Contacts of the helix formed by residues 416 - 435 (chain B) 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 LYS 416 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B PRO* 3.8 25.4 - - + -
381B ARG* 3.8 15.0 - - - +
414B ASP* 2.8 14.5 + - - +
415B ALA* 1.3 91.8 + - + +
417B TRP* 1.3 68.2 + - - +
418B ARG* 3.1 4.9 - - + +
419B VAL* 2.8 26.6 + - + +
420B ARG* 3.1 10.4 + - - -
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Residues in contact with TRP 417 (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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417A TRP* 4.9 1.1 - + - -
421A LEU* 3.7 31.4 - - + -
456A TYR* 4.1 27.5 - + - -
457A ALA* 3.3 42.8 - - + -
460A GLU* 4.2 14.2 - - + +
461A ALA* 4.7 6.5 - - + -
415B ALA 3.7 0.6 + - - -
416B LYS* 1.3 69.6 - - + +
418B ARG* 1.3 97.6 + - + +
420B ARG* 2.8 32.2 + - - +
421B LEU* 2.5 51.7 + - + +
455B VAL* 3.8 12.6 - - + -
457B ALA* 5.2 2.7 - - + -
458B ILE* 3.4 18.1 - - + +
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Residues in contact with ARG 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A ARG* 4.0 12.1 - - - +
421A LEU* 4.5 0.2 - - - +
425A GLU* 2.1 55.0 + - - -
378B PRO* 6.4 0.9 - - + -
382B LEU* 3.8 32.2 - - + +
416B LYS* 3.0 4.9 + - + +
417B TRP* 1.3 117.4 - - + +
419B VAL* 1.3 59.3 + - + +
421B LEU* 3.4 10.1 + - - +
422B ALA* 2.9 39.2 + - - +
425B GLU* 3.8 20.4 + - - -
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Residues in contact with VAL 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B PRO* 4.3 15.5 - - + +
381B ARG* 3.7 34.3 - - + +
382B LEU* 4.7 6.5 - - + +
385B ILE* 3.8 14.6 - - + -
411B LEU* 3.7 18.6 - - + +
414B ASP* 3.5 32.5 - - + +
416B LYS* 2.8 15.3 + - + +
418B ARG* 1.3 71.3 - - + +
420B ARG* 1.3 70.5 + - - +
422B ALA* 3.2 7.8 + - - +
423B ILE* 3.1 17.7 + - - +
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Residues in contact with ARG 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B LEU 4.3 5.2 - - - -
412B ALA 3.6 23.3 - - - +
413B GLU* 4.5 2.7 - - - +
414B ASP* 3.1 32.6 + - + +
415B ALA 3.1 24.2 + - - -
416B LYS 3.1 8.1 + - - +
417B TRP* 2.8 35.0 + - - +
419B VAL* 1.3 74.4 - - - +
421B LEU* 1.3 69.9 + - - +
423B ILE* 2.8 16.3 + - - +
424B ILE* 3.0 13.5 + - - +
450B TRP* 4.7 10.8 - - - +
453B ASP* 3.0 41.8 + - - -
455B VAL* 3.5 7.7 - - - +
458B ILE* 3.5 9.5 - - + +
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Residues in contact with LEU 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A TRP* 3.8 31.0 - - + -
418A ARG* 4.5 4.5 - - - +
421A LEU* 4.2 8.7 - - + -
417B TRP* 2.5 32.1 + - + +
418B ARG* 3.5 18.8 - - - +
420B ARG* 1.3 72.6 - - - +
422B ALA* 1.3 64.3 + - - +
424B ILE* 3.0 7.4 + - + +
425B GLU* 2.9 55.0 + - + +
457B ALA 5.4 0.7 - - - +
458B ILE* 3.2 14.5 - - + +
461B ALA* 3.8 28.3 - - + -
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Residues in contact with ALA 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B LEU* 4.6 11.0 - - + -
385B ILE* 3.9 28.1 - - + +
418B ARG* 2.9 28.3 + - - +
