Contacts of the helix formed by residues 341 - 356 (chain B) in PDB entry 3PU8
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 SER 341 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B GLY 5.0 0.9 + - - -
123B PHE 4.4 9.9 + - - -
124B THR* 6.0 0.9 - - - +
317B SER* 3.4 30.1 + - - -
338B HIS* 3.3 20.0 + - - -
339B SER 3.3 0.2 - - - -
340B LEU* 1.3 85.3 + - - +
342B VAL* 1.3 59.4 + - - +
343B GLU* 3.2 2.9 - - - +
344B MET* 3.9 8.8 - - - +
345B GLN* 2.8 36.6 + - - +
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Residues in contact with VAL 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B TRP* 3.8 24.5 - - + -
338B HIS 4.1 0.4 + - - -
339B SER* 3.7 19.7 - - - +
340B LEU 3.8 0.8 - - - -
341B SER* 1.3 75.6 - - - +
343B GLU* 1.3 63.8 + - - +
345B GLN* 3.7 9.2 + - - +
346B MET* 3.1 24.7 + - + +
373B MET* 5.7 2.5 - - + -
394B HIS 5.3 0.7 - - - +
395B LEU* 6.4 0.9 - - + -
398B GLY* 3.8 33.4 - - - +
401B ILE* 3.7 24.9 - - + -
402B LEU* 4.1 17.5 - - + -
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Residues in contact with GLU 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B SER* 3.2 0.8 - - - -
342B VAL* 1.3 80.3 - - - +
344B MET* 1.3 57.5 + - - +
346B MET* 3.3 4.5 + - - +
347B ARG* 2.9 30.0 + - + +
397B GLN* 6.0 2.0 - - - -
401B ILE* 3.5 28.4 - - + +
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Residues in contact with MET 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B PRO* 3.7 31.0 - - + +
278B ILE* 3.9 21.3 - - + -
317B SER* 3.3 37.5 - - - +
318B GLY* 3.7 11.2 - - - -
341B SER* 3.4 9.9 + - - +
343B GLU* 1.3 79.9 - - - +
345B GLN* 1.3 57.6 + - - +
347B ARG* 3.3 10.1 + - - +
348B ALA* 2.9 31.4 + - - +
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Residues in contact with GLN 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B TRP* 3.6 28.5 - - - -
253B GLY 3.6 20.0 - - - +
254B GLY* 3.6 11.4 - - - +
256B SER* 5.2 0.2 + - - -
317B SER* 3.5 14.2 + - - +
336B PHE 4.6 0.5 - - - +
337B LEU* 3.3 15.5 - - - +
338B HIS* 2.9 45.4 + - - +
341B SER* 2.8 26.1 + - - +
342B VAL* 3.7 5.8 - - - +
344B MET* 1.3 75.7 - - - +
346B MET* 1.3 57.9 + - + +
348B ALA* 3.8 0.5 - - - +
349B TYR* 3.0 27.7 + - - +
366B PHE* 3.9 9.8 - - + -
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Residues in contact with MET 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B EDO 3.5 38.4 - - - +
342B VAL* 3.1 20.2 + - + +
343B GLU 3.7 3.8 - - - +
345B GLN* 1.3 72.0 - - + +
347B ARG* 1.3 61.6 + - - +
349B TYR* 3.2 10.1 + - + +
350B GLU* 2.8 41.2 + - - +
366B PHE* 4.1 17.7 - - - -
370B CYS* 4.4 11.7 - - - -
401B ILE* 3.6 25.8 - - + +
402B LEU* 4.6 5.8 - - + -
405B ALA* 4.1 15.0 - - + -
409B TRP* 4.0 12.8 - - + -
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Residues in contact with ARG 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B SER* 3.4 36.4 + - - +
278B ILE* 3.7 41.7 - - + +
279B SER* 3.6 15.8 + - - +
282B GLU* 4.8 2.0 + - - -
343B GLU* 2.9 19.8 + - + +
344B MET* 3.6 11.9 - - - +
346B MET* 1.3 76.3 - - - +
348B ALA* 1.3 63.0 + - - +
350B GLU* 3.2 19.6 + - - +
351B VAL* 3.0 39.4 + - - +
354B ARG* 4.1 11.5 - - - +
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Residues in contact with ALA 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ILE* 4.1 22.0 - - + -
254B GLY* 3.4 34.3 - - - +
278B ILE* 6.2 0.4 - - - -
318B GLY* 5.0 4.5 - - - -
344B MET* 2.9 18.3 + - + +
347B ARG* 1.3 73.4 - - - +
349B TYR* 1.3 58.5 + - - +
351B VAL* 3.1 9.4 + - - +
