Contacts of the helix formed by residues 416 - 434 (chain N) in PDB entry 5KZ5
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 416 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321N ARG* 3.5 24.7 + - - +
324N LYS* 3.7 15.4 + - - -
325N LEU* 3.3 22.8 - - - +
328N ARG* 3.4 35.5 + - - -
415N THR* 1.4 72.7 - - - +
417N GLU* 1.3 72.3 + - - +
418N GLU 3.3 0.2 - - - -
419N VAL* 3.3 20.3 + - - +
420N ASP* 3.4 12.5 + - - +
52c LEU* 6.0 4.7 - - + +
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Residues in contact with GLU 417 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C TYR* 6.4 0.2 - - - -
76C MET* 3.8 19.5 - - + +
78C LEU* 3.9 11.4 - - - +
321N ARG* 4.7 2.1 + - - -
415N THR* 3.2 28.2 - - - +
416N GLU* 1.3 91.5 + - - +
418N GLU* 1.4 60.9 + - + +
420N ASP* 3.4 5.9 + - - +
421N TYR 3.3 15.6 + - - -
50c GLY* 3.9 10.1 - - - +
51c SER* 3.5 39.9 - - - +
52c LEU* 5.4 4.7 - - + -
86c VAL* 5.7 2.2 - - + -
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Residues in contact with GLU 418 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329N LEU* 5.2 3.8 - - + -
410N ILE* 3.7 16.0 - - + +
413N PHE* 3.1 29.6 - - - +
414N THR* 3.5 16.1 - - - +
415N THR* 3.3 12.8 + - - +
417N GLU* 1.4 74.3 - - - +
419N VAL* 1.4 59.3 + - + +
421N TYR* 3.2 5.6 - - - +
422N THR* 3.0 32.8 + - - +
425N LYS* 5.0 0.9 + - - +
50c GLY 3.8 7.2 - - - +
86c VAL* 3.1 37.3 - - + +
87c ASP* 3.2 24.4 - - + +
110c LYS* 4.2 3.6 + - - -
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Residues in contact with VAL 419 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325N LEU* 3.9 36.3 - - + +
328N ARG* 3.8 26.0 - - + +
329N LEU* 4.7 12.8 - - + +
332N ASN* 3.3 21.8 + - - +
414N THR* 6.0 1.3 - - + -
415N THR 3.6 15.5 - - - +
416N GLU* 3.3 17.2 + - - +
418N GLU* 1.4 76.6 - - + +
420N ASP* 1.4 58.7 + - - +
422N THR* 3.4 16.5 + - - -
423N VAL* 3.4 14.1 - - + +
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Residues in contact with ASP 420 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416N GLU 3.4 8.0 + - - +
417N GLU 3.5 9.4 - - - +
418N GLU 3.3 0.4 - - - -
419N VAL* 1.4 75.2 - - - +
421N TYR* 1.3 62.7 + - - +
423N VAL* 3.3 19.6 + - - +
424N GLU* 3.4 21.8 + - - +
51c SER* 3.2 9.3 + - - -
52c LEU* 3.2 54.3 + - + +
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Residues in contact with TYR 421 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417N GLU 3.3 11.1 + - - +
418N GLU* 3.2 11.9 - - - +
420N ASP* 1.3 76.8 - - - +
422N THR* 1.4 57.3 + - - +
424N GLU* 3.2 6.8 + - - +
425N LYS* 3.0 39.6 + - - +
50c GLY 3.4 24.0 - - - +
51c SER* 3.5 15.2 - - - -
77c ILE* 3.6 4.3 - - - -
78c GLN* 3.1 31.8 + - + +
87c ASP* 3.3 57.0 + - + -
88c ALA* 4.1 0.2 - - - -
89c ARG* 3.4 50.6 + - + +
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Residues in contact with THR 422 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329N LEU* 3.1 23.8 - - + +
332N ASN* 4.5 10.8 - - + -
333N ILE* 3.6 33.0 - - + -
371N LYS* 5.7 0.9 - - - +
418N GLU* 3.0 14.8 + - - +
419N VAL 3.5 10.5 - - - -
420N ASP 3.3 0.4 - - - -
421N TYR* 1.4 72.0 - - - +
423N VAL* 1.4 63.2 + - - +
425N LYS* 3.3 39.1 + - + +
426N CYS* 3.4 14.4 + - - -
90c PHE* 6.4 0.4 - - + -
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Residues in contact with VAL 423 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332N ASN* 3.5 25.1 - - + +
336N SER* 5.1 4.6 + - - +
419N VAL* 3.4 16.8 - - + +
420N ASP* 3.3 14.0 + - - +
422N THR* 1.4 75.9 - - - +
424N GLU* 1.4 68.9 + - - +
426N CYS* 3.7 13.4 + - - +
427N ILE* 3.8 17.4 + - + +
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Residues in contact with GLU 424 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420N ASP* 3.6 21.4 - - - +
421N TYR 3.2 8.3 + - - +
423N VAL* 1.4 83.6 - - - +
425N LYS* 1.4 62.4 + - - +
427N ILE* 3.1 36.5 - - - +
428N GLN* 3.4 14.5 + - + +
51c SER* 4.4 13.2 - - - +
89c ARG* 3.7 22.8 + - - +
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Residues in contact with LYS 425 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371N LYS* 3.9 9.9 - - - +
418N GLU 5.0 0.6 + - - -
