Contacts of the helix formed by residues 445 - 463 (chain A) in PDB entry 6KW5
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 445 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A LEU* 3.8 19.2 - - + +
429A LEU* 3.3 39.0 - - + +
430A ARG 4.4 0.2 + - - -
433A ARG* 2.6 40.5 + - - -
441A PRO* 3.5 11.9 - - + +
442A THR* 3.3 20.2 + - - +
444A GLU* 1.3 78.4 - - - +
446A ARG* 1.3 57.3 + - - +
447A GLU 3.3 1.1 - - - -
448A LEU* 2.9 7.7 + - - -
449A TYR* 2.4 37.1 + - - +
235D TYR* 3.8 19.5 + - + -
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Residues in contact with ARG 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A PRO* 5.9 3.1 - - - -
440A LYS* 5.9 1.4 - - - +
441A PRO* 4.0 29.8 + - + +
442A THR 3.5 14.2 + - - +
443A THR* 4.6 12.9 - - - +
445A GLU* 1.3 81.5 - - + +
447A GLU* 1.3 57.4 + - - +
449A TYR* 2.9 22.4 + - - +
450A PHE* 3.1 37.1 - - + -
234D VAL 4.6 3.2 + - - -
235D TYR* 3.0 37.1 + - + +
50J ARG* 3.1 49.5 + - - +
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Residues in contact with GLU 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A PRO 6.0 1.1 - - - -
401A TYR* 6.2 1.5 - - - -
402A ILE* 3.3 44.3 - - + +
443A THR 3.3 24.0 + - - +
444A GLU* 4.3 9.2 - - - +
446A ARG* 1.3 79.1 - - - +
448A LEU* 1.3 58.8 + - - +
449A TYR 3.7 0.3 + - - -
450A PHE* 4.3 6.2 + - - +
451A LYS* 3.8 17.0 + - - +
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Residues in contact with LEU 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A SER* 3.3 30.2 + - - +
425A LYS* 4.0 31.0 - - + +
426A LEU* 3.7 30.5 - - + +
429A LEU* 5.3 4.5 - - + -
444A GLU 3.3 19.7 + - - +
445A GLU* 2.9 9.5 + - + +
447A GLU* 1.3 76.6 - - - +
449A TYR* 1.3 62.4 + - - +
450A PHE 3.7 0.2 - - - -
451A LYS* 4.0 13.6 - - + +
452A VAL* 3.3 21.7 + - - +
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Residues in contact with TYR 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A LEU* 4.8 13.5 - - + -
445A GLU 2.4 24.3 + - - +
446A ARG* 2.9 9.1 + - - +
448A LEU* 1.3 69.5 - - - +
450A PHE* 1.3 89.4 + + - +
452A VAL* 2.9 29.5 + - + +
453A LYS* 3.2 30.2 + - + +
233D ASN* 4.8 5.4 + - - -
235D TYR* 3.6 42.8 - + + -
236D ASP* 5.1 6.5 - - + -
122J LEU* 4.3 17.6 - - + +
125J LEU* 5.6 1.6 - - + -
126J GLU* 2.5 47.7 + - + -
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Residues in contact with PHE 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A PRO* 4.1 35.0 - - + +
399A SER* 3.7 33.7 - - - -
446A ARG* 3.1 44.7 + - + +
447A GLU* 4.8 5.4 - - - +
449A TYR* 1.3 95.2 - + - +
451A LYS* 1.3 52.6 + - - +
453A LYS* 2.9 13.7 + - + +
454A ARG* 2.7 40.4 + - - +
235D TYR 4.7 0.4 - - - -
236D ASP* 3.6 45.8 - - + -
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Residues in contact with LYS 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A ILE* 5.8 10.3 - - + +
404A ASP 5.3 4.8 + - - +
406A GLU* 3.3 26.2 + - - +
407A ILE* 4.6 9.2 - - + -
418A LEU* 3.7 36.3 - - + +
422A SER* 4.9 10.3 - - - +
447A GLU 3.8 17.9 + - - +
448A LEU* 4.0 14.1 - - + +
450A PHE* 1.3 77.6 - - - +
452A VAL* 1.3 60.4 + - + +
