Contacts of the helix formed by residues 340 - 353 (chain A) in PDB entry 4PK7
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 GLN 340 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A ALA* 3.6 30.4 - - + +
305A ARG* 3.6 9.6 - - - +
338A ASP* 3.1 10.2 + - - +
339A LYS* 1.3 93.8 + - + +
341A GLY* 1.3 67.8 + - - +
342A GLU* 3.3 4.1 - - + +
343A VAL* 3.1 10.3 + - + +
344A ARG* 3.0 26.1 + - - +
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Residues in contact with GLY 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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339A LYS 4.2 0.2 + - - -
340A GLN* 1.3 70.9 + - - +
342A GLU* 1.3 66.2 + - - +
344A ARG* 3.0 25.3 + - - +
345A LEU* 2.9 22.1 + - - +
383A GLU* 4.0 24.0 + - - +
386A VAL* 3.3 12.8 - - - +
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Residues in contact with GLU 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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302A ALA* 4.5 4.7 - - - +
303A GLU* 4.1 33.4 + - - +
306A ALA* 4.4 18.0 - - + +
340A GLN* 4.5 4.9 - - + +
341A GLY* 1.3 76.8 - - - +
343A VAL* 1.3 64.9 + - + +
344A ARG 3.4 0.2 + - - -
345A LEU* 3.5 9.6 + - + +
346A LYS* 3.4 29.2 + - - +
383A GLU* 5.0 2.2 + - - -
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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
----------------------------------------------------------
302A ALA* 3.5 38.1 - - + +
305A ARG* 4.0 18.6 - - + +
306A ALA* 4.0 14.1 - - + +
309A ILE* 4.7 2.2 - - + -
335A THR* 3.1 33.7 - - + -
338A ASP* 3.4 29.4 - - + +
340A GLN* 3.1 4.3 + - + +
342A GLU* 1.3 75.5 - - + +
344A ARG* 1.3 62.1 + - - +
345A LEU 3.4 0.2 + - - -
346A LYS* 3.4 4.6 + - - +
347A CYS* 3.3 20.1 + - - -
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Residues in contact with ARG 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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335A THR 4.1 2.7 - - - +
336A MET* 3.3 28.4 - - - +
338A ASP 2.9 33.1 + - - +
339A LYS* 3.3 22.6 + - - +
340A GLN 3.0 12.1 + - - +
341A GLY* 3.0 23.5 + - - +
343A VAL* 1.3 76.2 - - - +
345A LEU* 1.3 62.1 + - - +
347A CYS* 3.2 17.4 + - - +
348A LEU* 3.4 16.3 + - - +
374A ARG* 3.6 13.6 - - - +
378A MET* 4.7 5.8 - - - +
381A ASP* 2.7 40.0 + - - -
382A LYS* 5.0 5.5 - - - +
383A GLU* 4.2 7.1 - - - +
386A VAL* 4.2 9.9 - - + -
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Residues in contact with LEU 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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341A GLY 2.9 11.7 + - - +
342A GLU* 3.6 12.8 - - + +
344A ARG* 1.3 73.6 - - - +
346A LYS* 1.3 65.1 + - + +
348A LEU* 2.7 25.8 + - - +
349A THR* 2.8 21.6 + - - +
385A ASP* 3.4 29.4 - - + +
386A VAL* 3.6 16.7 - - + +
389A GLN* 3.3 33.2 - - + -
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Residues in contact with LYS 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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306A ALA* 3.9 32.8 + - + +
309A ILE* 3.9 16.4 - - + +
310A GLU* 3.3 37.8 + - + +
342A GLU* 3.4 19.1 + - - +
343A VAL* 3.4 11.5 + - - +
344A ARG 3.4 0.2 - - - -
345A LEU* 1.3 86.7 - - + +
347A CYS* 1.3 62.7 + - - +
349A THR* 4.0 14.3 - - + +
350A ALA* 3.0 24.8 + - - +
