Contacts of the helix formed by residues 416 - 434 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321P ARG* 3.3 30.4 + - - +
324P LYS* 3.3 28.7 + - - +
325P LEU* 3.5 21.4 - - - +
328P ARG* 3.2 49.1 + - - +
415P THR* 1.4 76.9 - - - +
417P GLU* 1.4 69.8 + - - +
420P ASP* 3.7 6.8 + - - +
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Residues in contact with GLU 417 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H ARG* 3.4 9.1 + - - -
78I LEU* 3.3 25.4 - - + +
321P ARG* 4.5 2.6 + - - -
415P THR* 3.3 20.6 - - - +
416P GLU* 1.4 87.2 - - - +
418P GLU* 1.4 63.3 + - - +
420P ASP* 3.4 7.0 + - - +
421P TYR* 3.2 43.7 + - + +
86i VAL* 6.3 0.2 - - + -
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Residues in contact with GLU 418 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78I LEU* 4.4 4.8 - - + +
79I ARG* 3.4 14.0 + - - -
410P ILE* 6.0 2.3 - - - +
413P PHE* 3.0 30.8 - - - +
414P THR* 3.9 5.9 + - + +
415P THR* 3.2 20.7 + - - +
417P GLU* 1.4 77.5 - - - +
419P VAL* 1.3 61.3 + - - +
421P TYR* 3.2 12.0 + - + +
422P THR* 3.0 31.7 + - - +
84i LYS* 4.1 2.3 + - - -
86i VAL* 4.1 25.2 - - + +
87i ASP* 5.7 1.6 - - + +
110i LYS* 3.2 33.6 + - - +
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Residues in contact with VAL 419 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325P LEU* 3.8 27.4 - - + +
328P ARG* 3.6 37.9 - - + +
329P LEU* 3.9 24.0 - - + -
414P THR* 3.5 26.5 - - + -
415P THR 3.1 16.9 + - - +
416P GLU 4.1 0.2 - - - +
417P GLU 3.4 0.2 - - - -
418P GLU* 1.3 72.9 - - - +
420P ASP* 1.3 61.6 + - - +
422P THR* 3.2 9.8 + - - -
423P VAL* 3.2 24.3 + - + +
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Residues in contact with ASP 420 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328P ARG* 3.1 28.6 + - - +
416P GLU 3.7 7.4 + - - +
417P GLU* 3.4 12.1 + - - +
418P GLU 3.3 0.2 - - - -
419P VAL* 1.3 77.2 - - - +
421P TYR* 1.3 57.8 + - + +
423P VAL* 3.5 7.4 + - - +
424P GLU* 3.1 36.6 + - - +
51i SER* 3.7 24.1 + - - -
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Residues in contact with TYR 421 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76I MET* 5.6 3.5 - - - +
417P GLU* 3.2 32.0 - - + +
418P GLU* 3.2 8.9 + - + +
420P ASP* 1.3 75.8 - - + +
422P THR* 1.3 59.7 + - - +
424P GLU 3.3 0.5 + - - -
425P LYS 3.0 24.4 + - - -
50i GLY* 3.3 4.6 - - - -
51i SER* 3.1 51.8 + - - +
52i LEU 4.8 2.6 - - - -
53i ASP* 4.7 10.2 - - + +
55i THR* 4.6 13.5 + - - +
78i GLN* 4.3 14.5 + - + -
86i VAL* 3.8 33.0 - - + +
87i ASP* 3.2 38.1 - - + +
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Residues in contact with THR 422 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329P LEU* 4.0 23.1 - - + +
333P ILE* 4.0 19.5 - - + -
408P PHE* 4.0 19.5 - - + -
410P ILE* 4.7 4.6 - - + +
418P GLU* 3.0 21.8 + - - +
419P VAL 3.2 7.5 + - - -
421P TYR* 1.3 75.6 - - - +
423P VAL* 1.4 62.9 + - - +
425P LYS* 3.5 37.9 + - - +
426P CYS* 3.7 11.1 + - - -
87i ASP* 4.2 2.3 + - - -
110i LYS* 6.1 0.9 - - - -
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Residues in contact with VAL 423 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328P ARG* 5.5 0.4 - - - +
329P LEU* 4.4 10.3 - - - +
332P ASN* 3.6 50.3 - - + +
333P ILE* 4.3 11.8 - - + +
336P SER* 5.7 2.2 - - - -
419P VAL* 3.2 21.0 + - + +
420P ASP* 3.7 10.3 - - - +
421P TYR 3.3 0.2 - - - -
422P THR* 1.4 75.5 - - - +
424P GLU* 1.4 67.5 + - - +
426P CYS* 3.5 12.1 + - - +
427P ILE* 3.6 20.8 + - + +
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Residues in contact with GLU 424 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420P ASP* 3.1 27.7 + - - +
421P TYR 3.3 5.4 + - - +
423P VAL* 1.4 79.6 - - + +
425P LYS* 1.3 63.7 - - - +
427P ILE* 3.2 34.1 + - - +
428P GLN* 3.1 40.6 + - + +
50i GLY* 3.7 3.4 - - - -
51i SER* 3.6 35.5 + - - +
89i ARG* 5.5 0.9 + - - -
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Residues in contact with LYS 425 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372P ASP* 3.3 44.2 - - + +
408P PHE* 5.1 3.9 - - - -
421P TYR 3.0 5.8 + - - -
422P THR* 3.5 30.9 + - - +
424P GLU* 1.3 76.7 - - - +
