Contacts of the helix formed by residues 500 - 518 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B ASP* 3.6 17.9 - - - +
499B ALA* 1.3 83.0 - - - +
501B VAL* 1.3 67.3 + - + +
502B ASP* 3.8 17.3 - - - +
503B GLY* 2.7 36.7 + - - -
504B SER* 3.6 10.6 + - - -
740B LYS* 5.7 6.8 - - + +
14E G 5.7 1.2 + - - +
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Residues in contact with VAL 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASP* 4.6 15.0 - - - +
24A TYR* 3.2 31.3 - - + -
27A SER* 3.5 33.9 - - - +
28A VAL* 5.2 2.7 - - + -
32A ARG* 5.0 7.6 - - - +
500B ASP* 1.3 74.7 - - + +
502B ASP* 1.3 74.7 + - - +
503B GLY 3.1 1.6 - - - -
504B SER* 2.6 24.6 + - - -
505B HIS 3.0 6.2 + - - -
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Residues in contact with ASP 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.2 25.5 + - - -
32A ARG* 4.0 21.4 + - - -
80A HIS* 5.5 2.3 - - - -
449B LYS* 4.7 13.5 + - - -
500B ASP* 3.5 14.1 + - - +
501B VAL* 1.3 79.2 - - - +
503B GLY* 1.3 62.5 + - - +
505B HIS* 3.4 7.0 - - - +
506B ILE* 2.9 26.9 + - - +
13E A 4.3 3.7 - - - +
14E G 3.8 31.5 + - - +
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Residues in contact with GLY 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B THR* 3.3 24.7 - - - +
498B ASP* 3.8 11.0 - - - -
500B ASP* 2.7 24.4 + - - -
501B VAL 3.1 0.4 - - - -
502B ASP* 1.3 72.1 - - - +
504B SER* 1.3 56.5 + - - +
506B ILE* 3.1 7.1 - - - +
507B ARG* 2.9 29.8 + - - +
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Residues in contact with SER 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A SER* 3.6 37.4 + - - -
21A TYR* 5.9 0.2 - - - -
23A ASP* 5.2 3.3 + - - +
24A TYR* 3.9 6.1 + - - +
498B ASP 4.7 0.8 + - - -
500B ASP 3.6 9.4 + - - -
501B VAL* 2.6 25.6 + - - +
503B GLY* 1.3 75.5 - - - +
505B HIS* 1.3 57.1 + - - +
507B ARG* 3.3 16.3 + - - +
508B THR* 2.9 34.2 + - - -
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Residues in contact with HIS 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TYR* 4.5 12.2 - + - +
24A TYR* 3.2 47.0 - + + -
449B LYS* 4.1 31.9 + - + -
501B VAL 3.0 13.7 + - - +
502B ASP* 3.4 9.0 - - - +
503B GLY 3.2 0.2 - - - -
504B SER* 1.3 76.5 + - - +
506B ILE* 1.3 66.2 + - - +
508B THR* 3.2 6.1 + - - -
509B LEU* 3.0 50.2 + - + +
21G A 3.6 11.8 + - - -
22G C 3.0 30.7 + - - -
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Residues in contact with ILE 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B LEU* 5.9 4.3 - - + -
448B GLY 4.2 7.9 - - - +
449B LYS* 3.9 36.8 - - + -
450B ILE* 4.1 15.0 - - + +
497B THR* 3.7 18.4 - - + +
502B ASP 2.9 15.1 + - - +
503B GLY* 3.1 16.4 - - - +
505B HIS* 1.3 79.6 - - + +
507B ARG* 1.3 56.3 + - - +
509B LEU* 3.6 14.2 - - + +
510B LEU* 2.9 44.1 + - + +
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Residues in contact with ARG 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLU* 5.5 7.4 + - - +
20A SER* 4.6 18.4 + - - -
495B ILE* 5.1 10.5 + - + +
497B THR* 3.7 41.3 + - - +
498B ASP 4.0 7.6 + - - -
503B GLY 2.9 16.8 + - - +
504B SER* 3.4 13.3 - - - +
506B ILE* 1.3 78.3 - - - +
508B THR* 1.3 58.5 + - - +
510B LEU* 3.3 8.3 + - - +
511B LEU* 2.9 50.4 + - + +
529B ILE* 4.5 31.6 - - + +
530B ALA 4.7 10.1 + - - -
531B GLN* 5.4 4.0 - - - +
532B PRO* 5.3 3.2 - - - +
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Residues in contact with THR 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.8 34.3 + - + +
20A SER* 4.1 4.7 - - - -
21A TYR* 3.9 40.2 + - + +
504B SER 2.9 14.3 + - - -
505B HIS 3.2 8.0 + - - -
507B ARG* 1.3 76.0 - - - +
509B LEU* 1.3 64.0 + - + +
511B LEU* 3.3 9.2 + - - +
512B THR* 3.0 24.9 + - + +
777B PHE* 4.4 14.4 - - + -
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Residues in contact with LEU 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TYR* 5.9 0.9 - - + -
449B LYS* 5.1 1.6 - - + -
450B ILE* 3.1 33.9 - - + +
451B LEU 6.0 0.2 - - - +
452B ASN* 3.8 24.5 - - - +
505B HIS* 3.0 58.0 + - + +
506B ILE* 3.6 24.0 - - + +
507B ARG 3.3 0.2 - - - -
508B THR* 1.3 81.0 - - + +
510B LEU* 1.3 64.4 + - + +
512B THR* 3.0 11.0 - - - +
513B PHE* 3.0 23.0 + - - +
777B PHE* 5.0 6.7 - - + -
21G A 4.6 9.9 - - - -
22G C 4.5 2.0 - - - +
