Contacts of the helix formed by residues 536 - 559 (chain G) in PDB entry 7CR3
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 LEU 536 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360G TRP* 6.1 0.4 - - + -
364G GLU* 5.5 13.9 - - + +
535G GLY* 1.3 70.8 - - - +
537G LYS* 1.3 80.2 + - + +
539G SER* 3.5 8.1 - - - -
540G ILE* 3.0 40.0 + - + +
19H LEU* 5.3 1.3 - - - +
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Residues in contact with LYS 537 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360G TRP* 3.2 48.9 - - + -
535G GLY 4.9 5.8 - - - +
536G LEU* 1.3 89.9 - - + +
538G VAL* 1.3 58.5 + - - +
540G ILE* 3.8 2.1 - - - +
541G ARG* 2.9 61.9 + - - +
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Residues in contact with VAL 538 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535G GLY* 3.2 12.5 - - - +
537G LYS* 1.3 76.3 - - - +
539G SER* 1.3 63.5 + - - +
541G ARG* 3.6 13.9 - - - +
542G ALA* 2.8 29.5 + - - +
12H GLU* 3.1 41.1 - - - +
13H PHE* 3.6 28.0 - - + -
15H GLU* 5.4 0.4 - - - +
16H ALA* 3.6 27.7 - - + +
69H PHE* 4.9 2.2 - - + -
73H MET* 4.2 10.3 - - + -
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Residues in contact with SER 539 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535G GLY 2.4 29.6 + - - -
536G LEU* 3.5 9.7 - - - -
537G LYS 3.2 0.2 - - - -
538G VAL* 1.3 79.6 - - - +
540G ILE* 1.3 65.4 + - - +
542G ALA* 3.9 1.7 - - - +
543G VAL* 3.1 24.8 + - - +
16H ALA* 5.6 2.0 - - - -
19H LEU* 3.4 23.0 - - - +
20H PHE* 4.3 16.4 - - - -
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Residues in contact with ILE 540 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349G THR* 4.4 8.5 - - + -
360G TRP* 5.5 10.3 - - + +
363G TYR* 3.6 56.1 - - + +
364G GLU* 5.0 1.6 - - - +
536G LEU* 3.0 27.4 + - + +
537G LYS* 4.0 2.9 - - - +
539G SER* 1.3 77.0 - - - +
541G ARG* 1.3 57.6 + - - +
543G VAL* 3.2 11.9 - - + +
544G CYS* 2.9 33.3 + - + +
547G ARG* 5.3 2.0 - - - +
40H LEU* 3.8 24.2 - - + -
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Residues in contact with ARG 541 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349G THR* 2.3 52.0 + - - +
350G ASN* 4.3 1.5 - - - +
351G LEU* 3.4 39.1 - - - +
360G TRP* 3.3 20.7 - - + -
537G LYS* 2.9 55.0 + - - +
538G VAL* 3.5 16.3 - - - +
539G SER 3.1 0.2 - - - -
540G ILE* 1.3 77.4 - - - +
542G ALA* 1.3 57.4 + - - +
544G CYS* 3.1 3.2 + - - +
545G VAL* 2.8 36.8 + - + +
9H GLN* 5.7 4.0 - - - +
12H GLU* 6.3 0.4 - - - -
73H MET* 4.3 13.2 - - + -
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Residues in contact with ALA 542 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538G VAL 2.8 20.6 + - - +
539G SER 3.9 0.2 - - - +
541G ARG* 1.3 72.2 - - - +
543G VAL* 1.3 63.0 + - - +
545G VAL* 3.1 4.0 + - - +
546G MET* 3.0 32.0 + - + +
20H PHE* 3.7 17.7 - - + -
69H PHE* 3.5 33.7 - - + -
72H MET* 3.7 0.4 - - - +
73H MET* 3.7 15.2 - - - -
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Residues in contact with VAL 543 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539G SER 3.1 13.4 + - - +
540G ILE* 3.2 21.5 - - + +
542G ALA* 1.3 77.6 - - - +
544G CYS* 1.3 60.5 + - - +
546G MET* 3.5 13.1 + - + +
547G ARG* 2.9 49.8 + - - +
20H PHE* 4.2 8.0 - - + -
33H LEU* 5.6 1.1 - - + +
36H VAL* 5.3 9.2 - - + -
37H MET* 4.1 32.8 - - + -
40H LEU* 5.4 3.6 - - + -
52H MET* 4.4 11.7 - - + -
