Contacts of the helix formed by residues 377 - 392 (chain A) in PDB entry 2PKG
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 CYS 377 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A GLN* 3.8 34.7 - - + +
342A LYS* 5.1 0.9 - - - +
375A ASP* 2.8 16.5 + - - +
376A GLU* 1.3 78.9 - - - +
378A PRO* 1.3 66.2 - - - +
379A GLU* 3.2 28.5 - - - -
380A VAL* 3.2 20.9 + - + +
381A ARG* 3.0 28.3 + - - +
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Residues in contact with PRO 378 (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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376A GLU 3.8 2.7 - - - +
377A CYS* 1.3 81.7 - - - +
379A GLU* 1.3 55.4 + - - +
380A VAL 2.8 5.6 - - - -
381A ARG* 3.1 29.1 - - + +
382A LEU* 2.5 41.2 + - + +
416A LYS* 3.9 25.4 - - + -
418A ARG* 6.4 1.6 - - + -
419A VAL* 4.3 14.8 - - + +
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Residues in contact with GLU 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A SER* 3.5 22.1 + - - +
377A CYS* 3.2 13.4 - - - -
378A PRO* 1.3 78.6 - - - +
380A VAL* 1.3 57.1 + - - +
382A LEU* 3.7 12.6 - - - +
383A ASN* 3.0 46.9 + - - +
468B LYS* 3.9 33.6 + - - +
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Residues in contact with VAL 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A GLN 4.6 0.7 - - - +
342A LYS* 4.1 13.7 - - + -
343A SER* 3.7 31.4 - - - +
346A ALA* 4.2 7.6 - - + -
372A GLN* 3.9 25.1 - - + +
375A ASP* 3.5 30.1 - - + +
377A CYS* 3.2 21.6 + - + +
378A PRO 2.8 1.4 - - - -
379A GLU* 1.3 75.5 - - - +
381A ARG* 1.3 69.9 + - - +
382A LEU 2.8 0.7 - - - -
383A ASN* 2.6 18.7 + - - +
384A ILE* 2.9 11.6 + - - +
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Residues in contact with ARG 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A GLN 4.1 4.9 - - - +
373A LEU* 3.5 27.3 - - - +
374A LYS 5.0 1.1 - - - -
375A ASP 3.2 24.3 + - - +
376A GLU* 3.2 18.5 + - - -
377A CYS 3.0 9.1 + - - +
378A PRO* 3.1 36.7 - - + +
380A VAL* 1.3 82.3 - - - +
382A LEU* 1.3 63.4 + - - +
384A ILE* 3.4 3.8 + - - +
385A ILE* 2.9 29.8 + - - +
411A LEU* 4.2 8.3 - - + -
414A ASP* 2.5 52.7 + - - -
415A ALA* 4.6 6.1 - - - +
416A LYS* 4.4 6.1 - - - +
419A VAL* 4.3 7.0 - - + -
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Residues in contact with LEU 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A PRO* 2.5 26.8 + - + +
379A GLU* 3.7 16.6 - - - +
380A VAL 2.8 0.2 + - - -
381A ARG* 1.3 75.9 - - - +
383A ASN* 1.3 68.5 + - - +
384A ILE 3.1 1.4 + - - -
385A ILE* 3.1 13.7 + - - +
386A SER* 3.3 16.8 + - - -
418A ARG* 3.8 49.4 - - + +
419A VAL* 4.8 6.3 - - + +
422A ALA* 4.4 21.3 - - + -
425B GLU* 5.1 1.3 - - - +
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Residues in contact with ASN 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A SER* 3.1 27.7 + - - -
344A ALA* 5.1 0.2 - - - +
346A ALA* 3.5 25.6 - - + +
347A SER* 3.3 19.0 - - - +
379A GLU* 3.0 32.4 + - - +
380A VAL 2.6 9.7 + - - +
382A LEU* 1.3 81.7 - - - +
384A ILE* 1.3 59.8 + - - +
386A SER* 3.8 10.7 + - - +
387A ASN* 3.9 14.6 + - - -
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Residues in contact with ILE 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ALA* 3.9 15.9 - - + +
349A ILE* 4.0 7.6 - - + -
350A MET* 2.8 47.5 - - + +
369A PHE* 4.1 8.3 - - - -
372A GLN* 3.1 49.6 - - + +
373A LEU* 3.1 44.2 - - + +
380A VAL 2.9 11.1 + - - +
381A ARG 4.0 2.9 - - - +
383A ASN* 1.3 75.6 - - - +
385A ILE* 1.3 68.0 + - - +
386A SER 3.2 0.5 + - - -
387A ASN 3.3 6.6 + - - -
388A LEU* 3.8 2.3 - - + +
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Residues in contact with ILE 385 (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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373A LEU* 4.2 14.1 - - + -
