Contacts of the helix formed by residues 512 - 530 (chain N) in PDB entry 5A31
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 LYS 512 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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506N VAL* 6.5 1.3 - - - -
509N TYR* 5.1 1.0 - - - +
510N GLY 4.5 15.0 - - - -
511N SER* 1.3 88.8 + - - +
513N ASP* 1.3 54.1 + - - +
514N LEU* 3.4 2.3 - - - +
515N PHE* 3.3 15.5 + - - +
516N ILE* 2.9 40.2 + - + +
548N ARG 4.5 4.9 + - - -
549N PHE* 3.3 63.5 + - + +
553N PRO* 6.0 5.4 - - + -
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Residues in contact with ASP 513 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511N SER* 3.7 0.6 - - - -
512N LYS* 1.3 74.3 - - - +
514N LEU* 1.3 86.9 + - - +
516N ILE* 3.3 10.9 + - - +
517N ASN* 2.9 34.3 + - - +
750N GLU* 5.7 1.6 - - - +
782N VAL* 5.9 1.3 - - + -
787N LEU 3.1 11.9 - - - +
788N ALA* 2.9 15.2 - - - +
789N GLU* 2.2 57.6 + - + +
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Residues in contact with LEU 514 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432N GLU* 6.2 0.2 - - - +
435N VAL* 5.6 5.6 - - + -
509N TYR* 5.5 16.8 - - + -
511N SER* 3.6 16.2 + - - +
512N LYS 3.4 1.2 - - - +
513N ASP* 1.3 102.0 + - - +
515N PHE* 1.3 67.0 + - + +
517N ASN* 3.3 12.1 - - + +
518N GLU* 3.1 36.3 + - + +
747N LYS* 5.3 15.7 - - + +
789N GLU* 4.2 6.7 - - + +
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Residues in contact with PHE 515 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435N VAL* 1.8 48.5 - - + -
438N ILE* 4.5 9.0 - - + -
439N VAL* 5.0 11.4 - - + +
505N LEU* 5.3 14.1 - - + -
508N ILE* 3.9 14.4 - - + -
509N TYR* 3.0 48.5 - + + -
512N LYS* 3.3 14.3 + - - +
514N LEU* 1.3 77.7 - - + +
516N ILE* 1.3 62.9 + - + +
518N GLU* 3.4 3.1 + - - +
519N TYR* 2.8 32.2 + - - +
545N LEU* 5.9 2.5 - - + -
549N PHE* 4.7 15.5 - + + -
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Residues in contact with ILE 516 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512N LYS 2.9 15.7 + - - +
513N ASP* 3.5 10.1 - - - +
515N PHE* 1.3 74.0 - - - +
517N ASN* 1.3 66.8 + - - +
519N TYR* 3.3 2.1 + - - +
520N ARG* 3.0 49.4 + - - +
545N LEU* 3.7 23.6 - - + -
549N PHE* 3.7 20.9 - - + -
553N PRO* 3.3 35.2 - - + +
554N MET* 3.4 26.9 - - + +
787N LEU* 6.1 4.5 - - + +
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Residues in contact with ASN 517 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513N ASP* 2.9 18.6 + - - +
514N LEU* 3.3 17.9 + - + +
516N ILE* 1.3 76.0 - - - +
518N GLU* 1.3 59.3 + - + +
520N ARG* 3.3 26.0 + - - +
521N SER* 2.8 40.8 + - - -
747N LYS 5.9 1.4 + - - -
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Residues in contact with GLU 518 (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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433N ASP* 6.2 0.5 - - - -
435N VAL* 5.3 15.2 - - + +
436N ARG* 3.7 46.1 + - + +
439N VAL* 6.6 0.2 - - + -
514N LEU* 3.1 21.7 + - + +
515N PHE* 4.0 5.6 - - - +
516N ILE 3.3 0.2 - - - -
517N ASN* 1.3 82.6 - - + +
519N TYR* 1.3 57.6 + - - +
521N SER* 3.8 8.3 - - - -
522N LEU* 2.8 31.8 + - - +
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Residues in contact with TYR 519 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439N VAL* 5.3 15.0 - - + +
515N PHE 2.8 18.8 + - - +
516N ILE 3.8 3.1 - - - +
518N GLU* 1.3 77.4 - - - +
520N ARG* 1.3 57.1 + - - +
522N LEU* 3.3 10.5 + - + +
523N LEU* 2.9 39.9 + - + +
538N GLU* 2.8 30.1 + - - -
541N ASN* 2.8 52.9 - - - +
542N VAL* 3.3 12.4 + - + +
545N LEU* 4.0 16.2 - - + -
554N MET* 3.1 35.0 - - + -
557N CYS* 3.7 4.0 - - + -
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Residues in contact with ARG 520 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516N ILE* 3.0 32.7 + - - +
517N ASN* 3.3 30.2 - - - +
519N TYR* 1.3 76.4 - - - +
521N SER* 1.3 59.9 + - - +
523N LEU* 3.4 3.6 + - - +
524N ALA* 2.9 29.3 + - - +
553N PRO 4.8 0.6 + - - -
554N MET* 4.2 4.9 - - + -
556N PHE* 3.2 62.4 - - + +
557N CYS* 3.0 35.4 - - - +
560N MET* 5.7 6.0 - - + +
600N PHE 5.8 0.4 - - - +
602N PRO* 5.1 15.3 - - + +
787N LEU* 5.7 6.7 - - - +
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Residues in contact with SER 521 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517N ASN* 2.8 28.1 + - - -
518N GLU* 3.9 10.1 - - - -