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Residues in contact with CYS 544 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342G SER* 3.7 2.4 + - - -
345G ARG* 3.3 48.7 - - - -
346G PHE* 3.4 14.4 - - - -
349G THR* 3.6 9.6 - - + +
540G ILE* 2.9 20.6 + - + +
541G ARG 3.5 4.3 - - - +
543G VAL* 1.3 75.6 - - - +
545G VAL* 1.3 61.1 + - - +
547G ARG* 3.1 23.6 + - - +
548G PHE* 2.8 26.0 + - - +
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Residues in contact with VAL 545 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346G PHE* 3.7 33.9 - - + -
349G THR* 5.8 0.2 - - - +
541G ARG* 2.8 23.3 + - + +
542G ALA 3.6 6.3 - - - +
544G CYS* 1.3 74.6 - - + +
546G MET* 1.3 57.5 + - - +
548G PHE* 3.2 10.2 + - + +
549G LEU* 2.9 34.8 + - + +
72H MET* 3.6 41.1 - - + +
73H MET* 4.2 13.7 - - + -
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Residues in contact with MET 546 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542G ALA* 3.0 39.5 + - + +
543G VAL* 3.6 6.3 - - - +
545G VAL* 1.3 75.9 - - - +
547G ARG* 1.3 56.6 + - - +
549G LEU* 3.2 6.3 + - - +
550G VAL* 3.0 30.7 + - - +
20H PHE* 3.8 26.0 - - + -
33H LEU* 4.5 5.8 - - - -
52H MET* 3.4 39.1 - - + +
55H GLU* 4.4 1.0 - - + +
56H VAL* 3.5 30.5 - - + -
64H ILE* 4.2 17.3 - - + -
69H PHE* 4.9 4.5 - - + -
72H MET* 3.6 17.9 - - + -
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Residues in contact with ARG 547 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342G SER* 3.5 8.1 + - - +
345G ARG* 3.0 40.3 - - - +
363G TYR* 3.7 18.3 + - - -
540G ILE* 4.9 2.4 + - - +
543G VAL* 2.9 51.7 + - + +
544G CYS* 3.1 32.4 + - - +
546G MET* 1.3 75.7 - - - +
548G PHE* 1.3 59.0 + - - +
550G VAL* 3.1 11.5 - - + +
551G SER* 3.0 28.1 + - - -
37H MET* 4.2 22.2 - - - +
40H LEU* 5.2 3.4 - - - +
52H MET* 3.9 15.3 - - + -
115H GLU* 5.2 5.8 - - - -
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Residues in contact with PHE 548 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339G LEU* 3.4 30.1 - - + -
342G SER* 3.1 22.1 + - - +
343G ALA* 3.5 30.1 - - + -
346G PHE* 4.3 26.0 - + + -
544G CYS 2.8 17.2 + - - +
545G VAL* 3.7 9.6 - - + +
547G ARG* 1.3 69.9 - - - +
549G LEU* 1.3 63.4 + - + +
551G SER* 3.3 2.8 + - - -
552G LYS* 2.8 61.2 + - + +
77H MET* 4.9 10.5 - - + -
80H THR* 5.7 5.8 - - + -
82H SER* 5.7 8.3 - - - -
86H ILE* 5.9 2.5 - - + -
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Residues in contact with LEU 549 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545G VAL* 2.9 23.5 + - + +
546G MET* 3.2 2.0 + - - +
548G PHE* 1.3 76.9 - - + +
550G VAL* 1.3 60.4 + - - +
552G LYS* 3.2 32.0 + - + +
553G ARG* 3.0 24.9 + - - +
55H GLU* 3.0 51.4 - - + +
72H MET* 3.6 34.5 - - + -
80H THR* 6.3 0.4 - - + -
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Residues in contact with VAL 550 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546G MET 3.0 10.6 + - - +
547G ARG* 3.1 27.6 - - + +
549G LEU* 1.3 75.7 - - - +
551G SER* 1.3 56.5 + - - +
553G ARG* 4.1 0.6 - - - +
554G LYS* 2.8 39.9 + - + +
48H GLU 4.5 0.9 - - - +
51H ASP* 3.5 16.4 - - + -
52H MET* 3.5 43.7 - - + +
55H GLU* 3.5 19.5 - - + +
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Residues in contact with SER 551 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335G PRO* 4.6 2.3 + - - +
338G GLY* 3.2 26.0 + - - -
339G LEU* 3.2 18.1 + - - +
342G SER* 4.3 4.3 - - - -
547G ARG 3.0 20.1 + - - -
548G PHE* 3.5 10.3 - - - -
