Contacts of the helix formed by residues 453 - 473 (chain B) in PDB entry 4RUH
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 ARG 453 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B GLN* 2.2 45.7 + - - +
16B ASP* 3.0 26.9 + - - -
19B ILE* 4.2 26.0 - - + +
120B GLU* 3.0 33.4 + - - +
123B GLY* 2.8 28.5 + - - +
125B LEU* 4.3 11.1 - - + +
451B LEU 3.6 1.2 + - - -
452B ASN* 1.3 71.8 - - - +
454B TYR* 1.3 63.6 + - - +
456B TYR* 4.0 0.6 - - - +
457B ILE* 3.0 35.0 + - + +
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Residues in contact with TYR 454 (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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198B TRP* 4.5 10.5 - + - -
404B VAL 5.2 1.4 + - - -
405B PHE* 3.4 40.3 + + - -
452B ASN* 4.0 4.2 - - + +
453B ARG* 1.3 78.8 - - - +
455B ASN* 1.3 73.3 + - - +
457B ILE* 4.9 2.0 - - - -
458B GLU* 2.8 55.8 + - + +
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Residues in contact with ASN 455 (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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198B TRP* 3.8 27.8 - - - -
405B PHE* 5.4 3.4 - - - -
437B VAL* 2.9 32.8 + - - +
438B GLY 3.9 2.0 - - - -
439B SER* 3.2 21.0 + - - -
451B LEU* 4.0 10.1 - - + -
452B ASN* 3.1 29.7 + - + +
453B ARG 3.4 0.2 - - - -
454B TYR* 1.3 87.5 - - - +
456B TYR* 1.3 60.3 + - - +
458B GLU* 4.9 0.9 - - - -
459B GLY* 2.8 31.0 + - - +
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Residues in contact with TYR 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TYR* 2.7 39.8 + + + -
19B ILE* 3.5 33.0 - - + -
21B LYS* 4.7 0.2 - - - +
22B LEU* 3.9 15.9 + - + +
125B LEU* 3.9 8.3 - - + -
135B GLY* 3.5 27.8 - - - -
138B ALA* 3.9 7.0 - - + +
139B GLY* 4.4 10.1 - - - -
142B ASN* 3.4 16.3 + - - -
437B VAL* 4.3 4.7 - - + +
451B LEU* 3.6 28.9 - - + +
452B ASN 2.9 19.2 + - - +
453B ARG 4.0 1.8 - - - +
455B ASN* 1.3 78.0 - - - +
457B ILE* 1.3 65.4 + - + +
459B GLY* 4.3 0.3 - - - -
460B THR* 2.9 27.9 + - - -
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Residues in contact with ILE 457 (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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11B ILE* 3.9 10.9 - - + +
12B ASP* 4.0 16.6 - - - +
15B GLN* 3.6 54.5 - - + +
18B TYR* 4.4 11.7 - - + -
19B ILE* 4.3 2.2 - - + -
453B ARG* 3.0 25.6 + - + +
454B TYR* 4.0 2.5 - - - +
456B TYR* 1.3 92.7 - - + +
458B GLU* 1.3 82.2 + - + +
460B THR* 3.3 18.9 + - - +
461B LYS* 3.6 6.9 + - - +
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Residues in contact with GLU 458 (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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404B VAL* 3.6 33.8 - - + +
405B PHE* 4.0 13.2 - - + -
454B TYR* 2.8 52.0 + - + +
455B ASN 4.5 0.2 - - - +
457B ILE* 1.3 79.6 - - + +
459B GLY* 1.3 56.0 + - - +
461B LYS* 2.4 62.3 + - - +
462B MET 2.9 10.7 + - - -
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Residues in contact with GLY 459 (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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405B PHE* 4.6 6.0 - - - -
437B VAL* 4.5 15.3 - - - -
455B ASN* 2.8 25.0 + - - +
456B TYR 4.3 0.4 - - - -
458B GLU* 1.3 73.6 - - - +
460B THR* 1.3 56.0 + - - +
462B MET* 3.1 12.6 + - - +
463B LEU* 2.8 39.7 + - - +
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Residues in contact with THR 460 (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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11B ILE* 3.7 24.5 - - + -
