Contacts of the helix formed by residues 417 - 435 (chain K) in PDB entry 5G04
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 GLU 417 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412K ALA* 3.1 13.5 + - - +
413K PHE* 5.4 0.2 - - - -
415K ASN* 3.4 33.3 + - + +
416K GLY* 1.3 72.8 - - - +
418K TRP* 1.3 51.2 + - - +
419K LYS* 3.4 2.7 - - - -
420K THR* 2.5 50.9 + - + +
421K ALA* 2.9 21.5 + - - +
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Residues in contact with TRP 418 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413K PHE* 4.8 11.1 + + - -
416K GLY* 2.8 41.5 + - - -
417K GLU* 1.3 71.3 - - - +
419K LYS* 1.3 58.5 + - - +
421K ALA* 3.3 1.8 + - - -
422K GLU* 2.9 29.6 + - - +
454K VAL* 3.6 11.9 - - + +
457K LYS* 3.3 53.9 - - + +
458K LEU* 3.4 21.6 - - + +
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Residues in contact with LYS 419 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417K GLU 3.4 0.4 - - - -
418K TRP* 1.3 79.6 - - - +
420K THR* 1.3 65.2 + - + +
422K GLU* 3.5 5.9 + - + +
423K LYS* 3.1 21.7 + - - +
458K LEU* 4.1 24.7 - - + +
460K LYS* 5.9 3.6 - - - +
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Residues in contact with THR 420 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412K ALA* 3.8 8.8 - - - +
417K GLU* 2.5 52.8 + - + +
419K LYS* 1.3 78.1 - - + +
421K ALA* 1.3 56.9 + - - +
423K LYS* 3.2 10.0 + - + +
424K TRP* 2.9 41.1 + - - -
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Residues in contact with ALA 421 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409K GLY* 3.5 24.2 - - - +
412K ALA* 3.9 6.7 - - - +
413K PHE* 3.9 13.7 - - - +
417K GLU 2.9 16.0 + - - +
418K TRP* 3.3 0.6 + - - -
420K THR* 1.3 76.3 + - - +
422K GLU* 1.3 63.0 + - - +
424K TRP* 3.1 2.8 + - - +
425K PHE* 2.9 33.7 + - + -
454K VAL* 3.5 21.1 - - + -
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Residues in contact with GLU 422 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418K TRP 2.9 17.4 + - - +
419K LYS* 3.9 8.0 + - + +
421K ALA* 1.3 72.5 - - - +
423K LYS* 1.3 59.3 + - - +
425K PHE* 3.8 3.7 - - - +
426K LEU* 2.9 52.6 + - + +
451K LEU* 4.5 3.8 - - + -
454K VAL* 3.5 29.7 - - + +
455K CYS* 3.5 18.6 - - - -
458K LEU* 3.4 26.4 - - + +
460K LYS* 3.6 22.3 + - - +
463K GLU* 4.4 2.3 - - - +
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Residues in contact with LYS 423 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419K LYS 3.1 15.5 + - - +
420K THR* 3.2 11.6 + - - +
422K GLU* 1.3 76.9 - - - +
424K TRP* 1.3 80.8 + - + +
426K LEU* 3.9 7.0 - - - +
427K ASP* 3.0 52.8 + - - +
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Residues in contact with TRP 424 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395K LEU* 3.7 28.3 - - + -
405K MET* 3.7 42.5 - - + +
408K VAL* 3.3 34.7 - - + +
409K GLY* 3.7 22.4 - - - -
412K ALA* 4.6 5.1 - - + +
420K THR* 2.9 30.5 + - - -
421K ALA 3.1 5.6 + - - +
423K LYS* 1.3 98.3 - - + +
425K PHE* 1.3 58.7 + - - +
427K ASP* 3.4 24.0 + - + +
428K ALA* 2.9 28.6 + - - +
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Residues in contact with PHE 425 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406K HIS* 3.4 47.3 - + - -
409K GLY* 3.5 22.7 - - - -
410K VAL* 3.7 12.3 - - + -
413K PHE* 4.9 0.4 - - + -
421K ALA* 2.9 38.5 + - + +
422K GLU 3.8 0.7 - - - +
424K TRP* 1.3 78.3 - - - +
426K LEU* 1.3 56.3 + - - +
428K ALA* 3.2 6.1 + - - +
429K LEU* 2.9 28.4 + - - +
447K LEU* 3.8 12.7 - - + +
450K ASN* 3.9 30.7 - - + -
451K LEU* 3.8 30.4 - - + +
454K VAL* 4.4 8.7 - - + -
9W LEU* 4.2 7.9 - - + -
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Residues in contact with LEU 426 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422K GLU* 2.9 44.3 + - + +
