Contacts of the helix formed by residues 455 - 479 (chain I) in PDB entry 6PST
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 SER 455 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I ILE* 4.8 6.3 - - - -
31I GLN* 4.7 3.8 - - - -
34I SER* 2.8 29.4 + - - -
145I ILE* 5.2 0.2 - - - -
146I VAL 5.1 0.2 - - - -
147I SER* 4.3 15.0 - - - +
453I ILE* 5.0 2.6 + - - +
454I ARG* 1.3 77.8 - - - +
456I VAL* 1.3 70.9 + - - +
457I GLY 3.3 1.1 - - - -
458I GLU* 3.5 6.2 + - - +
459I MET* 2.9 35.3 + - - +
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Residues in contact with VAL 456 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I GLN* 3.6 33.7 - - - +
34I SER* 4.7 0.4 - - - +
35I PHE* 4.1 7.4 - - + -
130I MET* 3.7 20.4 - - + -
136I PHE* 3.3 28.5 - - + -
145I ILE* 3.3 33.9 - - + +
455I SER* 1.3 74.6 - - - +
457I GLY* 1.3 64.8 + - - +
459I MET* 4.9 1.6 - - - -
460I ALA* 2.9 30.0 + - - +
505I PHE* 5.2 1.6 - - + -
506I PHE* 4.1 10.1 - - + -
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Residues in contact with GLY 457 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I SER* 3.0 33.3 + - - -
35I PHE* 4.4 1.1 - - - +
38I PHE* 3.6 22.6 - - - -
456I VAL* 1.3 78.3 - - - +
458I GLU* 1.3 56.2 + - - +
461I GLU* 2.9 32.2 + - - +
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Residues in contact with GLU 458 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I SER* 4.2 2.4 + - - +
452I ARG* 2.4 39.0 + - - -
453I ILE 4.3 6.9 - - - +
454I ARG* 3.8 23.8 + - + +
455I SER* 3.5 10.2 + - - +
456I VAL 3.3 0.2 - - - -
457I GLY* 1.3 72.8 - - - +
459I MET* 1.3 61.3 + - - +
461I GLU* 3.3 13.7 + - - +
462I ASN* 2.7 48.4 + - - +
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Residues in contact with MET 459 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145I ILE* 4.1 6.1 - - + -
146I VAL 3.0 28.9 - - - +
148I GLN* 3.9 25.8 - - + +
454I ARG* 4.0 18.2 - - + +
455I SER* 2.9 27.9 + - - +
456I VAL 4.3 0.9 - - - +
458I GLU* 1.3 75.7 - - - +
460I ALA* 1.3 61.9 + - - +
462I ASN* 3.2 11.6 + - - +
463I GLN* 3.0 29.8 + - - +
505I PHE* 3.7 24.7 - - + -
511I LEU* 3.3 30.5 - - + -
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Residues in contact with ALA 460 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I PHE* 5.3 0.4 - - + -
38I PHE* 3.9 22.6 - - + -
456I VAL 2.9 20.7 + - - +
457I GLY 4.1 0.2 - - - +
459I MET* 1.3 75.2 - - - +
461I GLU* 1.3 61.1 + - - +
463I GLN* 3.2 7.2 + - - +
464I PHE* 2.9 28.8 + - - +
502I VAL* 4.4 4.2 - - + +
505I PHE* 4.3 6.6 - - + -
506I PHE* 3.8 32.1 - - + -
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Residues in contact with GLU 461 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I PHE* 3.7 17.4 - - + -
46I GLN 5.5 0.5 - - - +
47I TYR* 5.3 1.0 - - - -
48I GLY* 3.6 37.1 + - - +
51I ALA* 3.9 5.9 - - - +
52I ALA* 4.7 3.8 - - + +
457I GLY 2.9 19.8 + - - +
458I GLU* 3.6 20.2 - - - +
460I ALA* 1.3 75.6 - - - +
462I ASN* 1.3 58.8 + - - +
464I PHE* 3.2 3.5 + - - +
465I ARG* 2.3 69.1 + - - +
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Residues in contact with ASN 462 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179I TYR* 5.6 4.4 + - - -
454I ARG* 4.8 17.2 - - - +
458I GLU* 2.7 34.7 + - - +
459I MET* 3.2 10.5 + - - +
461I GLU* 1.3 77.7 - - - +
463I GLN* 1.3 70.3 + - - +
465I ARG* 3.1 24.3 + - - +
466I VAL* 3.0 26.1 + - + +
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Residues in contact with GLN 463 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459I MET* 3.0 17.4 + - - +
460I ALA 3.2 6.5 + - - +