549G LEU 3.2 0.2 - - - -
550G VAL* 1.3 78.3 - - - +
552G LYS* 1.3 57.5 + - - +
554G LYS* 3.8 5.3 - - - +
555G PHE* 2.9 29.6 + - - +
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Residues in contact with LYS 552 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339G LEU* 3.5 22.9 - - + -
548G PHE* 2.8 55.3 + - + +
549G LEU* 3.2 28.3 + - + +
551G SER* 1.3 71.9 - - - +
553G ARG* 1.3 59.7 + - + +
555G PHE* 3.4 1.2 + - - +
556G LYS* 2.9 20.0 + - - +
80H THR* 4.2 27.5 + - - +
82H SER* 4.9 8.5 - - - -
85H GLU* 2.9 37.1 - - - +
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Residues in contact with ARG 553 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549G LEU 3.0 7.3 + - - +
550G VAL* 4.1 1.6 - - - +
552G LYS* 1.3 77.1 - - + +
554G LYS* 1.3 60.1 + - + +
556G LYS* 3.1 10.2 + - + +
557G GLU* 2.9 43.6 + - - +
54H ASN* 2.6 46.4 + - - +
55H GLU* 2.7 47.1 + - - +
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Residues in contact with LYS 554 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335G PRO* 4.2 14.8 - - + +
550G VAL* 2.8 26.4 + - + +
551G SER* 3.9 5.4 - - - +
553G ARG* 1.3 75.8 - - + +
555G PHE* 1.3 61.9 + - - +
557G GLU* 3.2 29.9 + - - +
558G SER* 3.0 26.4 + - - -
51H ASP* 6.0 7.2 - - - +
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Residues in contact with PHE 555 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332G ARG* 4.4 10.3 - - + -
335G PRO* 3.6 19.2 - - + +
336G ALA* 3.6 39.3 - - + -
339G LEU* 4.0 11.9 - - + -
551G SER 2.9 18.5 + - - +
552G LYS 3.5 3.4 - - - +
554G LYS* 1.3 76.7 - - - +
556G LYS* 1.3 56.0 + - - +
558G SER 3.7 0.5 - - - -
559G LEU* 2.9 70.7 + - + +
85H GLU* 3.3 39.9 - - + -
88H GLU* 4.1 3.6 - - + -
89H ALA* 3.5 27.4 - - + -
92H VAL* 5.2 0.2 - - + -
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Residues in contact with LYS 556 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552G LYS 2.9 12.4 + - - +
553G ARG* 3.1 13.0 + - + +
555G PHE* 1.3 74.6 - - - +
557G GLU* 1.3 65.3 + - + +
559G LEU* 3.3 16.5 - - + +
560G ARG* 2.4 50.3 + - - +
81H ASP 6.0 0.7 - - - -
84H GLU* 4.4 13.9 + - - +
85H GLU* 3.2 48.2 - - - +
88H GLU* 4.7 3.4 + - - -
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Residues in contact with GLU 557 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553G ARG* 2.9 35.8 + - - +
554G LYS* 3.2 33.0 + - - +
556G LYS* 1.3 79.9 - - + +
558G SER* 1.3 58.2 + - - +
559G LEU 3.1 4.4 + - - -
560G ARG* 3.5 15.3 + - - +
51H ASP* 5.1 6.2 - - - +
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Residues in contact with SER 558 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331G LYS 4.2 4.0 + - - -
332G ARG* 3.4 30.2 - - - +
335G PRO* 3.5 26.2 - - - +
554G LYS* 3.0 11.3 + - - -
555G PHE 3.7 1.6 - - - -
557G GLU* 1.3 72.6 - - - +
559G LEU* 1.3 59.6 + - - +
560G ARG 3.1 7.5 + - - -
561G PRO* 3.3 17.0 - - - +
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Residues in contact with LEU 559 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326G GLN* 5.5 0.3 + - - -
332G ARG* 2.4 57.7 + - - +
555G PHE* 2.9 50.9 + - + +
556G LYS* 3.3 24.0 - - + +
557G GLU 3.1 1.0 - - - -
558G SER* 1.3 77.4 - - - +
560G ARG* 1.3 88.8 + - - +
561G PRO* 3.4 2.2 - - - -
88H GLU* 4.0 30.1 - - + +
91H ARG* 5.3 0.9 - - - +
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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