419B VAL* 3.2 12.3 - - - +
420B ARG 2.9 0.6 + - - -
421B LEU* 1.3 76.2 - - - +
423B ILE* 1.3 63.8 + - - +
425B GLU* 3.0 16.7 + - - +
426B TYR* 3.1 12.1 + - - +
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Residues in contact with ILE 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B ILE* 3.6 22.9 - - + -
388B LEU* 5.2 2.7 - - + -
408B ILE* 4.0 29.2 - - + +
411B LEU* 3.4 46.2 - - + +
412B ALA* 3.9 14.6 - - + -
419B VAL 3.7 6.3 - - - +
420B ARG 2.8 9.6 + - - +
422B ALA* 1.3 75.7 - - - +
424B ILE* 1.3 63.5 + - - +
426B TYR* 3.0 18.8 + - + +
427B MET* 3.0 16.9 + - - +
430B LEU* 6.4 0.2 - - + -
446B LEU* 5.9 1.3 - - + -
450B TRP* 3.8 21.8 - - + -
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Residues in contact with ILE 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B ARG 3.0 14.6 + - - +
421B LEU* 3.1 11.7 - - + +
423B ILE* 1.3 76.6 - - - +
425B GLU* 1.3 60.4 + - + +
427B MET* 3.4 4.3 + - - +
428B PRO* 3.4 17.8 - - - +
450B TRP* 3.5 57.9 - - + +
458B ILE* 3.9 41.3 - - + +
461B ALA* 3.8 30.3 - - + +
462B ALA* 4.5 1.3 - - - +
465B ASN* 3.5 9.2 + - + -
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Residues in contact with GLU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A LEU* 5.1 2.1 - - - +
418A ARG* 2.5 46.0 + - - -
418B ARG* 3.8 16.1 + - - -
421B LEU* 2.9 32.5 + - + +
422B ALA* 3.0 7.4 + - - +
424B ILE* 1.3 79.0 - - + +
426B TYR* 1.3 61.3 + - - +
428B PRO* 3.7 14.8 - - - +
429B LEU* 5.7 0.9 - - - +
461B ALA* 5.4 3.1 - - + +
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Residues in contact with TYR 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B ILE* 5.2 6.1 - - + +
388B LEU* 3.5 47.3 + - + +
389B ASP* 3.6 33.0 - - - +
392B ASN* 4.5 0.9 + - - -
400B LEU* 3.8 18.4 - - + +
408B ILE* 3.8 8.7 - - + -
422B ALA 3.1 10.1 + - - +
423B ILE* 3.0 14.9 + - + +
425B GLU* 1.3 79.6 - - - +
427B MET* 1.3 64.6 + - - +
428B PRO 3.5 0.2 - - - -
429B LEU* 3.2 32.9 + - + +
430B LEU* 3.2 47.9 + - + +
433B GLN* 3.6 13.5 + - - -
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Residues in contact with MET 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ILE* 6.1 2.0 - - - -
423B ILE* 3.0 14.4 + - - +
424B ILE 3.5 9.4 - - - +
426B TYR* 1.3 75.1 - - - +
428B PRO* 1.3 73.6 - - + +
429B LEU 3.1 0.2 + - - -
430B LEU* 3.1 40.0 + - + -
431B ALA* 2.8 30.9 + - + +
439B PHE* 4.4 5.6 - - + -
443B LEU* 4.0 23.1 - - + -
446B LEU* 5.5 4.3 - - - -
447B CYS* 3.5 32.5 - - - -
450B TRP* 4.5 13.0 - - + -
465B ASN* 4.0 9.6 - - - +
469B LEU* 4.9 1.3 - - + -
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Residues in contact with PRO 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B ILE 3.4 6.3 - - - +
425B GLU* 3.7 12.6 - - - +
426B TYR 3.6 1.1 - - - -
427B MET* 1.3 85.7 - - + +
429B LEU* 1.3 61.2 + - + +
431B ALA* 3.7 1.9 - - - +
432B GLY 3.1 16.5 + - - -
465B ASN* 2.9 27.6 - - - +
468B LYS* 4.0 39.0 - - + -
469B LEU* 4.6 11.8 - - + +
472B LYS* 3.2 20.5 - - + +
