - - -
343A VAL* 3.0 27.9 + - + +
344A GLU* 3.6 11.2 - - + +
346A PHE* 1.3 75.2 - - - +
348A THR* 1.3 63.3 + - - +
350A THR* 3.3 4.2 + - - -
351A ALA* 3.0 26.5 + - - +
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Residues in contact with THR 348 (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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344A GLU 3.4 10.8 + - - -
345A HIS* 3.2 12.2 + - - -
347A GLU* 1.3 79.3 - - - +
349A ALA* 1.3 62.1 + - - +
350A THR 3.3 1.2 + - - -
351A ALA* 3.4 16.4 + - - +
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Residues in contact with ALA 349 (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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206A ALA 5.3 0.4 - - - +
207A ASP* 3.9 21.5 - - - +
210A ALA* 4.0 19.1 - - + +
345A HIS* 2.9 18.4 + - + +
346A PHE* 3.9 7.2 - - - +
347A GLU 3.3 0.2 - - - -
348A THR* 1.3 77.2 - - - +
350A THR* 1.3 58.2 + - - +
351A ALA 3.6 0.6 + - - -
352A SER* 5.8 0.2 + - - -
353A PHE* 3.8 15.9 - - - -
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Residues in contact with THR 350 (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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210A ALA* 3.9 14.6 - - + -
213A LEU* 4.2 2.5 - - + -
239A LEU* 4.2 2.8 - - - +
242A ARG* 2.9 32.0 + - - -
243A LEU* 4.0 8.2 - - - +
346A PHE* 2.6 41.8 + - + +
349A ALA* 1.3 79.4 - - - +
351A ALA* 1.3 64.7 + - - +
352A SER 3.1 4.8 + - - -
353A PHE* 3.2 43.7 + - + +
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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