Contacts of the helix formed by residues 500 - 518 (chain D) in PDB entry 6RKU
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 500 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498D ASP* 3.6 17.3 - - + +
499D ALA* 1.3 83.4 - - - +
501D VAL* 1.3 67.6 + - + +
502D ASP* 3.8 17.6 - - - +
503D GLY* 2.7 35.4 + - - -
504D SER* 3.6 10.7 + - - -
740D LYS* 5.7 6.8 - - + +
14F G 5.5 1.9 + - - +
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Residues in contact with VAL 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ASP* 4.8 11.2 - - - +
24C TYR* 3.3 34.5 - - + -
27C SER* 3.7 31.6 - - - +
28C VAL* 5.3 2.5 - - + -
32C ARG* 5.0 7.9 - - - +
500D ASP* 1.3 73.9 - - + +
502D ASP* 1.3 74.7 + - - +
503D GLY 3.1 1.8 - - - -
504D SER* 2.6 24.6 + - - -
505D HIS 3.0 5.5 + - - -
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Residues in contact with ASP 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C TYR* 3.3 23.4 + - - -
32C ARG* 4.0 15.1 + - - -
80C HIS* 5.5 0.7 - - - -
449D LYS* 4.7 10.1 + - - -
500D ASP* 3.8 13.0 - - - +
501D VAL* 1.3 82.5 - - - +
503D GLY* 1.3 62.7 + - - +
505D HIS* 3.2 8.4 + - - +
506D ILE* 2.9 26.4 + - - +
13F A 4.0 3.2 - - - +
14F G 3.0 46.4 + - - +
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Residues in contact with GLY 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497D THR* 3.3 25.4 - - - +
498D ASP* 3.8 9.9 - - - -
500D ASP* 2.7 24.9 + - - -
501D VAL 3.1 0.2 - - - -
502D ASP* 1.3 72.3 - - - +
504D SER* 1.3 55.5 + - - +
506D ILE* 3.1 7.5 - - - +
507D ARG* 2.9 30.0 + - - +
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Residues in contact with SER 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C SER* 3.8 36.4 + - - -
21C TYR* 6.0 0.2 - - - -
23C ASP* 5.4 2.1 - - - +
24C TYR* 4.0 5.9 + - - +
498D ASP 4.7 0.8 + - - -
500D ASP 3.6 8.4 + - - -
501D VAL* 2.6 25.5 + - - +
503D GLY* 1.3 75.0 - - - +
505D HIS* 1.3 56.7 + - - +
507D ARG* 3.4 17.0 - - - +
508D THR* 2.9 33.1 + - - -
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Residues in contact with HIS 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C TYR* 4.6 13.8 - + - +
24C TYR* 3.3 45.0 + + + -
449D LYS* 4.1 33.8 + - + +
501D VAL 3.0 13.6 + - - +
502D ASP* 3.4 9.4 - - - +
503D GLY 3.2 0.4 - - - -
504D SER* 1.3 78.8 + - - +
506D ILE* 1.3 65.8 + - + +
508D THR* 3.2 6.7 + - - -
509D LEU* 3.0 54.3 + - + +
21H A 4.3 10.8 + - - -
22H C 3.9 20.9 - - - -
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Residues in contact with ILE 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446D LEU* 5.9 4.0 - - + -
448D GLY 4.2 7.6 - - - +
449D LYS* 3.9 37.0 - - + -
450D ILE* 4.1 16.6 - - + +
497D THR* 3.7 18.8 - - + +
502D ASP 2.9 14.9 + - - +
503D GLY* 3.1 16.2 - - - +
505D HIS* 1.3 79.3 - - + +
507D ARG* 1.3 57.8 + - - +
509D LEU* 3.3 14.6 + - + +
510D LEU* 2.9 42.9 + - + +
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Residues in contact with ARG 507 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C GLU* 5.8 4.7 + - - +
20C SER* 4.8 15.1 + - - -
495D ILE* 5.1 10.5 + - + +
497D THR* 3.7 41.0 + - - +
498D ASP 4.0 7.4 + - - -
499D ALA* 5.9 0.2 - - - +
503D GLY 2.9 17.9 + - - +
504D SER* 3.4 15.5 - - - +
505D HIS 3.1 0.2 - - - -
506D ILE* 1.3 78.0 - - - +
508D THR* 1.3 57.0 + - - +
510D LEU* 3.3 8.4 + - - +
511D LEU* 2.9 49.0 + - + +
529D ILE* 4.5 31.7 - - + +
530D ALA 4.7 10.3 + - - -
531D GLN* 5.4 3.6 - - - +
532D PRO* 5.3 3.8 - - - +
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Residues in contact with THR 508 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 3.9 32.4 + - + +
20C SER* 4.2 6.2 - - - -
21C TYR* 4.1 37.6 + - + +
504D SER 2.9 14.4 + - - -
505D HIS* 3.6 9.4 - - - -
507D ARG* 1.3 75.8 - - - +
509D LEU* 1.3 65.0 + - + +
511D LEU* 3.3 10.1 + - - +
512D THR* 3.0 25.3 + - + +
777D PHE* 4.4 14.1 - - + -
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Residues in contact with LEU 509 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C TYR* 6.0 0.7 - - + -
449D LYS* 5.1 2.7 - - + -
450D ILE* 3.1 32.1 - - + +
451D LEU 6.0 0.2 - - - +
452D ASN* 3.8 25.4 - - - +
505D HIS* 3.0 58.0 + - + +
506D ILE* 3.6 24.2 - - + +
508D THR* 1.3 80.6 - - + +
510D LEU* 1.3 62.4 + - + +
512D THR* 3.0 9.8 - - - +
513D PHE* 3.0 24.1 + - - +