520N ARG* 1.3 72.2 - - - +
522N LEU* 1.3 68.0 + - - +
524N ALA* 3.4 8.9 - - - +
525N ASP* 3.3 22.0 + - - +
602N PRO* 4.2 17.0 - - - +
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Residues in contact with LEU 522 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439N VAL* 5.2 14.4 - - + -
518N GLU* 2.8 22.9 + - - +
519N TYR* 3.4 12.1 - - + +
521N SER* 1.3 69.4 - - - +
523N LEU* 1.3 83.0 + - + +
525N ASP* 2.6 35.8 + - + +
526N ARG* 3.0 47.7 + - + +
541N ASN* 6.1 0.2 - - - +
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Residues in contact with LEU 523 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519N TYR* 2.9 37.7 + - + +
520N ARG* 3.6 7.4 - - - +
522N LEU* 1.3 86.0 - - + +
524N ALA* 1.3 58.4 + - - +
526N ARG* 3.2 8.1 + - - +
527N LEU* 2.8 36.3 + - - +
538N GLU* 2.8 50.9 - - + +
557N CYS* 3.5 33.7 - - + +
560N MET* 5.6 3.1 - - + -
561N LEU* 3.6 20.2 - - + -
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Residues in contact with ALA 524 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520N ARG 2.9 18.0 + - - +
521N SER* 3.4 11.7 - - - +
522N LEU 2.9 0.4 + - - -
523N LEU* 1.3 76.0 - - - +
525N ASP* 1.3 60.6 + - - +
527N LEU* 4.7 0.7 - - - -
528N LEU* 2.9 24.0 + - - +
560N MET* 5.9 3.5 - - - +
601N TRP* 3.2 43.9 - - + -
602N PRO* 4.9 11.4 - - + -
603N PRO* 5.0 2.9 - - + -
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Residues in contact with ASP 525 (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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521N SER 3.3 10.1 + - - +
522N LEU* 2.6 18.0 + - + +
524N ALA* 1.3 78.4 - - - +
526N ARG* 1.3 57.8 + - - +
528N LEU* 3.8 20.8 - - + +
529N HIS* 3.0 28.2 + - - +
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Residues in contact with ARG 526 (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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522N LEU* 3.0 54.9 + - + +
523N LEU* 3.5 13.7 - - - +
525N ASP* 1.3 74.1 - - - +
527N LEU* 1.3 57.5 + - + +
529N HIS* 4.0 3.4 - - - +
530N GLN* 2.7 38.2 + - - -
531N PHE* 3.7 37.0 + - + +
534N SER* 4.5 14.1 + - - +
537N ARG* 5.8 7.2 - - - +
538N GLU* 4.8 4.5 - - - +
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Residues in contact with LEU 527 (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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523N LEU 2.8 20.3 + - - +
524N ALA* 3.6 5.6 - - - +
526N ARG* 1.3 79.7 - - + +
528N LEU* 1.3 64.2 + - - +
530N GLN* 3.4 21.2 + - - +
533N PHE* 6.5 0.4 - - + -
534N SER* 5.0 5.4 - - - +
538N GLU* 5.0 0.7 - - - +
560N MET* 3.9 7.0 - - + +
561N LEU* 3.5 40.4 - - + -
564N MET* 2.4 63.0 - - + +
594N VAL* 5.4 7.1 - - - +
601N TRP* 3.5 19.7 - - + -
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Residues in contact with LEU 528 (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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11B VAL* 4.3 26.5 - - + -
524N ALA 2.9 18.0 + - - +
525N ASP* 3.8 22.7 - - + +
526N ARG 3.4 0.4 - - - -
527N LEU* 1.3 74.2 - - - +
529N HIS* 1.3 62.4 + - - +
530N GLN* 5.1 0.3 - - - +
594N VAL* 6.1 0.7 - - + -
596N LEU* 5.0 0.4 - - + -
601N TRP* 4.0 22.9 - - + -
603N PRO* 6.1 0.9 - - + -
638N LYS* 4.6 4.9 - - - +
641N LEU* 3.4 48.7 - - + +
643N LEU* 3.9 25.1 - - + +
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Residues in contact with HIS 529 (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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525N ASP 3.0 16.2 + - - +
526N ARG* 4.2 3.1 - - - +
528N LEU* 1.3 75.4 - - - +
530N GLN* 1.3 76.4 + - + +
531N PHE* 4.1 13.5 - - - +
643N LEU* 5.6 8.1 - - + +
727N MET* 5.6 10.8 - - + -
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Residues in contact with GLN 530 (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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9B ASN* 4.3 15.8 + - - +
526N ARG 2.7 22.1 + - - +
527N LEU* 3.4 18.3 + - - +
528N LEU 5.1 0.2 - - - +
529N HIS* 1.3 80.4 + - + +
531N PHE* 1.3 85.2 + - - +
532N SER* 4.2 12.7 + - - +
533N PHE* 4.2 23.6 - - + -
534N SER* 3.8 10.0 + - - -
592N TYR* 4.6 18.2 + - - +
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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
------------------------------------------------------------
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