462I ASN* 1.3 82.0 - - - +
464I PHE* 1.3 61.6 + - - +
466I VAL* 3.2 14.7 + - - +
467I GLY* 3.0 19.1 + - - -
498I ILE 5.1 0.5 - - - +
501I ALA* 3.8 31.4 + - + +
502I VAL* 4.2 15.0 - - + -
505I PHE* 3.8 35.3 - - + +
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Residues in contact with PHE 464 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I PHE* 4.8 5.4 - + + -
49I LEU* 3.7 22.7 - - + -
52I ALA* 3.9 16.4 - - + -
53I PHE* 3.4 37.2 - + - -
96I LEU* 3.4 30.1 - - + -
124I MET* 4.4 4.7 - - - -
127I ILE* 5.5 5.4 - - + -
460I ALA 2.9 16.7 + - - +
461I GLU* 3.6 8.1 - - - +
463I GLN* 1.3 77.3 - - - +
465I ARG* 1.3 57.6 + - - +
467I GLY* 3.3 1.7 + - - +
468I LEU* 2.9 36.2 + - + +
498I ILE* 3.4 28.9 - - + -
502I VAL* 4.4 15.9 - - + +
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Residues in contact with ARG 465 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I ALA* 4.1 13.1 - - - +
52I ALA* 3.5 24.2 - - + +
55I SER* 3.7 25.2 + - - +
56I VAL* 5.1 0.2 - - - +
179I TYR* 5.4 6.4 + - - -
461I GLU* 2.3 51.0 + - - +
462I ASN* 3.1 26.5 + - - +
464I PHE* 1.3 74.4 - - - +
466I VAL* 1.3 66.7 + - + +
468I LEU* 3.1 7.3 + - - +
469I VAL* 2.9 31.3 + - + +
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Residues in contact with VAL 466 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462I ASN* 3.0 17.1 + - + +
463I GLN* 3.2 18.6 + - - +
465I ARG* 1.3 75.9 - - + +
467I GLY* 1.3 64.5 + - - +
469I VAL* 3.0 29.7 - - + +
470I ARG* 3.1 19.6 + - - +
501I ALA* 4.5 12.6 - - + -
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Residues in contact with GLY 467 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463I GLN 3.0 13.7 + - - -
464I PHE 3.3 3.8 + - - -
466I VAL* 1.3 77.9 - - - +
468I LEU* 1.3 61.0 + - - +
470I ARG* 3.2 7.8 + - - +
471I VAL* 2.9 28.1 + - - +
497I PRO 4.1 17.0 - - - -
498I ILE* 4.0 17.1 - - - +
501I ALA* 4.7 3.1 - - - +
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Residues in contact with LEU 468 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52I ALA 3.7 11.9 - - - +
53I PHE* 3.5 32.1 - - + -
56I VAL* 3.4 44.3 - - + +
57I PHE* 4.1 2.9 - - + -
124I MET* 4.9 5.6 - - + -
464I PHE* 2.9 32.7 + - + +
465I ARG* 3.1 8.9 + - + +
467I GLY* 1.3 76.3 - - - +
469I VAL* 1.3 62.8 + - - +
471I VAL* 3.1 17.0 + - + +
472I GLU 2.9 22.7 + - - -
498I ILE* 4.0 19.3 - - + -
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Residues in contact with VAL 469 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I VAL* 4.2 9.9 - - + -
465I ARG* 2.9 18.3 + - + +
466I VAL* 3.0 24.9 - - + +
468I LEU* 1.3 75.1 - - - +
470I ARG* 1.3 65.1 + - + +
472I GLU* 3.0 20.9 + - - +
473I ARG* 3.1 26.5 + - - +
33P A 5.0 7.4 - - - +
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Residues in contact with ARG 470 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466I VAL* 3.1 20.3 + - - +
467I GLY* 3.2 11.2 + - - +
469I VAL* 1.3 85.7 - - + +
471I VAL* 1.3 60.2 + - - +
473I ARG* 3.6 17.2 + - - +
474I ALA* 3.8 5.0 + - - +
497I PRO* 3.3 40.2 + - + -
500I ALA* 6.3 0.4 - - - +
501I ALA* 6.4 0.4 - - - +
33P A 3.3 59.8 + - - +
34P T 3.6 23.7 + - + +
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Residues in contact with VAL 471 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I VAL* 5.2 0.9 - - + -
57I PHE* 5.0 6.7 - - + -
59I ILE* 4.6 7.9 - - + -
124I MET* 5.2 2.7 - - + -
467I GLY 2.9 7.8 + - - +
468I LEU* 3.1 19.3 + - + +
470I ARG* 1.3 75.7 - - - +
472I GLU* 1.3 69.1 + - - +
474I ALA* 3.3 4.5 + - - +
475I VAL* 3.0 34.0 + - + +
493I ILE* 4.5 15.9 - - + -