454A ARG* 3.4 28.3 + - - +
455A ILE* 3.3 28.3 + - + +
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Residues in contact with VAL 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A VAL* 4.3 25.4 - - + +
422A SER* 3.3 32.3 - - - +
423A LEU* 4.3 12.6 - - + -
426A LEU* 4.5 13.5 - - + -
448A LEU 3.3 12.3 - - - +
449A TYR* 2.9 9.3 + - + +
451A LYS* 1.3 77.8 - - + +
453A LYS* 1.3 59.5 + - - +
454A ARG 3.2 0.2 - - - -
455A ILE* 3.0 25.1 + - - +
456A LEU* 3.3 13.5 + - + +
122J LEU* 3.7 23.3 - - + -
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Residues in contact with LYS 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A TYR* 3.2 35.4 + - + +
450A PHE* 2.9 16.8 + - + +
452A VAL* 1.3 78.1 - - - +
454A ARG* 1.3 61.3 + - - +
456A LEU* 4.1 2.9 - - - +
457A LYS* 3.2 21.4 + - - +
236D ASP* 5.4 1.4 + - - -
239D GLN* 4.3 18.0 - - - +
352D GLU* 3.6 45.1 + - - +
355D LEU* 3.6 32.0 - - + +
356D SER* 4.1 15.6 - - - -
122J LEU* 4.5 16.6 - - + -
126J GLU* 4.9 0.7 - - - +
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Residues in contact with ARG 454 (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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399A SER* 2.4 40.3 + - - +
402A ILE* 3.7 11.1 - - - +
403A GLY 3.5 19.6 + - - -
404A ASP* 3.3 19.8 + - - +
407A ILE* 3.4 29.5 - - + +
450A PHE* 2.7 18.6 + - - +
451A LYS* 3.4 35.1 - - - +
453A LYS* 1.3 72.6 - - - +
455A ILE* 1.3 58.1 + - - +
457A LYS* 3.0 28.5 + - - +
458A GLU* 3.0 31.6 + - + +
352D GLU* 5.2 2.0 - - - -
93J TYR* 3.6 19.4 + - - +
100J LEU* 6.3 2.0 - - - -
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Residues in contact with ILE 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ILE* 4.1 30.5 - - + -
410A PHE* 6.0 1.1 - - + -
411A ARG* 3.9 20.9 - - - +
415A PRO* 4.1 11.7 - - + +
418A LEU* 4.0 30.5 - - + -
419A VAL* 3.9 26.9 - - + +
451A LYS* 3.3 23.1 - - + +
452A VAL* 3.0 9.4 + - - +
454A ARG* 1.3 76.6 - - - +
456A LEU* 1.3 59.2 + - + +
458A GLU* 3.0 18.8 + - - +
459A VAL* 3.3 17.5 + - + +
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Residues in contact with LEU 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A VAL* 4.7 15.5 - - + -
423A LEU* 6.3 0.4 - - + -
452A VAL* 3.3 15.7 + - + +
453A LYS 4.3 4.3 - - - +
455A ILE* 1.3 76.8 - - + +
457A LYS* 1.3 60.0 + - - +
459A VAL* 4.3 7.3 + - + +
460A ILE* 3.3 30.3 + - + +
355D LEU* 4.5 13.5 - - + -
110J TYR* 4.4 20.6 - - + +
115J LEU* 5.6 7.6 - - + -
118J HIS* 4.6 26.9 - - + +
119J LEU* 4.6 16.6 - - + -
122J LEU* 3.8 29.8 - - + -
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Residues in contact with LYS 457 (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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453A LYS 3.2 15.0 + - - +
454A ARG* 3.0 20.0 + - - +
456A LEU* 1.3 76.7 - - - +
458A GLU* 1.3 79.0 + - - +
460A ILE* 3.0 9.5 + - - +
461A LEU* 2.8 31.9 + - + +
348D GLU* 2.7 47.3 + - + +
351D ILE* 3.8 18.3 - - + +
352D GLU* 3.1 34.3 + - + +
355D LEU* 4.1 10.5 - - + +
93J TYR* 4.6 10.3 + - - -