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Residues in contact with LEU 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B LEU* 5.0 12.8 - - + +
446B LEU* 4.5 18.2 - - + -
450B ILE* 3.7 30.1 - - + -
467B VAL* 6.1 3.6 - - + -
495B ILE* 4.4 28.7 - - + -
497B THR* 5.6 0.9 - - - +
506B ILE* 2.9 33.3 + - + +
507B ARG* 3.8 4.5 - - - +
509B LEU* 1.3 76.1 - - + +
511B LEU* 1.3 63.5 + - - +
513B PHE* 3.3 11.7 + - + +
514B PHE* 3.0 44.3 + - + -
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Residues in contact with LEU 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU* 6.1 0.2 - - - +
16A GLU* 5.8 5.6 - - + -
17A LEU* 4.3 28.7 - - + +
495B ILE* 4.3 20.4 - - + -
507B ARG* 2.9 39.2 + - + +
508B THR* 3.8 7.0 - - - +
509B LEU 3.3 0.2 - - - -
510B LEU* 1.3 76.4 - - - +
512B THR* 1.3 57.2 + - - +
514B PHE* 3.3 8.5 + - + +
515B TYR* 2.9 28.6 + - - +
527B VAL* 4.5 12.6 - - + -
529B ILE* 4.5 14.6 - - + -
765B VAL* 5.6 11.0 - - + -
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Residues in contact with THR 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.5 8.2 - - - +
452B ASN* 5.0 11.2 - - - +
453B VAL* 4.9 10.4 - - + +
454B GLU* 4.8 6.6 + - - +
508B THR* 3.0 18.4 + - - +
509B LEU* 3.0 21.1 - - - +
511B LEU* 1.3 74.2 - - - +
513B PHE* 1.3 65.3 + - - +
515B TYR* 4.4 5.6 - - - -
516B ARG* 2.9 33.8 + - - +
774B ASP* 4.0 24.5 + - - +
777B PHE* 5.1 16.9 - - + -
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Residues in contact with PHE 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B ILE* 5.6 11.2 - - + -
451B LEU 5.5 4.0 - - - +
453B VAL* 3.5 28.0 - - + -
467B VAL* 4.8 20.6 - - + -
468B ALA* 5.8 7.2 - - + -
509B LEU 3.0 14.6 + - - +
510B LEU* 3.4 19.1 - - + +
511B LEU 3.2 0.2 - - - -
512B THR* 1.3 77.8 - - - +
514B PHE* 1.3 80.9 + + - +
516B ARG 3.3 0.3 + - - -
517B GLN* 2.9 55.9 + - + +
518B MET* 5.7 5.4 - - + -
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Residues in contact with PHE 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B LEU* 4.5 18.8 - - + -
467B VAL* 4.9 14.1 - - + -
471B ILE* 4.8 14.4 - - + -
493B ILE* 4.1 25.6 - - + -
495B ILE* 4.3 22.7 - - + -
510B LEU* 3.0 39.3 + - + -
511B LEU* 3.3 11.4 + - + +
513B PHE* 1.3 87.9 - + - +
515B TYR* 1.3 64.3 + - - +
517B GLN* 4.8 2.0 - - - -
518B MET* 2.9 46.7 + - + +
521B ILE* 4.8 9.2 - - + -
522B VAL* 4.3 14.6 - - + -
527B VAL* 5.0 8.5 - - + -
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Residues in contact with TYR 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLU* 5.4 15.5 - - + +
17A LEU* 6.5 0.2 - - + -
511B LEU 2.9 17.4 + - - +
512B THR* 3.8 6.7 - - - +
514B PHE* 1.3 77.9 - - - +
516B ARG* 1.3 78.9 + - - +
517B GLN 3.5 0.3 + - - -
518B MET 5.0 0.2 - - - -
519B PRO* 3.9 27.5 - - + +
522B VAL* 4.5 24.6 - - + +
767B VAL* 5.7 9.6 - - + -
769B ASP 4.5 12.8 + - - -
770B ALA* 4.9 7.6 - - - +
771B ILE 5.3 5.0 + - - -
774B ASP* 3.3 25.6 - - + +
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Residues in contact with ARG 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B VAL* 4.2 21.5 - - + +
454B GLU* 2.3 47.0 + - + +
512B THR* 2.9 29.7 + - - +
513B PHE 4.4 0.2 - - - +
515B TYR* 1.3 100.6 - - + +
517B GLN* 1.3 70.1 + - - +
519B PRO* 5.3 1.6 - - - -
774B ASP* 4.6 6.0 - - - +
775B GLN* 3.5 21.4 - - - +
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Residues in contact with GLN 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B VAL* 3.8 18.0 - - + +
474B LEU* 4.5 22.9 - - + +
513B PHE* 2.9 55.3 + - + +
514B PHE* 4.1 1.1 - - - +
516B ARG* 1.3 95.8 - - - +
518B MET* 1.3 74.3 + - + +
519B PRO* 3.5 9.1 - - - +
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Residues in contact with MET 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B VAL* 6.5 0.4 - - + -
468B ALA* 6.1 2.2 - - + -
471B ILE* 4.5 28.7 - - + -
472B THR* 4.2 18.6 - - - -
474B LEU* 4.8 19.3 - - + -
484B ASN* 4.1 31.0 - - - +
513B PHE* 5.7 5.6 - - + -
514B PHE* 2.9 33.4 + - + +
517B GLN* 1.3 86.3 - - + +
519B PRO* 1.3 66.0 - - - +
520B GLU 3.2 1.8 - - - +
521B ILE* 3.2 37.1 - - + +
522B VAL* 3.8 4.2 - - - +
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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
------------------------------------------------------------
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