352B GLU* 2.9 33.9 + - - +
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Residues in contact with TYR 349 (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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17B EDO 3.7 31.9 - - - -
253B GLY* 4.6 2.5 - - - -
254B GLY 4.8 0.2 - - - +
345B GLN 3.0 18.3 + - - +
346B MET* 3.5 6.5 - - + +
348B ALA* 1.3 77.7 - - - +
350B GLU* 1.3 56.4 + - - +
352B GLU* 3.3 26.8 + - + +
353B ARG* 2.9 51.6 + - + +
363B PHE 5.7 0.9 - - - -
366B PHE* 3.5 50.6 - + + +
367B GLU* 2.5 36.6 + - + +
409B TRP* 4.1 1.8 - + - -
421B GLU* 4.7 5.4 + - - -
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Residues in contact with GLU 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B EDO 3.1 37.5 + - - -
346B MET* 2.8 26.3 + - - +
347B ARG* 3.5 20.8 + - - +
349B TYR* 1.3 72.5 - - - +
351B VAL* 1.3 65.4 + - - +
353B ARG* 3.4 6.2 + - - +
354B ARG* 3.1 48.5 + - - +
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Residues in contact with VAL 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ILE* 5.6 2.5 - - + -
278B ILE* 4.0 15.7 - - + -
281B TYR* 4.4 15.3 - - + -
282B GLU* 3.6 25.3 - - + +
347B ARG* 3.0 33.3 + - - +
348B ALA* 3.5 9.9 - - - +
350B GLU* 1.3 76.8 - - - +
352B GLU* 1.3 65.0 + - - +
354B ARG* 3.1 25.7 + - - +
355B LEU* 3.0 40.3 + - + +
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Residues in contact with GLU 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ASP 4.5 0.2 - - - +
252B SER* 2.8 26.4 + - - -
253B GLY* 2.6 31.0 + - - -
254B GLY 4.3 0.9 + - - -
348B ALA* 2.9 12.5 + - - +
349B TYR* 3.4 29.1 - - + +
351B VAL* 1.3 80.0 - - + +
353B ARG* 1.3 64.6 + - + +
355B LEU* 3.4 11.6 + - + +
356B LYS* 3.2 18.7 + - - -
357B LEU* 4.4 7.0 + - + +
359B SER* 6.0 0.9 - - - -
362B GLN* 4.6 8.3 - - - +
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Residues in contact with ARG 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B EDO 3.7 23.8 + - - -
349B TYR* 2.9 49.5 + - + +
350B GLU* 3.7 6.1 - - - +
351B VAL 3.2 0.2 - - - -
352B GLU* 1.3 79.2 - - + +
354B ARG* 1.3 60.5 + - + +
356B LYS* 3.4 23.1 + - - +
367B GLU* 4.4 1.9 + - - -
417B GLU* 6.0 3.8 - - - +
418B HIS* 4.2 23.1 + - - -
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Residues in contact with ARG 354 (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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282B GLU* 2.8 45.3 + - - +
347B ARG* 4.1 10.7 - - - +
350B GLU* 3.1 35.9 + - - +
351B VAL* 3.1 23.8 + - - +
353B ARG* 1.3 78.4 - - + +
355B LEU* 1.3 61.2 + - - +
356B LYS* 3.6 12.8 + - - +
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Residues in contact with LEU 355 (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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281B TYR* 4.5 10.1 - - + +
282B GLU* 3.6 31.9 - - + +
285B ARG* 3.9 24.7 - - + -
286B SER* 3.6 26.0 - - - +
351B VAL* 3.0 38.8 + - + +
352B GLU* 3.8 9.2 - - + +
353B ARG 3.3 0.2 - - - -
354B ARG* 1.3 76.9 - - - +
356B LYS* 1.3 71.3 + - - +
357B LEU* 3.4 27.8 + - + +
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Residues in contact with LYS 356 (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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352B GLU 3.2 9.7 + - - -
353B ARG* 3.4 18.6 + - - +
354B ARG* 3.7 9.0 - - - +
355B LEU* 1.3 80.1 - - - +
357B LEU* 1.3 63.0 + - - +
358B GLY 3.2 4.3 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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