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Residues in contact with GLU 458 (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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407A ILE* 6.1 0.4 - - + -
411A ARG* 3.6 23.6 - - - +
454A ARG* 3.0 26.3 + - + +
455A ILE* 3.0 3.7 + - - +
457A LYS* 1.3 97.0 + - - +
459A VAL* 1.3 52.1 + - - +
461A LEU* 2.9 24.8 + - - +
462A ALA* 2.6 38.1 + - - +
93J TYR* 5.0 0.3 + - - -
97J LEU* 4.5 14.8 - - - +
100J LEU* 4.0 25.1 - - + +
101J ARG* 3.9 17.1 + - - +
104J ILE* 5.3 4.8 - - + +
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Residues in contact with VAL 459 (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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411A ARG* 3.6 23.6 - - - +
415A PRO* 4.5 15.7 - - + -
455A ILE* 3.3 13.7 + - + +
456A LEU* 4.6 7.4 - - + +
457A LYS 3.3 0.6 - - - -
458A GLU* 1.3 74.4 - - - +
460A ILE* 1.3 60.4 + - + +
462A ALA* 3.0 4.8 + - - +
463A LYS* 2.5 48.8 + - + +
464A LYS 3.5 2.6 + - - -
465A VAL* 3.7 26.7 - - + -
110J TYR* 4.6 18.4 - - + -
115J LEU* 5.8 1.6 - - + -
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Residues in contact with ILE 460 (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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456A LEU* 3.3 20.2 - - + +
457A LYS 3.0 10.1 + - - +
459A VAL* 1.3 77.3 - - + +
461A LEU* 1.3 60.3 + - - +
464A LYS* 4.4 19.3 + - - +
465A VAL* 5.7 3.1 - - + +
468A VAL* 4.2 27.8 - - + -
334D TRP* 3.6 37.3 - - + +
351D ILE* 3.8 28.1 - - + +
354D PHE* 5.6 5.2 - - + -
355D LEU* 4.4 18.2 - - + -
115J LEU* 5.9 8.1 - - + -
119J LEU* 5.7 4.0 - - + -
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Residues in contact with LEU 461 (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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457A LYS* 2.8 29.8 + - + +
458A GLU* 2.9 42.4 + - - +
460A ILE* 1.3 78.2 - - - +
462A ALA* 1.3 57.9 + - + +
464A LYS* 3.9 14.0 + - - -
347D VAL* 5.2 4.7 - - + -
348D GLU* 4.4 18.4 - - + +
351D ILE* 3.7 21.1 - - + -
101J ARG* 3.5 27.1 - - - +
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Residues in contact with ALA 462 (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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458A GLU 2.6 19.8 + - - +
459A VAL* 3.0 4.1 + - - +
461A LEU* 1.3 77.6 - - - +
463A LYS* 1.3 68.1 + - + +
464A LYS* 3.4 11.3 + - - +
104J ILE* 3.7 39.7 - - + -
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Residues in contact with LYS 463 (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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415A PRO* 6.4 1.8 - - + -
459A VAL* 2.5 40.6 + - + +
462A ALA* 1.3 80.6 - - + +
464A LYS* 1.3 67.8 + - - +
465A VAL* 4.1 8.7 - - + -
104J ILE* 4.7 10.5 - - + -
105J ASP 4.1 9.8 + - - +
106J LYS 3.5 11.7 + - - -
107J GLY* 3.4 13.5 - - - -
108J PHE* 3.1 39.3 - - + +
109J GLN* 4.1 20.9 + - - +
110J TYR* 5.3 4.3 - - + +
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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
------------------------------------------------------------
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