777D PHE* 5.0 8.5 - - + -
21H A 5.0 7.9 - - - +
22H C 5.3 0.9 - - - +
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Residues in contact with LEU 510 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422D LEU* 5.0 11.9 - - + -
446D LEU* 4.5 19.5 - - + -
450D ILE* 3.7 31.0 - - + -
467D VAL* 6.1 3.4 - - + -
495D ILE* 4.4 29.2 - - + -
497D THR* 5.6 1.3 - - - +
506D ILE* 2.9 33.1 + - + +
507D ARG* 3.8 4.3 - - - +
509D LEU* 1.3 76.5 - - + +
511D LEU* 1.3 63.0 + - - +
513D PHE* 3.3 11.9 + - + +
514D PHE* 3.0 43.6 + - + -
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Residues in contact with LEU 511 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C GLU* 6.1 4.9 - - + -
17C LEU* 4.5 25.6 - - + +
495D ILE* 4.3 20.0 - - + -
507D ARG* 2.9 39.8 + - + +
508D THR* 3.8 7.2 - - - +
510D LEU* 1.3 76.0 - - - +
512D THR* 1.3 57.5 + - - +
514D PHE* 3.3 8.1 + - + +
515D TYR* 2.9 29.6 + - - +
527D VAL* 4.5 12.6 - - + -
529D ILE* 4.5 14.8 - - + -
765D VAL* 5.6 11.2 - - + -
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Residues in contact with THR 512 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 4.7 8.0 - - - +
452D ASN* 5.0 11.4 - - - +
453D VAL* 4.7 11.3 - - + +
454D GLU* 4.8 6.8 + - - +
508D THR* 3.0 17.1 + - - +
509D LEU* 3.0 21.5 - - - +
511D LEU* 1.3 72.7 - - - +
513D PHE* 1.3 66.6 + - - +
515D TYR* 4.4 5.4 - - - -
516D ARG* 2.9 33.3 + - - +
774D ASP* 4.0 24.7 + - - +
777D PHE* 5.1 17.1 - - + -
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Residues in contact with PHE 513 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450D ILE* 5.6 11.2 - - + -
451D LEU 5.5 4.0 - - - +
453D VAL* 3.5 28.7 - - + -
467D VAL* 4.8 20.2 - - + -
468D ALA* 5.8 8.1 - - + -
509D LEU 3.0 14.9 + - - +
510D LEU* 3.4 18.2 - - + +
512D THR* 1.3 78.6 - - - +
514D PHE* 1.3 81.0 + + - +
516D ARG* 3.8 0.3 - - - -
517D GLN* 2.9 58.0 + - + +
518D MET* 5.7 5.2 - - + -
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Residues in contact with PHE 514 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422D LEU* 4.5 19.5 - - + -
467D VAL* 4.9 14.1 - - + -
471D ILE* 4.8 13.7 - - + -
493D ILE* 4.1 27.1 - - + -
495D ILE* 4.3 23.1 - - + -
510D LEU* 3.0 39.5 + - + -
511D LEU* 3.7 11.4 - - + +
513D PHE* 1.3 87.0 - + - +
515D TYR* 1.3 64.4 + - - +
517D GLN* 4.8 2.5 - - - -
518D MET* 2.9 48.0 + - + +
521D ILE* 4.8 9.0 - - + -
522D VAL* 4.3 14.8 - - + -
527D VAL* 5.0 7.4 - - + -
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Residues in contact with TYR 515 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C GLU* 5.6 14.4 - - + +
511D LEU 2.9 17.0 + - - +
512D THR* 3.8 6.3 - - - +
513D PHE 3.2 0.2 - - - -
514D PHE* 1.3 79.0 - - - +
516D ARG* 1.3 77.7 + - + +
517D GLN 3.5 0.2 + - - -
518D MET 5.0 0.4 - - - -
519D PRO* 3.9 27.9 - - + +
522D VAL* 4.5 23.5 - - + +
767D VAL* 5.7 9.4 - - + -
769D ASP 4.5 13.6 + - - -
770D ALA* 4.9 7.6 - - - +
771D ILE 5.3 5.3 + - - -
774D ASP* 3.3 26.7 - - + +
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Residues in contact with ARG 516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453D VAL* 4.2 21.8 - - + +
454D GLU* 2.3 48.4 + - + +
512D THR* 2.9 29.3 + - - +
513D PHE 4.4 0.2 - - - +
515D TYR* 1.3 100.6 - - + +
517D GLN* 1.3 69.6 + - - +
519D PRO* 5.3 1.3 - - - -
774D ASP* 4.6 5.6 - - - +
775D GLN* 3.5 20.1 - - - +
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Residues in contact with GLN 517 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453D VAL* 3.8 18.4 - - + +
474D LEU* 4.5 23.1 - - + +
513D PHE* 2.9 56.8 + - + +
514D PHE* 4.1 1.6 - - - +
516D ARG* 1.3 94.8 - - - +
518D MET* 1.3 72.7 + - + +
519D PRO* 3.5 8.9 - - - +
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Residues in contact with MET 518 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467D VAL* 6.5 0.4 - - + -
468D ALA* 6.1 2.2 - - + -
471D ILE* 4.5 28.5 - - + -
472D THR* 4.2 17.5 - - - -
474D LEU* 4.8 20.0 - - + -
484D ASN* 4.1 31.0 - - - +
513D PHE* 5.7 5.2 - - + -
514D PHE* 2.9 33.7 + - + +
517D GLN* 1.3 85.9 - - + +
519D PRO* 1.3 66.4 - - - +
520D GLU 3.2 1.3 - - - +
521D ILE* 3.2 37.7 - - + +
522D VAL* 3.8 4.0 - - - +
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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