423K LYS* 3.9 6.3 - - - +
425K PHE* 1.3 76.0 - - - +
427K ASP* 1.3 58.4 + - - +
429K LEU* 3.3 14.5 + - + +
430K GLU* 3.0 42.6 + - + +
451K LEU* 4.5 9.4 - - + +
467K TYR* 4.1 19.5 - - - +
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Residues in contact with ASP 427 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405K MET* 3.5 30.5 - - - +
423K LYS* 3.0 34.9 + - - +
424K TRP* 3.4 19.7 - - + +
426K LEU* 1.3 75.1 - - - +
428K ALA* 1.3 62.0 + - - +
430K GLU* 3.3 18.2 + - - +
431K LYS* 3.1 34.5 + - - +
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Residues in contact with ALA 428 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402K PRO* 4.0 25.9 - - + +
405K MET* 4.0 14.8 - - + -
406K HIS* 4.1 5.4 - - + +
424K TRP 2.9 14.1 + - - +
425K PHE* 3.4 10.1 - - - +
427K ASP* 1.3 77.5 - - - +
429K LEU* 1.3 57.4 + - - +
431K LYS* 3.3 6.2 + - - +
432K ILE* 2.9 30.4 + - - +
444K TRP* 5.9 0.7 - - + -
447K LEU* 4.0 17.3 - - + -
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Residues in contact with LEU 429 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H PHE* 4.1 15.3 - - + -
425K PHE 2.9 11.9 + - - +
426K LEU* 3.5 15.3 - - + +
428K ALA* 1.3 76.5 - - - +
430K GLU* 1.3 56.1 + - - +
432K ILE* 3.1 15.1 - - + +
433K LYS* 2.8 63.7 + - + +
447K LEU* 4.2 13.1 - - + +
448K LEU* 4.4 10.1 - - + -
451K LEU* 3.8 23.3 - - + -
467K TYR* 4.1 22.2 - - + +
470K GLN* 5.8 0.7 - - - +
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Residues in contact with GLU 430 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426K LEU* 3.0 29.1 + - + +
427K ASP* 3.3 20.7 + - - +
429K LEU* 1.3 75.9 - - - +
431K LYS* 1.3 65.2 + - + +
433K LYS* 3.3 22.1 + - + +
434K ALA* 3.5 10.9 + - - +
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Residues in contact with LYS 431 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400K GLU* 3.9 28.7 + - + +
402K PRO* 4.3 16.2 - - + -
405K MET* 3.9 28.9 - - - -
427K ASP* 3.1 23.9 + - - +
428K ALA* 3.7 6.7 - - - +
430K GLU* 1.3 76.2 - - + +
432K ILE* 1.3 58.7 + - - +
435K ILE* 2.8 62.2 + - + +
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Residues in contact with ILE 432 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H PHE* 3.9 29.5 - - + +
402K PRO* 4.3 15.0 - - + +
428K ALA 2.9 16.9 + - - +
429K LEU* 3.1 33.9 - - + +
431K LYS* 1.3 74.5 - - - +
433K LYS* 1.3 65.3 + - - +
434K ALA 3.3 0.2 + - - -
436K GLY* 3.0 29.6 - - - +
444K TRP* 3.3 47.1 - - + +
447K LEU* 4.1 9.0 - - + -
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Residues in contact with LYS 433 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H PHE* 3.6 49.7 + - - +
99H LYS* 5.3 10.9 - - - +
429K LEU* 2.8 53.8 + - + +
430K GLU* 3.5 12.8 - - + +
431K LYS 3.3 0.4 - - - -
432K ILE* 1.3 78.1 - - - +
434K ALA* 1.3 59.8 + - + +
436K GLY 4.4 4.3 - - - +
437K ASN* 5.7 1.4 - - - +
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Residues in contact with ALA 434 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430K GLU 3.5 10.3 + - - +
433K LYS* 1.3 82.1 - - + +
435K ILE* 1.3 70.2 + - + +
436K GLY* 3.4 4.9 - - - -
437K ASN* 4.4 5.0 + - - +
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Residues in contact with ILE 435 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244K ASN* 4.0 19.5 - - + +
246K ASP* 3.7 25.7 - - - +
400K GLU* 3.6 31.9 - - + +
402K PRO* 5.7 4.0 - - + -
431K LYS* 2.8 59.8 + - + +
434K ALA* 1.3 74.0 - - + +
436K GLY* 1.3 57.4 + - - +
437K ASN 3.7 2.4 + - - -
438K GLU* 5.1 0.2 - - - +
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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