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Residues in contact with LEU 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B ASP* 4.6 19.7 - - + +
425B GLU 5.7 0.4 - - - +
426B TYR* 3.2 31.6 + - + +
428B PRO* 1.3 77.5 - - + +
430B LEU* 1.3 55.5 + - - +
432B GLY* 2.9 5.4 + - - -
433B GLN* 2.8 62.7 + - + +
472B LYS* 4.1 14.3 - - - +
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Residues in contact with LEU 430 (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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397B ILE* 5.9 0.4 - - + -
400B LEU* 5.4 5.2 - - + -
405B LEU* 3.9 10.1 - - + -
408B ILE* 3.8 26.0 - - + -
423B ILE* 6.4 0.2 - - + -
426B TYR* 3.2 47.9 + - + +
427B MET* 3.1 28.4 + - + +
429B LEU* 1.3 79.3 - - - +
431B ALA* 1.3 52.2 + - - +
433B GLN* 3.2 14.5 + - + +
434B LEU* 2.7 61.2 + - + -
443B LEU* 4.3 2.2 - - + -
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Residues in contact with ALA 431 (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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427B MET* 2.8 25.6 + - + +
428B PRO 3.7 4.5 - - - +
430B LEU* 1.3 68.6 - - - +
432B GLY* 1.3 69.6 + - - +
434B LEU* 3.0 6.0 + - - +
435B GLY* 2.7 26.5 + - - +
439B PHE* 3.5 35.2 - - + -
443B LEU* 4.9 0.2 - - - -
469B LEU* 3.9 6.5 - - + -
473B PHE* 3.6 17.1 - - + -
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Residues in contact with GLY 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B PRO 3.1 9.0 + - - -
429B LEU* 2.9 8.5 + - - -
431B ALA* 1.3 79.1 - - - +
433B GLN* 1.3 61.8 + - - +
435B GLY* 3.3 10.2 + - - -
472B LYS* 4.1 24.8 - - - +
473B PHE* 4.4 5.3 - - - -
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Residues in contact with GLN 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B ASP 4.4 5.9 + - - -
392B ASN* 2.5 33.6 + - - +
393B GLU* 4.7 7.7 + - - -
397B ILE* 3.7 29.8 - - + +
400B LEU* 4.8 1.0 - - - +
426B TYR* 3.6 16.1 + - - -
429B LEU* 2.8 47.5 + - + +
430B LEU* 3.5 14.2 - - - +
431B ALA 3.1 0.2 - - - -
432B GLY* 1.3 75.0 - - - +
434B LEU* 1.3 61.4 + - - +
435B GLY* 3.3 1.0 + - - -
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Residues in contact with LEU 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B ILE* 3.5 32.5 - - + +
401B SER* 4.4 11.4 - - - -
405B LEU* 3.4 20.4 - - + -
430B LEU* 2.7 44.3 + - + +
431B ALA* 3.8 4.3 - - - +
433B GLN* 1.3 72.9 - - - +
435B GLY* 1.3 66.5 - - - +
437B GLU* 3.6 3.1 - - - +
438B PHE* 3.5 40.2 - - + +
443B LEU* 3.9 15.3 - - + -
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Residues in contact with GLY 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B ALA 2.7 13.9 + - - +
432B GLY 3.3 6.9 + - - -
433B GLN 3.2 5.1 - - - -
434B LEU* 1.3 79.8 - - - +
436B VAL* 1.3 60.6 + - - -
437B GLU* 2.7 19.2 - - - +
439B PHE* 3.2 17.7 + - - +
473B PHE* 4.1 2.9 - - - -
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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
------------------------------------------------------------
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