Contacts of the helix formed by residues 503 - 515 (chain K) in PDB entry 6D84
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 ASP 503 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501K THR* 2.8 18.6 + - - +
502K GLU* 1.3 83.6 - - - +
504K GLU* 1.3 64.6 + - + +
505K VAL 3.3 0.9 - - - -
506K LEU 4.1 0.9 - - - -
507K ASP* 3.2 22.3 + - - +
540K THR* 3.2 17.4 + - - +
543K ARG* 2.8 41.2 + - - +
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Residues in contact with GLU 504 (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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460K TYR* 3.6 20.0 + - - +
501K THR* 3.6 18.3 - - + +
503K ASP* 1.3 76.4 - - + +
505K VAL* 1.3 60.6 + - - +
506K LEU 3.3 0.7 - - - -
507K ASP* 3.5 13.0 - - + +
508K ILE* 2.9 31.4 + - - +
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Residues in contact with VAL 505 (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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460K TYR* 4.2 17.3 - - + +
480K ILE* 4.1 17.5 - - + +
487K LEU* 3.7 28.0 - - + -
488K VAL* 4.1 7.9 - - + -
500K VAL* 4.9 1.6 - - - -
501K THR* 4.1 9.6 - - + +
502K GLU* 3.5 31.0 - - - +
503K ASP 3.3 0.2 - - - -
504K GLU* 1.3 78.5 - - - +
506K LEU* 1.3 59.2 + - + +
508K ILE* 3.3 20.7 - - + +
509K LEU* 3.9 12.5 - - - +
533K LEU* 5.2 0.7 - - + -
537K PHE* 4.3 20.2 - - + -
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Residues in contact with LEU 506 (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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502K GLU 3.3 28.0 - - - +
503K ASP 3.9 0.8 + - - -
504K GLU 3.3 0.2 - - - -
505K VAL* 1.3 80.6 - - - +
507K ASP* 1.3 58.8 + - - +
508K ILE 3.3 0.4 - - - -
509K LEU* 3.3 7.6 + - + +
510K GLU* 3.0 29.8 + - - +
530K ILE* 3.7 29.6 - - + +
533K LEU* 4.2 26.2 - - + -
537K PHE* 4.1 24.7 - - + -
540K THR* 5.0 6.5 - - - +
543K ARG* 3.6 22.0 - - - +
544K ILE* 3.7 21.8 - - + -
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Residues in contact with ASP 507 (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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503K ASP 3.2 20.7 + - - +
504K GLU* 3.3 14.6 + - + +
506K LEU* 1.3 76.1 - - - +
508K ILE* 1.3 59.4 + - - +
510K GLU* 3.7 21.0 - - - +
511K SER* 2.8 33.3 + - - -
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Residues in contact with ILE 508 (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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460K TYR* 4.0 19.7 - - + +
463K ILE* 3.3 47.3 - - + +
464K LEU* 3.7 17.3 - - + +
467K TYR* 6.3 2.0 - - + -
480K ILE* 5.9 2.2 - - + -
504K GLU 2.9 16.5 + - - +
505K VAL* 3.3 18.8 - - + +
507K ASP* 1.3 76.9 - - - +
509K LEU* 1.3 66.9 + - + +
511K SER* 2.6 23.8 + - - +
512K VAL* 3.0 24.9 + - + +
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Residues in contact with LEU 509 (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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463K ILE* 5.6 5.2 - - + -
476K ALA 5.3 0.9 - - - -
477K ALA* 4.3 26.7 - - + +
480K ILE* 3.8 33.2 - - + -
505K VAL 3.9 12.6 - - - +
506K LEU* 3.3 6.7 + - - +
507K ASP 3.3 0.2 - - - -
508K ILE* 1.3 83.9 - - + +
510K GLU* 1.3 57.8 + - - +
512K VAL* 3.2 13.9 + - + +
513K LEU* 2.9 32.1 + - - +
526K ALA* 4.6 13.4 - - + +
529K ALA* 4.2 20.6 - - + -
530K ILE* 4.7 18.2 - - + -
533K LEU* 4.8 4.9 - - + -
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Residues in contact with GLU 510 (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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506K LEU* 3.0 18.3 + - - +
507K ASP* 3.8 21.8 - - - +
509K LEU* 1.3 77.7 - - - +
511K SER* 1.3 55.6 + - - +
513K LEU* 3.1 14.2 + - + +
514K ILE* 2.9 53.6 + - + +
530K ILE* 5.7 2.0 - - + +
543K ARG* 5.8 2.6 + - - +
546K LYS* 4.3 10.9 + - - -
547K VAL* 4.0 34.9 - - + +
550K ILE* 5.5 4.3 - - - +
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Residues in contact with SER 511 (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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467K TYR* 4.8 10.9 - - - -
507K ASP* 2.8 22.1 + - - -
508K ILE* 2.6 27.9 + - - +
510K GLU* 1.3 72.3 - - - +
512K VAL* 1.3 62.6 + - - +
514K ILE* 4.3 8.5 - - - +
515K SER* 2.9 28.1 + - - -
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Residues in contact with VAL 512 (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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467K TYR* 3.8 29.2 - - + -
473K VAL* 4.9 17.9 - - + -
508K ILE* 3.0 25.8 + - + +
509K LEU* 3.4 17.0 - - + +
511K SER* 1.3 77.5 - - - +
513K LEU* 1.3 58.7 + - + +
515K SER* 2.8 13.6 + - - +
517K MET 4.8 4.3 - - - +
518K SER* 2.6 34.5 + - - +
522K THR* 4.6 21.1 - - + +
523K ARG* 6.0 0.2 - - + -
526K ALA* 5.4 5.2 - - + -
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Residues in contact with LEU 513 (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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509K LEU 2.9 19.8 + - - +
510K GLU* 3.1 18.1 + - + +
512K VAL* 1.3 78.6 - - + +
514K ILE* 1.3 63.5 + - + +
523K ARG* 3.4 50.2 + - + +
526K ALA* 3.7 21.8 - - + -
527K LEU* 3.7 33.9 - - + -
530K ILE* 5.0 10.3 - - + -
547K VAL* 4.7 17.7 - - + -
551K TYR* 4.8 12.8 - - + +
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Residues in contact with ILE 514 (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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510K GLU* 2.9 42.6 + - + +
511K SER* 4.4 6.3 - - - +
512K VAL 3.4 0.2 - - - -
513K LEU* 1.3 76.7 - - + +
515K SER* 1.3 64.4 + - - +
516K ASN* 3.5 2.4 + - - +
523K ARG* 4.4 2.6 + - - -
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Residues in contact with SER 515 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467K TYR* 3.2 40.3 - - - -
511K SER 2.9 16.2 + - - -
512K VAL 2.8 23.4 + - - +
514K ILE* 1.3 77.8 - - - +
516K ASN* 1.3 60.4 + - - +
517K MET* 3.1 5.0 + - - -
518K SER* 2.9 25.3 + - - -
523K ARG* 3.2 8.2 + - - -
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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
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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