Contacts of the helix formed by residues 523 - 535 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468I ILE* 4.3 19.6 - - + +
469I GLU* 6.2 1.3 - - + -
452K SER* 3.9 13.1 + - - +
514K TYR* 3.7 12.8 - - - -
521K PHE* 3.2 6.3 - - - +
522K SER* 1.3 81.5 - - - +
524K ILE* 1.3 63.6 + - - +
525K PRO* 3.2 15.5 - - + +
526K GLN* 2.9 63.9 + - - +
527K LEU* 3.3 9.2 + - - +
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Residues in contact with ILE 524 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455K LEU* 4.0 21.3 - - + -
460K TRP* 4.2 4.5 - - + -
482K VAL* 4.5 3.1 - - + -
492K TYR* 3.4 53.4 - - + -
507K ILE* 4.0 20.2 - - + -
514K TYR* 3.5 32.2 - - + -
523K ASN* 1.3 70.3 - - - +
525K PRO* 1.3 74.5 - - + +
527K LEU* 3.0 8.2 + - + +
528K ILE* 2.8 38.1 + - + +
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Residues in contact with PRO 525 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469I GLU* 5.6 1.6 - - - +
452K SER* 3.7 14.1 - - - +
453K LYS 3.7 19.1 - - - +
455K LEU* 4.0 17.7 - - + +
458K GLN* 3.7 32.1 - - + +
460K TRP* 3.9 12.4 - - + -
523K ASN* 3.2 16.2 - - + +
524K ILE* 1.3 92.3 - - + +
526K GLN* 1.3 56.4 + - - +
528K ILE* 4.0 0.3 - - - +
529K ASP* 2.8 33.3 + - - +
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Residues in contact with GLN 526 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452K SER* 3.8 17.6 + - - +
521K PHE* 3.9 17.5 - - + +
522K SER* 3.2 34.5 + - - -
523K ASN* 2.9 35.6 + - - +
525K PRO* 1.3 75.7 - - - +
527K LEU* 1.3 58.7 + - - +
529K ASP* 3.9 3.6 - - - +
530K HIS* 2.9 29.3 + - - +
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Residues in contact with LEU 527 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507K ILE* 3.6 34.1 - - + -
514K TYR* 4.2 3.4 - - + +
515K ARG* 4.0 20.4 - - - +
516K PHE* 3.7 28.0 - - + +
519K THR 4.8 0.9 - - - +
521K PHE* 3.6 39.0 - - + -
523K ASN 3.3 8.5 + - - +
524K ILE* 3.0 9.3 + - - +
526K GLN* 1.3 78.7 - - - +
528K ILE* 1.3 64.3 + - + +
530K HIS* 3.3 2.4 + - - +
531K HIS* 3.2 46.9 + - + +
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Residues in contact with ILE 528 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460K TRP* 3.8 37.7 - - + +
480K PHE* 3.7 30.3 - - + -
482K VAL* 3.9 17.0 - - + -
494K LEU* 4.0 21.5 - - + -
507K ILE* 4.7 2.9 - - + -
516K PHE* 4.7 12.6 - - + -
524K ILE* 2.8 29.5 + - + +
527K LEU* 1.3 77.3 - - + +
529K ASP* 1.3 59.5 + - - +
531K HIS* 3.1 5.9 + - - +
532K TYR* 2.8 28.3 + - + +
546K LEU* 4.2 8.2 - - + +
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Residues in contact with ASP 529 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452K SER* 5.8 1.6 - - - +
460K TRP* 5.5 0.4 - - + -
525K PRO 2.8 19.8 + - - +
526K GLN* 4.0 4.7 - - - +
528K ILE* 1.3 77.1 - - - +
530K HIS* 1.3 51.7 + - - +
532K TYR* 4.2 13.1 - - - -
533K THR* 2.7 58.0 + - - +
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Residues in contact with HIS 530 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519K THR* 5.8 4.1 + - - -
521K PHE* 3.6 33.9 - + + -
526K GLN 2.9 18.7 + - - +
527K LEU 3.5 3.4 - - - +
528K ILE 3.2 0.4 - - - -
529K ASP* 1.3 75.7 - - - +
531K HIS* 1.3 77.7 + + - +
533K THR* 3.9 3.8 - - - -
534K THR* 2.6 52.1 + - + +
536K GLN* 3.2 41.6 + - - +
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Residues in contact with HIS 531 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516K PHE* 3.7 24.2 - + - +
527K LEU* 3.2 36.8 + - + +
528K ILE* 3.1 7.4 + - - +
530K HIS* 1.3 94.2 - + - +
532K TYR* 1.3 61.4 + - - +
534K THR* 4.0 3.6 - - - -
535K LYS* 3.0 30.1 + - - +
536K GLN* 2.9 24.5 + - + +
537K VAL 3.2 23.1 + - - -
538K ILE* 3.7 18.3 - - + +
546K LEU* 3.8 24.3 + - + +
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Residues in contact with TYR 532 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480K PHE* 3.9 25.6 - + + -
528K ILE* 2.8 18.6 + - + +
529K ASP* 3.9 17.5 - - - +
531K HIS* 1.3 78.3 - - - +
533K THR* 1.3 64.5 + - + +
535K LYS* 2.9 45.4 + - - +
546K LEU* 4.1 8.0 - - + +
547K LEU 3.3 23.5 + - - -
549K PRO* 3.8 24.9 - - + +
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Residues in contact with THR 533 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529K ASP* 2.7 46.7 + - - +
530K HIS* 3.3 6.2 + - - -
532K TYR* 1.3 86.4 - - + +
534K THR* 1.3 67.7 + - - +
535K LYS* 3.6 6.4 + - - +
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Residues in contact with THR 534 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530K HIS* 2.6 39.5 + - + +
533K THR* 1.3 83.5 + - - +
535K LYS* 1.3 68.2 + - - +
536K GLN* 3.1 39.6 + - - +
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Residues in contact with LYS 535 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531K HIS 3.0 12.6 + - - +
532K TYR* 2.9 40.5 + - - +
533K THR 4.3 4.9 - - - +
534K THR* 1.3 79.6 - - - +
536K GLN* 1.3 65.7 + - - +
537K VAL* 3.6 2.6 + - - +
545K VAL* 3.7 30.7 - - + +
546K LEU 2.8 29.1 + - - +
547K LEU* 3.8 17.3 + - + +
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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
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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