Contacts of the helix formed by residues 480 - 500 (chain N) in PDB entry 1CZA
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 THR 480 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478N HIS* 4.2 20.4 + - + +
479N LEU* 1.3 77.1 - - - +
481N LYS* 1.3 64.7 + - - +
482N ASP* 3.4 9.1 + - - +
483N MET* 3.0 26.6 + - + +
484N LEU* 2.9 23.5 + - - +
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Residues in contact with LYS 481 (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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480N THR* 1.3 72.5 - - - +
482N ASP* 1.4 61.0 + - - +
484N LEU* 3.2 11.9 + - - +
485N LEU* 2.8 47.4 + - + +
881N GLU* 4.0 41.5 + - - +
882N LEU* 4.4 7.4 - - + -
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Residues in contact with ASP 482 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480N THR* 3.2 8.3 + - - +
481N LYS* 1.4 83.2 - - - +
483N MET* 1.3 63.5 + - - +
485N LEU* 3.4 17.8 + - - +
486N GLU* 3.1 21.5 + - - +
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Residues in contact with MET 483 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479N LEU* 3.8 24.9 - - + -
480N THR* 3.0 28.8 + - + +
482N ASP* 1.3 78.0 - - + +
484N LEU* 1.3 57.5 + - - +
486N GLU* 3.0 20.4 + - + +
487N VAL* 2.8 31.6 + - + +
490N ARG* 4.8 2.0 - - - +
720N ASP* 4.6 15.3 - - - +
721N ILE* 3.9 20.0 - - + -
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Residues in contact with LEU 484 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479N LEU* 3.7 36.6 - - + +
480N THR 2.9 20.4 + - - +
481N LYS* 3.6 8.1 - - - +
483N MET* 1.3 72.8 - - - +
485N LEU* 1.3 64.7 + - - +
487N VAL* 3.1 6.4 + - + +
488N LYS* 2.9 23.6 + - - +
832N GLN* 3.8 52.3 - - + +
833N LEU* 4.5 3.6 - - + +
836N ALA* 3.8 10.0 - - + +
878N THR* 4.4 11.0 - - + -
882N LEU* 3.8 19.0 - - + +
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Residues in contact with LEU 485 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481N LYS* 2.8 42.3 + - + +
482N ASP* 3.7 17.0 - - - +
484N LEU* 1.3 73.0 - - - +
486N GLU* 1.4 56.6 + - - +
488N LYS* 3.4 15.0 + - + +
489N LYS* 3.0 27.2 + - - +
881N GLU 5.4 1.1 - - - +
882N LEU* 3.7 39.0 - - + +
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Residues in contact with GLU 486 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482N ASP 3.1 12.2 + - - +
483N MET* 3.0 20.1 + - + +
485N LEU* 1.4 72.4 - - - +
487N VAL* 1.3 69.1 + - - +
489N LYS* 3.2 28.0 + - - +
490N ARG* 2.9 70.2 + - - +
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Residues in contact with VAL 487 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479N LEU* 5.7 0.7 - - + -
483N MET* 2.8 30.5 + - + +
484N LEU* 3.1 9.6 + - + +
486N GLU* 1.3 77.5 - - + +
488N LYS* 1.3 64.0 + - - +
490N ARG* 3.2 12.5 + - - +
491N MET* 2.9 22.6 + - + +
712N PHE* 3.8 21.9 - - + -
718N LEU* 4.5 8.3 - - + -
721N ILE* 4.3 22.9 - - + -
741N TYR* 4.8 4.9 - - + -
833N LEU* 4.2 18.4 - - + +
836N ALA* 3.8 20.4 - - + -
837N GLY 5.2 0.4 - - - +
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Residues in contact with LYS 488 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484N LEU 2.9 12.6 + - - +
485N LEU* 3.4 22.1 - - + +
487N VAL* 1.3 78.6 - - - +
489N LYS* 1.4 63.9 + - - +
491N MET* 3.3 0.7 + - - -
492N ARG* 3.1 21.1 + - + +
836N ALA* 3.5 20.6 - - + +
839N ALA* 3.7 16.4 - - + -
840N ALA* 3.5 21.2 - - - +
843N ASP* 2.6 32.1 + - - -
847N GLU* 6.0 0.2 - - - -
882N LEU* 2.7 29.3 + - + +
883N SER* 3.0 11.8 + - - -
884N PRO* 5.4 0.6 - - - +
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Residues in contact with LYS 489 (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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485N LEU 3.0 14.7 + - - +
486N GLU* 3.5 31.8 + - - +
488N LYS* 1.4 78.8 - - - +
490N ARG* 1.3 57.9 + - + +
492N ARG* 3.4 6.8 + - - +
493N ALA* 2.9 28.4 + - + +
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Residues in contact with ARG 490 (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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483N MET* 4.8 5.7 - - - +
486N GLU* 2.9 54.5 + - - +
487N VAL* 3.6 12.6 - - - +
489N LYS* 1.3 75.2 - - + +
491N MET* 1.3 66.2 + - - +
493N ALA* 3.2 7.4 + - - +
494N GLU* 2.9 27.1 + - + +
712N PHE* 3.8 14.6 - - + -
717N CYS* 2.8 42.7 + - + -
718N LEU* 4.2 10.3 - - - +
720N ASP* 2.8 41.2 + - - -
721N ILE* 5.5 0.4 - - - +
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Residues in contact with MET 491 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487N VAL 2.9 13.2 + - - +