18B TYR* 4.9 4.4 - - + -
139B GLY* 3.5 34.8 - - - +
142B ASN* 4.0 13.0 + - + +
143B ALA* 3.6 16.5 - - + +
456B TYR* 2.9 20.3 + - - -
457B ILE* 3.3 11.2 + - - +
458B GLU 3.1 0.6 - - - -
459B GLY* 1.3 75.1 - - - +
461B LYS* 1.3 53.9 + - - +
463B LEU* 3.4 5.3 + - - -
464B ALA* 2.7 35.5 + - - +
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Residues in contact with LYS 461 (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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8B PHE* 3.6 47.5 - - + +
11B ILE* 3.6 31.9 - - + -
12B ASP* 2.6 41.4 + - - -
404B VAL* 3.6 7.6 - - + -
457B ILE* 3.9 5.6 - - - +
458B GLU* 2.4 50.5 + - - +
460B THR* 1.3 77.4 - - - +
462B MET* 1.3 49.7 + - - +
464B ALA* 3.2 3.1 + - - +
465B ALA* 2.7 35.5 + - - +
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Residues in contact with MET 462 (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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400B ALA* 3.6 19.6 - - - +
401B MET* 3.5 46.0 - - + +
404B VAL* 3.4 17.4 - - + +
405B PHE* 4.4 6.7 - - + -
435B LEU* 3.7 28.3 - - + +
436B PRO 3.6 15.3 - - - +
437B VAL* 4.4 4.5 - - + -
458B GLU 2.9 11.5 + - - +
459B GLY* 3.4 13.9 - - - +
461B LYS* 1.3 75.8 - - - +
463B LEU* 1.3 72.3 + - + +
465B ALA* 3.0 4.2 + - - +
466B TYR* 2.7 32.9 + - - +
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Residues in contact with LEU 463 (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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136B PRO 3.7 23.3 - - - +
139B GLY* 3.9 7.4 - - - -
140B TRP* 3.8 53.5 - - + +
143B ALA* 4.5 4.0 - - + -
194B SER* 4.1 12.6 - - - +
435B LEU* 4.4 5.8 - - + -
437B VAL* 4.1 11.9 - - + -
459B GLY 2.8 24.1 + - - +
460B THR* 3.9 3.4 - - - +
462B MET* 1.3 95.0 - - + +
464B ALA* 1.3 61.7 + - - +
466B TYR* 3.4 6.5 + - - +
467B LEU* 3.1 30.7 + - - +
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Residues in contact with ALA 464 (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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7B LEU* 4.1 21.8 - - + -
8B PHE* 4.7 1.8 - - + -
11B ILE* 4.4 8.3 - - + -
143B ALA* 3.8 18.5 - - + +
147B TYR* 2.6 35.1 + - + -
460B THR 2.7 22.7 + - - +
461B LYS* 3.4 10.5 - - - +
463B LEU* 1.3 74.7 - - - +
465B ALA* 1.3 58.5 + - - +
467B LEU* 3.6 1.4 + - - -
468B TYR 3.5 4.3 + - - -
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Residues in contact with ALA 465 (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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4B LEU* 5.0 7.9 - - + -
8B PHE* 4.3 16.3 - - + -
400B ALA* 3.7 21.8 - - + +
403B THR* 4.8 8.1 - - + -
404B VAL* 4.5 0.7 - - + -
461B LYS 2.7 19.7 + - - +
462B MET* 3.4 6.1 - - - +
464B ALA* 1.3 71.1 - - - +
466B TYR* 1.3 56.6 + - - +
468B TYR* 3.2 8.7 + - + +
469B GLU* 2.8 40.5 + - + +
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Residues in contact with TYR 466 (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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94B VAL* 3.9 15.6 - - + +
140B TRP* 3.5 20.9 - + - -
190B TYR* 4.0 0.5 - - - +
192B CYS* 3.4 25.6 - - + +
393B HIS* 2.3 43.6 + + - -
396B ALA* 4.6 1.8 - - + -
397B GLY* 4.5 9.4 - - - -
400B ALA* 3.4 11.8 - - + +
433B MET* 3.4 15.5 - - + -
435B LEU* 3.7 23.6 - - + -
462B MET 2.7 16.2 + - - +
463B LEU 3.5 9.2 - - - +
464B ALA 3.4 0.2 - - - -
465B ALA* 1.3 73.5 - - - +
467B LEU* 1.3 66.3 + - + +
469B GLU* 3.1 3.8 + - - +
470B VAL* 2.8 61.3 + - + +