381A ARG 2.9 19.1 - - - +
382A LEU* 3.1 6.4 + - - +
384A ILE* 1.3 78.5 - - - +
386A SER* 1.3 64.3 + - - +
387A ASN 3.2 1.4 + - - -
388A LEU* 3.4 29.4 + - + +
389A ASP* 4.1 4.2 - - - +
411A LEU* 4.0 6.3 - - + -
419A VAL* 3.9 24.5 - - + -
422A ALA* 3.9 36.6 - - + +
423A ILE* 4.0 28.5 - - + -
426A TYR* 4.9 9.0 - - + +
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Residues in contact with SER 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A LEU* 3.3 19.1 + - - +
383A ASN* 4.1 8.5 - - - -
384A ILE 3.1 1.6 - - - -
385A ILE* 1.3 80.0 - - - +
387A ASN* 1.3 68.3 + - - +
389A ASP* 3.7 15.9 - - - +
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Residues in contact with ASN 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A SER* 3.0 27.7 + - - +
350A MET* 3.4 30.9 - - + +
351A GLY 6.0 0.2 - - - -
383A ASN 3.9 11.3 + - - -
384A ILE 3.3 3.8 + - - -
385A ILE 3.3 1.0 - - - -
386A SER* 1.3 85.5 + - - +
388A LEU* 1.3 65.6 + - - +
389A ASP* 3.3 3.6 - - - -
390A CYS* 3.1 23.4 + - + +
391A VAL* 4.0 3.6 + - - +
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Residues in contact with LEU 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A MET* 3.7 23.8 - - + -
373A LEU* 4.9 9.0 - - + -
384A ILE* 3.8 8.5 + - + +
385A ILE* 3.4 29.2 + - + +
386A SER 3.5 0.2 - - - -
387A ASN* 1.3 70.7 - - - +
389A ASP* 1.3 55.3 + - - +
390A CYS 2.3 31.4 + - - -
391A VAL* 3.1 15.8 + - + +
392A ASN* 3.5 4.0 + - - +
400A LEU* 5.5 1.6 - - + -
404A LEU* 4.0 26.0 - - + -
408A ILE* 3.8 22.4 - - + -
426A TYR* 3.7 36.3 + - + +
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Residues in contact with ASP 389 (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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385A ILE 4.1 3.3 - - - +
386A SER 3.7 20.5 - - - +
387A ASN 3.3 0.6 + - - +
388A LEU* 1.3 69.9 + - - +
390A CYS* 1.3 60.7 + - - +
392A ASN* 4.2 2.3 - - - +
393A GLU* 4.3 7.8 - - - +
426A TYR* 3.5 33.8 - - - +
429A LEU* 3.5 24.6 - - + +
433A GLN* 4.1 14.3 + - - +
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Residues in contact with CYS 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A MET* 4.5 15.7 - - + -
351A GLY* 6.1 0.7 - - - -
353A SER* 5.1 1.6 - - - -
354A PRO* 4.8 16.8 - - - -
387A ASN* 3.1 16.7 + - + +
388A LEU 2.3 12.3 + - - -
389A ASP* 1.3 68.5 - - - +
391A VAL* 1.3 64.1 + - + +
392A ASN* 2.3 21.6 + - - -
393A GLU* 2.3 35.2 + - - +
394A VAL* 5.2 1.8 - - - -
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Residues in contact with VAL 391 (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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350A MET* 3.8 27.6 - - + +
353A SER* 4.3 11.2 - - - +
361A THR* 5.4 0.2 - - + -
366A LEU* 6.6 0.2 - - + -
369A PHE* 3.8 28.7 - - + -
387A ASN 4.4 1.8 - - - +
388A LEU* 3.1 25.5 + - + +
390A CYS* 1.3 79.2 - - - +
392A ASN* 1.3 59.2 + - - +
393A GLU 2.8 1.3 - - - -
394A VAL* 2.8 30.1 + - - +
395A ILE* 2.9 28.3 + - + +
400A LEU* 4.7 6.5 - - + -
404A LEU* 4.6 13.5 - - + -
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Residues in contact with ASN 392 (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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388A LEU 4.1 7.6 - - - +
389A ASP 4.2 2.4 + - - +
390A CYS 2.3 14.3 + - - +
391A VAL* 1.3 76.3 - - + +
393A GLU* 1.3 64.7 + - - +
395A ILE* 3.0 20.4 - - - +
396A GLY* 4.8 0.2 - - - -
397A ILE* 3.4 36.7 + - - +
400A LEU* 3.4 24.3 - - + +
426A TYR* 4.8 1.8 - - - +
433A GLN* 2.3 45.0 - - - +
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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