421N TYR* 3.0 34.6 + - - +
422N THR* 3.3 32.1 + - + +
424N GLU* 1.4 73.8 - - - +
426N CYS* 1.3 62.1 + - - +
428N GLN* 3.3 5.5 + - - +
429N HIS* 2.9 35.3 + - + +
87c ASP* 3.0 33.4 + - - -
89c ARG* 3.9 30.2 - - + +
90c PHE* 3.3 41.1 - - + +
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Residues in contact with CYS 426 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332N ASN 4.5 6.5 - - - -
333N ILE* 4.6 6.7 - - - -
336N SER* 3.2 36.8 - - - +
337N LEU* 4.0 16.6 - - + +
371N LYS* 3.4 24.9 - - - +
422N THR* 3.4 18.6 + - - -
423N VAL* 3.9 9.2 - - - +
424N GLU 3.3 0.8 - - - -
425N LYS* 1.3 78.8 - - - +
427N ILE* 1.4 60.8 + - - +
429N HIS* 3.2 13.3 + - - +
430N VAL* 3.3 18.4 + - - +
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Residues in contact with ILE 427 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336N SER* 5.1 5.4 - - - +
423N VAL* 3.8 12.1 + - + +
424N GLU* 3.1 41.1 - - - +
426N CYS* 1.4 77.8 - - + +
428N GLN* 1.4 72.3 + - - +
429N HIS 3.6 0.2 + - - -
430N VAL* 3.6 10.0 + - + +
431N LYS* 3.6 22.5 + - - +
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Residues in contact with GLN 428 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ARG* 5.8 0.7 + - - -
424N GLU* 3.4 14.8 + - - +
425N LYS* 3.3 6.9 + - - +
426N CYS 3.3 0.6 - - - -
427N ILE* 1.4 91.3 - - - +
429N HIS* 1.4 64.0 + - + +
431N LYS* 3.2 50.4 + - - +
432N ARG* 3.3 18.8 + - + +
74c LYS* 5.0 1.4 + - - -
76c GLN* 3.2 30.8 + - + +
89c ARG* 3.4 20.1 - - - +
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Residues in contact with HIS 429 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337N LEU* 5.4 3.4 - - + -
368N MET* 3.7 24.4 + - + +
369N ALA* 5.2 2.0 - - - +
371N LYS* 3.6 40.9 - - + +
425N LYS* 2.9 32.3 + - + +
426N CYS 3.2 9.4 + - - +
428N GLN* 1.4 75.1 - - + +
430N VAL* 1.4 63.5 + - + +
432N ARG* 3.2 11.1 + - + +
433N LEU* 3.2 29.6 + - + +
89c ARG* 6.0 1.6 - - + -
90c PHE* 3.0 32.3 + + - -
91c LYS* 3.8 22.4 - - + +
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Residues in contact with VAL 430 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336N SER 5.5 7.4 - - - +
337N LEU* 5.5 6.1 - - + -
338N PRO* 6.1 4.0 - - + -
426N CYS 3.3 14.3 + - - +
427N ILE* 3.8 10.8 - - + +
428N GLN 3.4 0.2 - - - -
429N HIS* 1.4 75.3 - - + +
431N LYS* 1.4 61.5 + - + +
433N LEU* 3.3 13.2 + - + +
434N ARG* 3.3 29.6 + - + +
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Residues in contact with LYS 431 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427N ILE 3.6 11.9 + - - +
428N GLN* 3.2 49.0 + - - +
430N VAL* 1.4 76.0 - - + +
432N ARG* 1.3 62.0 + - - +
434N ARG* 3.3 42.1 - - - +
435N GLU* 3.2 30.0 + - - +
74c LYS* 5.3 6.7 - - - +
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Residues in contact with ARG 432 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368N MET* 3.6 24.6 - - + +
428N GLN* 3.3 16.0 + - + +
429N HIS* 3.2 13.1 + - - +
431N LYS* 1.3 77.1 - - - +
433N LEU* 1.4 61.9 + - - +
435N GLU* 3.4 24.8 + - - -
436N MET* 3.8 1.6 + - - -
439N LEU* 3.4 49.0 - - - +
63c LEU* 4.0 6.3 - - - +
72c VAL* 4.1 5.7 - - - +
73c MET* 3.6 27.9 + - - +
74c LYS* 3.4 45.2 - - - +
91c LYS* 4.0 22.1 - - + +
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Residues in contact with LEU 433 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365N SER* 3.9 26.0 - - - +
368N MET* 3.7 38.1 - - + -
369N ALA* 4.5 17.5 - - + +
429N HIS* 3.2 16.5 + - + +
430N VAL* 3.3 13.0 + - + +
432N ARG* 1.4 76.5 - - - +
434N ARG* 1.4 63.5 + - - +
435N GLU 3.5 0.3 + - - -
436N MET* 3.6 27.4 + - + +
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Residues in contact with ARG 434 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430N VAL* 3.3 16.3 + - + +
431N LYS* 3.3 44.1 - - - +
433N LEU* 1.4 76.8 - - - +
435N GLU* 1.4 85.8 + - - +
436N MET* 3.1 6.7 + - - +
437N SER 4.1 4.9 + - - +
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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
------------------------------------------------------------
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