498I ILE* 3.2 32.8 - - + -
34P T 3.1 30.2 - - + +
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Residues in contact with GLU 472 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I SER 5.1 0.7 - - - +
56I VAL* 3.0 35.0 - - + +
59I ILE* 3.5 34.8 - - + +
468I LEU 2.9 12.3 + - - +
469I VAL* 3.0 13.8 + - - +
471I VAL* 1.3 76.2 - - - +
473I ARG* 1.3 64.2 + - - +
475I VAL* 4.1 0.2 - - - +
476I LYS* 2.9 53.3 + - - +
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Residues in contact with ARG 473 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469I VAL* 3.1 25.2 + - - +
470I ARG* 3.6 10.5 - - - +
471I VAL 3.2 0.2 - - - -
472I GLU* 1.3 78.7 - - - +
474I ALA* 1.3 62.7 + - - +
476I LYS* 3.8 5.1 - - - +
477I GLU* 3.1 23.9 + - - +
56O C 5.6 2.7 - - - +
32P A 3.6 36.2 + - - -
33P A 3.9 33.8 + - - -
34P T 5.5 2.9 - - - +
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Residues in contact with ALA 474 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470I ARG 3.8 2.8 + - - +
471I VAL 3.3 5.8 + - - +
473I ARG* 1.3 80.2 - - - +
475I VAL* 1.3 58.1 + - - +
477I GLU* 3.1 15.1 - - - +
478I ARG* 2.9 30.8 + - - +
492I MET 5.3 0.4 - - - -
34P T 3.1 62.5 - - + +
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Residues in contact with VAL 475 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59I ILE* 3.5 26.9 - - + -
68I LEU* 3.6 25.6 - - + -
471I VAL* 3.0 22.8 + - + +
472I GLU 4.1 0.2 - - - +
474I ALA* 1.3 73.4 - - + +
476I LYS* 1.3 67.3 + - - +
478I ARG* 3.4 4.7 + - - +
479I LEU* 2.9 50.9 + - + +
492I MET* 4.1 16.8 - - + +
493I ILE* 4.0 21.8 - - + -
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Residues in contact with LYS 476 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59I ILE* 3.5 18.6 - - + +
60I GLN* 4.3 17.3 - - - +
61I SER* 5.6 0.2 - - - +
62I TYR 4.8 3.7 + - - +
472I GLU* 2.9 47.3 + - - +
473I ARG* 3.8 4.5 - - - +
475I VAL* 1.3 77.9 - - - +
477I GLU* 1.3 63.1 + - - +
479I LEU* 3.2 8.7 + - - +
480I SER* 2.9 19.6 + - - -
56O C 3.9 26.6 + - - +
57O T 2.3 36.1 + - - +
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Residues in contact with GLU 477 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473I ARG* 3.1 10.7 + - - +
474I ALA* 3.1 31.6 - - - +
476I LYS* 1.3 77.1 - - - +
478I ARG* 1.3 59.8 + - + +
480I SER* 2.8 29.8 + - - -
481I LEU* 3.1 18.6 - - + +
55O C 4.3 21.5 + - - +
56O C 4.7 4.6 - - - -
32P A 5.7 5.2 - - - -
34P T 4.0 19.4 + - - +
35P G 4.4 10.0 - - - +
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Residues in contact with ARG 478 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474I ALA 2.9 19.8 + - - +
475I VAL* 4.0 3.1 - - - +
477I GLU* 1.3 79.3 - - + +
479I LEU* 1.3 58.2 + - - +
480I SER 3.1 0.2 - - - -
481I LEU* 2.5 48.1 + - - +
482I GLY* 4.6 1.2 - - - -
483I ASP* 4.0 4.5 + - - +
484I LEU* 3.8 21.4 - - - +
487I LEU* 3.3 41.5 - - + +
492I MET* 3.8 31.6 - - + +
34P T 5.9 2.0 - - - +
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Residues in contact with LEU 479 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59I ILE* 4.6 5.4 - - + -
60I GLN 4.8 0.2 - - - -
61I SER* 3.4 36.8 - - - +
62I TYR 4.0 0.3 + - - -
65I ASN* 3.8 1.9 + - - -
66I SER* 3.8 20.4 - - - +
68I LEU* 4.5 13.2 - - + +
102I LEU* 3.9 18.8 - - + -
475I VAL* 2.9 42.3 + - + +
476I LYS* 3.5 5.8 - - - +
478I ARG* 1.3 74.3 - - - +
480I SER* 1.3 56.4 + - - +
483I ASP* 2.7 34.9 - - + +
487I LEU* 5.6 3.1 - - + -
492I MET* 3.8 22.7 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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