488N LYS 3.3 8.3 + - - +
490N ARG* 1.3 75.7 - - - +
492N ARG* 1.4 51.6 + - - +
494N GLU* 3.0 4.3 + - - +
495N MET* 2.7 45.6 + - - +
509N VAL* 4.5 11.9 - - - -
707N MET* 4.1 17.3 - - + -
709N TRP* 3.8 20.2 - - + -
712N PHE* 3.4 45.9 - - + -
741N TYR* 3.5 26.7 - - + +
837N GLY* 4.1 13.7 - - - +
840N ALA* 3.8 17.5 - - + -
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Residues in contact with ARG 492 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488N LYS* 3.1 14.6 + - + +
489N LYS* 3.7 9.9 - - - +
491N MET* 1.4 76.3 - - - +
493N ALA* 1.4 62.7 + - - +
495N MET* 3.2 12.6 + - - +
496N GLU* 2.8 50.6 + - + +
840N ALA* 4.0 10.2 + - + +
843N ASP* 5.3 1.0 - - - +
844N LYS* 3.6 43.5 - - - +
847N GLU* 3.0 30.1 + - - +
848N ASN* 3.9 18.8 - - - +
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Residues in contact with ALA 493 (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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489N LYS* 2.9 16.1 + - + +
490N ARG* 3.6 10.1 - - - +
492N ARG* 1.4 78.3 - - - +
494N GLU* 1.3 63.7 + - + +
496N GLU* 3.2 10.5 + - - +
497N LEU* 3.1 29.8 + - + +
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Residues in contact with GLU 494 (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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490N ARG* 2.9 18.0 + - - +
491N MET 3.0 7.4 + - - +
493N ALA* 1.3 74.0 - - - +
495N MET* 1.3 67.5 + - - +
497N LEU* 3.2 25.9 + - - +
498N GLY* 3.0 20.6 + - - -
507N ALA* 5.0 0.3 - - - +
508N VAL* 3.8 20.7 + - - +
509N VAL* 3.7 28.0 + - + +
712N PHE* 3.8 22.0 - - + -
715N ASN* 3.0 26.4 + - - -
717N CYS* 3.9 9.9 - - - +
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Residues in contact with MET 495 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491N MET* 2.7 27.6 + - + +
492N ARG* 3.5 16.2 - - - +
494N GLU* 1.3 77.2 - - - +
496N GLU* 1.4 62.9 + - - +
498N GLY 3.4 0.3 + - - -
499N LEU* 3.2 28.8 + - - +
509N VAL* 4.9 0.9 - - + +
511N MET* 3.7 17.4 - - + +
686N TYR* 3.6 38.1 - - + -
707N MET* 3.7 28.9 - - + -
840N ALA* 4.4 2.0 - - - +
841N VAL* 4.0 29.6 - - + -
844N LYS* 3.7 23.8 - - + -
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Residues in contact with GLU 496 (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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492N ARG* 2.8 55.7 + - + +
493N ALA* 3.2 9.6 + - - +
495N MET* 1.4 77.6 - - - +
497N LEU* 1.3 63.7 + - + +
499N LEU* 3.3 1.9 + - - +
500N ARG* 2.4 79.7 + - - +
844N LYS* 3.6 17.7 + - - -
848N ASN* 5.5 0.2 + - - -
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Residues in contact with LEU 497 (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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493N ALA* 3.1 20.3 + - + +
494N GLU* 3.2 32.9 + - - +
496N GLU* 1.3 77.8 - - + +
498N GLY* 1.3 62.2 + - - +
500N ARG* 3.5 3.3 - - - +
503N THR* 2.6 59.3 + - + +
504N HIS 3.4 1.0 + - - -
507N ALA* 3.7 16.2 - - + -
715N ASN* 5.8 1.1 - - - +
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Residues in contact with GLY 498 (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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494N GLU 3.0 11.3 + - - -
496N GLU 3.4 0.2 - - - -
497N LEU* 1.3 79.1 - - - +
499N LEU* 1.3 57.9 + - - +
504N HIS* 2.8 30.1 - - - -
507N ALA* 3.6 10.4 - - - +
509N VAL 3.4 22.0 - - - -
510N LYS 3.7 2.3 - - - +
511N MET* 3.6 13.1 - - - +
695N MET* 4.6 2.3 - - - +
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Residues in contact with LEU 499 (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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495N MET 3.2 19.3 + - - +
496N GLU* 3.3 6.9 + - - +
498N GLY* 1.3 76.4 - - - +
500N ARG* 1.3 64.2 + - - +
501N LYS 3.8 0.2 + - - -
511N MET* 3.7 24.7 - - + +
686N TYR* 3.6 8.5 - - - +
688N GLU* 3.6 29.6 - - + +
692N ASN* 3.5 21.4 - - + +
693N VAL* 4.3 8.4 - - + -
694N GLU* 3.4 27.4 + - - +
695N MET* 3.9 6.4 + - - +
705N ILE* 4.1 25.8 - - + -
844N LYS* 3.9 14.8 - - - +
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Residues in contact with ARG 500 (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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496N GLU* 2.4 62.1 + - - +
497N LEU* 3.5 1.3 - - - +
498N GLY 3.4 0.4 - - - -
499N LEU* 1.3 86.3 - - - +
501N LYS* 1.3 56.5 + - - +
502N GLN* 4.5 3.8 - - + +
503N THR* 3.2 21.4 + - + +
504N HIS* 2.7 37.1 + - - +
692N ASN* 5.3 6.3 + - - +
694N GLU* 3.5 23.3 + - + +
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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