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Residues in contact with CYS 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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309A ILE* 3.8 13.5 - - - -
332A VAL* 3.9 12.4 - - + +
335A THR* 3.5 46.0 - - - -
336A MET* 3.6 22.9 - - + -
343A VAL 3.3 15.7 + - - -
344A ARG 3.2 6.9 + - - +
345A LEU 3.1 1.4 - - - -
346A LYS* 1.3 76.5 - - - +
348A LEU* 1.3 62.8 + - - +
350A ALA* 3.7 2.6 - - - +
351A LEU* 3.2 27.6 + - - +
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Residues in contact with LEU 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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336A MET* 4.6 4.9 - - + -
344A ARG 3.4 8.3 + - - +
345A LEU* 2.7 14.6 + - - +
347A CYS* 1.3 73.6 - - - +
349A THR* 1.3 65.0 + - - +
351A LEU* 3.1 10.1 + - + +
352A GLN* 2.9 29.9 + - - +
375A ILE* 4.9 3.1 - - + -
378A MET* 4.2 24.0 - - + -
386A VAL* 3.5 27.1 - - + +
389A GLN* 3.9 16.8 - - + +
390A ALA* 3.5 37.0 - - + +
393A LEU* 4.0 22.8 - - + +
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Residues in contact with THR 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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310A GLU* 5.7 4.0 - - + +
345A LEU* 2.8 28.3 + - - +
346A LYS* 4.0 16.6 - - + +
348A LEU* 1.3 72.5 - - - +
350A ALA* 1.3 63.1 + - - +
352A GLN* 3.4 16.2 + - - +
353A GLY* 3.2 18.7 + - - -
389A GLN* 4.9 7.2 + - - +
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Residues in contact with ALA 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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309A ILE 4.3 8.5 - - - +
310A GLU* 5.2 1.8 - - - +
313A GLY* 3.8 30.9 - - - +
316A MET* 5.3 1.6 - - + -
332A VAL* 4.7 11.7 - - + -
346A LYS 3.0 19.7 + - - +
347A CYS* 3.7 6.7 - - - +
349A THR* 1.3 79.2 - - - +
351A LEU* 1.3 62.5 + - + +
353A GLY* 3.3 14.0 + - - -
354A LEU* 3.7 13.3 - - - +
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Residues in contact with LEU 351 (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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316A MET* 5.9 1.1 - - + -
329A LEU* 4.5 12.1 - - + -
332A VAL* 4.1 14.4 - - + -
336A MET* 4.4 13.0 - - - -
347A CYS 3.2 13.6 + - - +
348A LEU* 3.1 9.6 + - + +
350A ALA* 1.3 76.2 - - - +
352A GLN* 1.3 69.8 + - - +
354A LEU* 2.8 20.1 + - + +
355A TYR* 3.2 17.9 - - + -
364A LEU* 4.6 10.8 - - + -
367A PHE* 3.7 32.5 - - + -
368A THR* 5.5 2.5 - - - +
375A ILE* 4.1 13.7 - - + -
393A LEU* 3.8 31.6 - - + -
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Residues in contact with GLN 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LEU 2.9 20.2 + - - +
349A THR* 3.6 16.9 + - - +
351A LEU* 1.3 74.2 - - - +
353A GLY* 1.3 56.5 + - - +
355A TYR* 3.0 6.9 + - - +
356A TYR* 3.0 29.4 + - + +
389A GLN* 2.8 57.8 + - - +
392A LYS* 3.6 7.6 - - - +
393A LEU* 3.6 27.2 - - + +
396A LEU* 3.8 20.0 - - + +
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Residues in contact with GLY 353 (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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317A LYS* 3.2 37.6 - - - +
349A THR 3.2 10.9 + - - -
350A ALA 3.3 6.3 + - - -
351A LEU 3.0 1.2 - - - -
352A GLN* 1.3 79.4 - - - +
354A LEU* 1.3 61.8 + - - +
355A TYR 3.4 1.1 - - - -
356A TYR* 3.3 17.8 - - - +
358A LYS 5.2 1.6 - - - +
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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