426P CYS* 1.4 61.4 + - - +
428P GLN* 3.4 2.1 + - - +
429P HIS* 2.9 48.1 + - + +
50i GLY* 4.0 2.8 - - - -
87i ASP* 3.0 34.0 + - - +
88i ALA* 3.3 32.5 - - + +
89i ARG* 4.6 4.5 - - - -
90i PHE* 4.6 6.1 - - + -
106i THR* 6.3 0.9 - - + -
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Residues in contact with CYS 426 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333P ILE* 3.8 35.2 - - + -
336P SER* 6.2 0.7 - - - -
337P LEU* 4.2 24.8 - - + +
368P MET* 5.2 0.5 - - - +
372P ASP* 4.2 24.7 - - - -
408P PHE* 5.4 0.2 - - - -
422P THR 3.7 13.7 + - - -
423P VAL 3.5 7.5 + - - +
424P GLU 3.3 0.6 - - - -
425P LYS* 1.4 79.5 - - - +
427P ILE* 1.4 63.8 + - + +
429P HIS* 3.3 24.9 + - - +
430P VAL* 3.4 12.8 + - - +
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Residues in contact with ILE 427 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336P SER* 3.4 28.3 - - - +
337P LEU* 5.6 1.1 - - + -
423P VAL* 3.6 15.2 + - + +
424P GLU* 3.2 49.7 + - - +
426P CYS* 1.4 75.9 - - + +
428P GLN* 1.4 70.1 + - - +
430P VAL* 3.3 20.9 + - + +
431P LYS* 3.4 17.3 + - + +
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Residues in contact with GLN 428 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424P GLU* 3.1 34.0 + - + +
425P LYS 3.7 7.6 - - - +
426P CYS 3.3 0.2 - - - -
427P ILE* 1.4 78.6 - - - +
429P HIS* 1.3 63.3 + - - +
431P LYS* 3.2 42.3 + - - +
432P ARG* 3.4 25.9 + - + +
50i GLY* 5.3 0.4 - - - +
89i ARG* 3.3 61.6 + - + +
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Residues in contact with HIS 429 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368P MET* 3.6 35.1 + - + +
372P ASP* 3.6 21.1 + - + +
425P LYS* 2.9 28.7 + - + +
426P CYS* 3.4 11.6 + - - +
427P ILE 3.2 0.4 - - - -
428P GLN* 1.3 75.1 - - - +
430P VAL* 1.4 57.7 + - - +
432P ARG* 3.3 3.1 + - - -
433P LEU* 3.0 23.0 + - - +
89i ARG* 3.6 7.7 - - + -
90i PHE* 3.0 68.1 + + - -
91i LYS* 3.0 18.7 + - - +
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Residues in contact with VAL 430 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336P SER 5.5 2.7 - - - +
337P LEU* 3.7 22.9 - - + -
338P PRO* 6.1 4.5 - - + -
368P MET* 4.4 11.0 - - + -
426P CYS 3.5 15.5 - - - +
427P ILE* 3.3 14.1 + - + +
429P HIS* 1.4 75.3 - - - +
431P LYS* 1.4 61.3 + - + +
433P LEU* 3.2 22.5 + - + +
434P ARG* 3.3 16.4 + - + +
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Residues in contact with LYS 431 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427P ILE* 3.4 11.9 + - + +
428P GLN* 3.2 49.2 + - - +
429P HIS 3.4 0.6 - - - -
430P VAL* 1.4 75.5 - - + +
432P ARG* 1.3 66.0 + - + +
434P ARG* 3.1 49.0 + - - +
435P GLU* 3.4 17.4 - - - +
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Residues in contact with ARG 432 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60I ARG* 6.3 1.2 - - - +
428P GLN* 3.4 15.7 + - + +
429P HIS* 3.3 9.4 + - - +
430P VAL 3.3 0.2 - - - -
431P LYS* 1.3 83.4 - - - +
433P LEU* 1.4 55.1 + - - +
435P GLU* 3.1 36.4 + - - +
436P MET* 3.2 11.3 + - - -
439P LEU* 3.4 43.5 - - + +
63i LEU* 5.7 3.0 - - - +
74i LYS* 3.6 38.6 - - - +
76i GLN* 4.9 11.0 - - - +
90i PHE 5.1 3.1 - - - +
91i LYS* 3.7 33.8 - - + +
93i PHE* 6.0 0.2 - - - -
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Residues in contact with LEU 433 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361P VAL* 5.6 5.6 - - + -
364P GLU* 3.5 38.8 - - + +
365P SER* 4.3 10.3 - - - +
368P MET* 4.1 22.7 - - + -
429P HIS 3.0 13.7 + - - +
430P VAL* 3.2 17.4 + - + +
432P ARG* 1.4 72.3 - - - +
434P ARG* 1.4 63.8 + - - +
436P MET* 3.2 23.3 - - + +
91i LYS* 3.6 19.0 - - + +
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Residues in contact with ARG 434 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430P VAL* 3.3 9.9 + - + +
431P LYS* 3.1 46.7 + - - +
433P LEU* 1.4 78.4 - - - +
435P GLU* 1.4 86.1 + - - +
436P MET* 3.3 1.6 + - - +
437P SER* 3.2 14.6 + - - +
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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
------------------------------------------------------------
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