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Residues in contact with LEU 467 (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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94B VAL* 5.0 4.7 - - + -
96B ILE* 4.9 6.5 - - + -
140B TRP* 3.6 27.6 - - + -
143B ALA* 4.8 4.9 - - + -
144B LEU* 3.6 29.8 - - + -
147B TYR* 4.2 17.7 - - + +
154B ILE* 5.2 1.1 - - + -
155B PRO* 3.9 8.9 - - + +
156B VAL* 3.8 30.1 - - + +
158B VAL* 5.1 1.6 - - + -
463B LEU 3.1 16.6 - - - +
464B ALA* 3.7 7.9 - - - +
465B ALA 3.2 0.4 - - - -
466B TYR* 1.3 89.2 - - + +
468B TYR* 1.3 62.3 + - - +
470B VAL* 3.3 7.0 + - - +
471B SER* 3.2 17.7 + - - -
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Residues in contact with TYR 468 (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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4B LEU* 4.1 29.4 - - + -
147B TYR* 3.2 22.5 + + - +
155B PRO* 3.7 15.2 - - + +
464B ALA 4.1 0.9 - - - +
465B ALA* 3.2 7.4 + - + +
467B LEU* 1.3 77.7 - - - +
469B GLU* 1.3 84.2 + - + +
471B SER* 2.6 26.8 + - - -
472B GLN* 3.0 41.4 + - + +
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Residues in contact with GLU 469 (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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396B ALA* 3.5 27.4 - - - +
399B ARG* 3.6 41.9 + - + +
400B ALA* 4.0 8.1 - - - +
403B THR* 4.3 10.4 + - - -
465B ALA* 2.8 26.2 + - + +
466B TYR 3.6 1.6 - - - +
468B TYR* 1.3 88.8 - - + +
470B VAL* 1.3 61.5 + - - +
472B GLN* 3.3 11.9 + - - +
473B LEU* 3.0 22.5 + - - +
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Residues in contact with VAL 470 (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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92B LYS* 3.8 14.1 + - + +
94B VAL* 3.9 6.7 - - + -
156B VAL* 3.8 17.0 - - + -
190B TYR* 3.8 31.2 - - + -
393B HIS* 4.7 3.4 - - + -
396B ALA* 4.0 11.2 - - + +
466B TYR* 2.8 62.8 + - + +
467B LEU* 3.4 7.9 - - - +
469B GLU* 1.3 72.3 - - - +
471B SER* 1.3 58.0 + - - +
473B LEU* 3.0 25.2 + - + +
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Residues in contact with SER 471 (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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92B LYS* 3.9 16.4 + - - +
155B PRO* 3.3 44.8 - - - +
156B VAL* 4.0 4.5 - - - +
467B LEU 3.2 3.4 + - - -
468B TYR* 2.6 20.3 + - - -
470B VAL* 1.3 79.4 - - - +
472B GLN* 1.3 77.3 + - - +
473B LEU 4.3 0.2 - - - +
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Residues in contact with GLN 472 (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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399B ARG* 5.1 5.8 + - - +
468B TYR* 3.0 52.1 + - + +
469B GLU* 3.3 12.5 + - - +
470B VAL 3.2 0.2 - - - -
471B SER* 1.3 99.7 + - - +
473B LEU* 1.3 64.6 + - - +
474B LYS* 3.4 3.8 + - - +
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Residues in contact with LEU 473 (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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92B LYS* 2.8 30.1 + - - -
190B TYR* 3.3 33.9 - - + +
392B PRO* 3.4 41.1 - - + +
393B HIS* 4.2 2.7 - - - +
395B LEU* 3.7 26.7 - - + -
396B ALA* 4.6 8.3 - - + +
399B ARG* 4.9 8.3 - - - +
469B GLU 3.0 11.4 + - - +
470B VAL* 3.0 15.8 + - - +
471B SER 4.3 0.2 - - - +
472B GLN* 1.3 77.0 - - - +
474B LYS* 1.3 62.2 + - - +
475B ASP 3.7 13.2 - - - +
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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