Contacts of the helix formed by residues 405 - 424 (chain A) in PDB entry 4KM5
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 405 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A CYS* 1.3 73.2 - - - +
406A ARG* 1.3 62.6 + - - +
407A LYS 3.5 1.8 - - - +
408A ASP* 3.9 4.3 - - + -
409A CYS* 3.1 26.6 + - - -
455A TRP* 2.9 24.2 + - - -
456A ASP 3.4 16.6 - - - +
457A ARG* 3.8 17.7 - - - +
460A LEU* 3.7 28.5 - - + -
463A CYS* 3.7 30.7 - - - -
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Residues in contact with ARG 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A TRP* 4.0 10.9 - - - +
390A HIS* 3.7 38.4 + - + -
391A GLY* 3.5 11.7 - - - -
396A CYS* 3.8 1.0 - - - -
404A CYS* 3.5 30.4 - - - +
405A CYS* 1.3 75.1 - - - +
407A LYS* 1.3 67.3 + - + +
409A CYS 3.2 1.9 + - - -
410A LEU 3.2 10.7 + - - -
442A PHE* 3.1 29.4 - - + -
446A CYS* 4.4 11.0 - - - +
449A ASN 4.3 0.6 + - - -
450A PRO 3.3 19.8 + - - -
451A GLN 3.5 2.8 + - - -
452A ASP* 2.7 33.3 + - - +
455A TRP* 3.4 51.6 - - + +
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Residues in contact with LYS 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A LEU* 3.3 39.0 - - + +
388A ASN* 3.7 18.3 + - - +
390A HIS* 4.1 21.1 - - + +
404A CYS* 5.2 1.0 + - - -
405A CYS 3.5 0.2 - - - -
406A ARG* 1.3 78.8 - - + +
408A ASP* 1.3 60.6 + - - +
410A LEU* 3.2 11.5 + - + +
411A LYS* 3.0 52.2 + - - +
442A PHE* 5.1 0.4 - - - -
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Residues in contact with ASP 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ARG* 3.7 6.7 + - - -
169A LEU* 3.6 29.1 - - + +
405A CYS* 3.6 8.9 + - - +
406A ARG 3.2 0.4 - - - -
407A LYS* 1.3 81.9 - - - +
409A CYS* 1.3 56.1 + - - +
411A LYS* 3.2 13.1 + - - +
412A LEU* 2.9 36.2 + - - +
457A ARG* 2.3 41.1 + - - +
460A LEU* 4.0 15.3 - - + -
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Residues in contact with CYS 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A CYS 3.1 24.9 + - - +
406A ARG 3.2 4.9 + - - +
408A ASP* 1.3 75.8 - - - +
410A LEU* 1.3 57.1 + - - +
412A LEU* 4.0 5.6 - - - +
413A MET* 3.1 36.2 + - - +
442A PHE* 4.2 2.9 - - + -
455A TRP* 3.9 8.1 - - + -
460A LEU* 4.1 13.0 - - - -
463A CYS* 3.7 18.4 - - - -
464A PHE* 3.7 31.8 - - - -
467A CYS* 3.9 17.0 - - - -
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Residues in contact with LEU 410 (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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387A LEU* 3.8 39.0 - - + -
406A ARG 3.2 11.9 + - - +
407A LYS* 3.5 11.4 - - + +
408A ASP 3.2 0.2 - - - -
409A CYS* 1.3 76.6 - - - +
411A LYS* 1.3 61.1 + - + +
413A MET* 3.5 2.2 + - - +
414A LYS* 3.0 56.5 + - + +
438A VAL* 4.3 4.7 - - + -
439A LYS* 4.0 24.5 - - + -
442A PHE* 3.8 37.2 - - + -
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Residues in contact with LYS 411 (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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169A LEU* 4.3 18.8 - - + -
172A LEU* 5.1 7.6 - - + -
176A ARG* 3.4 37.3 - - - +
220A ILE* 4.5 15.2 - - + +
407A LYS* 3.0 41.8 + - - +
408A ASP* 3.2 14.9 + - - +
410A LEU* 1.3 78.8 - - + +
412A LEU* 1.3 54.0 + - - +
414A LYS* 3.2 9.7 + - + +
415A TYR* 2.7 38.4 + - - +
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Residues in contact with LEU 412 (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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165A LEU* 4.0 37.7 - - + +
