Contacts of the helix formed by residues 523 - 535 (chain G) in PDB entry 6KC4
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 ASN 523 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452G SER* 3.2 32.1 + - - +
453G LYS 5.2 1.3 - - - +
514G TYR* 3.6 11.4 - - - +
521G PHE* 3.1 9.0 + - - +
522G SER* 1.3 101.6 + - - +
524G ILE* 1.3 63.5 + - - +
525G PRO* 3.4 14.0 - - + +
526G GLN* 2.9 46.9 + - - +
527G LEU* 3.5 14.9 + - - +
468K ILE* 4.5 15.7 - - + -
469K GLU* 6.4 0.9 - - + -
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Residues in contact with ILE 524 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455G LEU* 4.0 20.6 - - + -
460G TRP* 4.3 3.8 - - + -
482G VAL* 4.6 2.0 - - + -
492G TYR* 3.4 54.5 - - + -
507G ILE* 4.1 21.8 - - + -
514G TYR* 3.5 31.3 - - + -
523G ASN* 1.3 69.2 - - - +
525G PRO* 1.3 75.3 - - + +
527G LEU* 3.0 9.1 + - + +
528G ILE* 2.9 38.2 + - + +
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Residues in contact with PRO 525 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453G LYS* 3.2 48.5 - - + +
455G LEU* 4.0 23.8 - - + +
458G GLN* 4.1 16.8 - - + -
460G TRP* 3.9 11.9 - - + -
523G ASN* 3.4 13.0 - - + +
524G ILE* 1.3 93.3 - - + +
526G GLN* 1.3 55.0 + - - +
529G ASP* 2.8 37.2 + - - -
469K GLU* 5.5 0.9 - - - +
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Residues in contact with GLN 526 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452G SER 5.7 0.2 - - - +
453G LYS* 6.1 0.2 - - - +
521G PHE* 3.3 36.9 - - + +
522G SER* 4.4 3.8 + - - -
523G ASN* 2.9 36.9 + - - +
524G ILE 3.2 0.4 - - - -
525G PRO* 1.3 76.3 - - - +
527G LEU* 1.3 58.3 + - - +
529G ASP* 4.0 5.6 - - - +
530G HIS* 3.0 30.5 + - + +
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Residues in contact with LEU 527 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507G ILE* 3.7 27.8 - - + -
514G TYR* 4.1 4.3 - - + +
515G ARG* 3.9 18.2 - - - +
516G PHE* 3.7 29.6 - - + +
519G THR 4.3 10.1 - - - +
521G PHE* 3.7 32.4 - - + -
523G ASN 3.5 8.5 + - - +
524G ILE* 3.0 9.5 + - - +
526G GLN* 1.3 78.6 - - - +
528G ILE* 1.3 65.6 + - + +
530G HIS* 3.3 2.8 + - - +
531G HIS* 3.2 48.2 + - + +
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Residues in contact with ILE 528 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460G TRP* 3.8 37.9 - - + +
480G PHE* 3.8 24.7 - - + -
482G VAL* 4.1 14.8 - - + -
494G LEU* 4.1 15.0 - - + -
507G ILE* 4.5 5.6 - - + -
516G PHE* 4.2 23.1 - - + -
524G ILE* 2.9 32.4 + - + +
527G LEU* 1.3 75.8 - - + +
529G ASP* 1.3 59.3 + - - +
531G HIS* 3.1 5.0 + - - +
532G TYR* 2.8 28.1 + - + +
546G LEU* 4.2 6.9 - - + +
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Residues in contact with ASP 529 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453G LYS* 2.5 39.6 + - - -
458G GLN* 4.8 1.0 - - - +
460G TRP* 4.2 19.1 + - - -
525G PRO 2.8 26.7 + - - +
526G GLN* 4.0 5.6 - - - +
528G ILE* 1.3 73.1 - - - +
530G HIS* 1.3 63.2 + - - +
532G TYR* 4.4 7.7 - - - +
533G THR* 2.9 36.4 + - + +
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Residues in contact with HIS 530 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519G THR* 5.8 4.1 + - - -
521G PHE* 4.1 28.3 - + + -
526G GLN* 3.0 19.6 + - + +
527G LEU 3.5 4.5 - - - +
528G ILE 3.2 0.2 - - - -
529G ASP* 1.3 76.3 - - - +
531G HIS* 1.3 72.2 + + - +
533G THR* 4.0 3.6 - - - -
534G THR* 2.6 62.3 + - + +
536G GLN* 2.6 31.7 + - - -
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Residues in contact with HIS 531 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516G PHE* 3.8 19.2 - + + +
527G LEU* 3.2 36.3 + - + +
528G ILE* 3.1 7.4 + - - +
530G HIS* 1.3 87.3 - + - +
532G TYR* 1.3 58.6 + - - +
534G THR* 4.1 3.8 - - - -
535G LYS* 2.9 30.1 + - - +
536G GLN* 2.8 40.5 + - + +
537G VAL 3.2 21.9 + - - -
538G ILE* 3.8 22.8 + - + +
546G LEU* 3.8 22.1 + - + +
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Residues in contact with TYR 532 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480G PHE* 3.8 27.4 - + + -
528G ILE* 2.8 18.7 + - + +
529G ASP* 3.9 8.3 - - - +
531G HIS* 1.3 77.9 - - - +
533G THR* 1.3 70.2 + - + +
535G LYS* 2.8 48.9 + - - +
546G LEU* 4.1 8.7 - - + +
547G LEU 3.4 24.3 + - - -
549G PRO* 3.7 26.1 - - + +
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Residues in contact with THR 533 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529G ASP* 2.9 28.1 + - + +
530G HIS* 3.5 5.4 + - - -
532G TYR* 1.3 91.7 - - + +
534G THR* 1.3 69.9 + - - +
535G LYS* 3.7 5.7 + - - +
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Residues in contact with THR 534 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530G HIS* 2.6 44.0 + - + +
533G THR* 1.3 84.3 - - - +
535G LYS* 1.3 68.6 + - - +
536G GLN* 3.2 22.0 + - - +
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Residues in contact with LYS 535 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531G HIS 2.9 12.1 + - - +
532G TYR* 2.8 42.6 + - - +
533G THR 3.4 5.4 - - - +
534G THR* 1.3 79.5 - - - +
536G GLN* 1.3 64.6 + - - +
537G VAL* 3.5 2.6 + - - +
545G VAL* 3.8 29.9 - - + +
546G LEU 2.8 28.6 + - - +
547G LEU* 4.1 14.9 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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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