168A VAL* 3.8 32.3 - - + -
169A LEU* 3.8 26.0 - - + -
172A LEU* 5.1 1.3 - - + -
408A ASP 2.9 21.2 + - - +
409A CYS 4.0 0.2 - - - +
411A LYS* 1.3 75.6 - - - +
413A MET* 1.3 58.3 + - - +
415A TYR* 4.4 2.7 - - - -
416A LEU* 2.9 23.6 + - - +
460A LEU* 4.4 10.8 - - + -
464A PHE* 3.5 25.6 - - + -
519A PHE* 3.2 22.4 - - + -
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Residues in contact with MET 413 (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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409A CYS 3.1 21.3 + - - +
410A LEU* 3.8 3.4 - - + +
412A LEU* 1.3 75.2 - - - +
414A LYS* 1.3 62.8 + - - +
416A LEU* 3.5 13.1 + - + +
417A LEU* 3.3 16.3 + - - +
438A VAL* 3.5 34.5 - - + +
441A ALA* 5.9 1.3 - - + -
442A PHE* 5.9 3.4 - - + -
464A PHE* 3.6 20.9 - - + -
467A CYS* 3.8 29.4 - - + +
468A VAL* 3.7 24.5 - - - -
471A PHE* 3.9 29.4 - - + -
508A ILE* 6.3 0.9 - - + -
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Residues in contact with LYS 414 (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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216A GLU* 5.3 5.5 + - - -
217A HIS 3.8 16.2 + - - -
218A VAL* 4.2 14.0 - - - +
220A ILE* 3.9 21.3 - - + +
410A LEU* 3.0 44.6 + - + +
411A LYS* 3.7 7.3 - - + +
413A MET* 1.3 73.0 - - - +
415A TYR* 1.3 64.8 + - - +
417A LEU* 3.4 4.3 + - - +
418A GLU* 3.1 34.7 + - - +
435A SER* 4.3 24.3 - - - +
438A VAL* 3.8 20.9 - - + -
439A LYS* 5.6 4.4 - - + +
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Residues in contact with TYR 415 (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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168A VAL* 3.9 23.3 - - + -
171A LYS* 3.7 18.4 + - - -
172A LEU* 4.3 16.3 - - + +
220A ILE* 3.5 27.1 - - + +
221A SER* 4.1 11.9 - - - -
411A LYS 2.7 21.3 + - - +
412A LEU* 3.9 5.2 - - + +
414A LYS* 1.3 71.1 - - - +
416A LEU* 1.3 64.7 + - - +
418A GLU* 4.1 11.4 - - - -
419A GLN* 3.1 68.2 + - + +
519A PHE* 3.5 41.2 + + - -
522A PHE* 4.7 9.9 - - - -
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Residues in contact with LEU 416 (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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412A LEU 2.9 19.2 + - - +
413A MET* 3.6 20.0 - - + +
415A TYR* 1.3 77.3 - - - +
417A LEU* 1.3 63.5 + - - +
419A GLN* 3.8 1.6 - - - +
420A LEU* 3.1 52.4 + - + +
464A PHE* 4.5 15.9 - - + -
468A VAL* 4.7 4.0 - - + -
508A ILE* 4.7 22.0 - - + -
511A GLU* 4.3 12.3 - - + -
516A PHE* 4.4 15.7 - - + -
518A VAL* 3.9 15.5 - - + -
519A PHE* 3.6 15.9 - - + -
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Residues in contact with LEU 417 (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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413A MET 3.3 10.0 + - - +
414A LYS 3.8 7.0 - - - +
415A TYR 3.4 0.2 - - - -
416A LEU* 1.3 80.3 - - - +
418A GLU* 1.3 58.9 + - + +
420A LEU* 3.2 7.9 + - + +
421A LYS* 2.8 48.6 + - + +
430A LEU* 5.1 0.9 - - + +
433A PHE* 4.1 21.1 - - + +
434A SER* 3.2 43.3 - - - +
435A SER* 4.0 3.6 - - - +
437A HIS* 5.6 0.7 - - + -
438A VAL* 3.8 17.7 - - + -
471A PHE* 5.7 4.5 - - + -
504A LEU* 4.5 23.6 - - + -
508A ILE* 6.2 0.7 - - + -
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Residues in contact with GLU 418 (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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218A VAL 3.1 17.0 - - - +
219A LYS* 3.9 21.1 - - + +
220A ILE* 3.1 32.3 + - - +
221A SER* 3.0 37.1 + - - -
414A LYS* 3.1 21.8 + - - +
415A TYR* 3.9 4.6 - - - +
416A LEU 3.3 0.2 - - - -
417A LEU* 1.3 79.6 - - + +
419A GLN* 1.3 59.6 + - - +
421A LYS* 3.2 11.1 + - + +
422A GLU* 2.9 31.1 + - - +
435A SER* 5.2 3.6 - - - -
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Residues in contact with GLN 419 (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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221A SER* 4.2 13.3 + - - -
415A TYR* 3.1 64.5 + - + +
416A LEU 3.8 3.8 - - - +
417A LEU 3.3 0.2 - - - -
418A GLU* 1.3 77.5 - - - +
420A LEU* 1.3 58.8 + - - +
422A GLU* 3.7 12.3 + - - +
423A ARG* 3.1 27.0 + - - +
518A VAL* 3.4 43.2 - - + +
519A PHE* 5.0 0.4 - - + +
522A PHE* 4.6 16.0 - - - -
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Residues in contact with LEU 420 (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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416A LEU* 3.1 46.0 + - + +
417A LEU* 3.5 9.2 - - + +
418A GLU 3.2 0.2 - - - -
419A GLN* 1.3 76.9 - - - +
421A LYS* 1.3 63.4 + - - +
423A ARG* 3.2 5.7 + - + -
424A PHE* 3.1 36.8 + - + -
430A LEU* 3.4 13.3 - - + +
504A LEU* 4.0 15.0 - - + -
507A GLN* 4.3 19.5 - - + -
508A ILE* 4.0 28.5 - - + +
511A GLU* 4.4 10.5 - - + +
518A VAL* 4.0 18.6 - - + -
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Residues in contact with LYS 421 (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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219A LYS* 5.3 10.6 - - - +
417A LEU* 2.8 37.1 + - + +
418A GLU* 3.2 9.6 + - + +
420A LEU* 1.3 72.3 - - - +
422A GLU* 1.3 60.2 + - - +
424A PHE 3.5 1.2 - - - -
425A LYS* 3.1 31.5 + - - +
430A LEU* 3.3 42.0 - - + +
431A ASP* 4.1 16.5 + - - +
433A PHE 3.3 18.1 + - - +
434A SER* 4.6 6.3 - - - +
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Residues in contact with GLU 422 (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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219A LYS* 6.0 1.6 - - - -
418A GLU 2.9 16.8 + - - +
419A GLN* 3.9 16.2 - - - +
421A LYS* 1.3 76.5 - - - +
423A ARG* 1.3 62.1 + - - +
425A LYS* 2.9 54.9 + - - +
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Residues in contact with ARG 423 (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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419A GLN 3.1 18.0 + - - +
420A LEU* 3.6 8.1 - - - +
421A LYS 3.2 0.4 - - - -
422A GLU* 1.3 79.5 - - - +
424A PHE* 1.3 84.7 + - + +
425A LYS* 3.5 1.5 + - - +
426A ASP* 4.8 5.4 - - - +
511A GLU* 5.8 2.6 + - - -
518A VAL* 4.7 16.6 - - - -
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Residues in contact with PHE 424 (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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420A LEU* 3.1 32.1 + - + +
421A LYS* 3.4 4.9 + - - -
423A ARG* 1.3 107.8 - - + +
425A LYS* 1.3 60.3 + - - +
426A ASP* 3.2 13.5 + - - +
427A LYS* 3.4 9.5 + - + +
428A LYS* 3.4 16.8 + - - -
429A HIS 4.6 2.4 + - - +
430A LEU* 3.9 21.3 + - + +
503A PHE* 3.5 29.2 - + + -
507A GLN* 3.2 38.6 - - + -
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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