Contacts of the helix formed by residues 5017 - 5041 (chain f) in PDB entry 2AXT
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 THR5017 (chain f).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5007e GLU* 3.3 31.4 + - + +
5008e ARG* 5.5 4.0 - - + -
5014f PRO* 5.3 13.0 - - + +
5015f ILE 5.0 4.3 - - - +
5016f PHE* 1.3 74.9 - - - +
5018f VAL* 1.3 81.8 + - - +
5019f ARG* 3.1 13.8 + - + +
5020f TRP* 2.9 34.4 + - + +
5021f VAL* 3.2 11.3 + - - +
5051f HEM 4.2 8.7 - - - +
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Residues in contact with VAL5018 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5021d TRP* 5.3 5.2 - - + -
5026d ARG* 3.6 53.8 - - + +
5027d PHE 5.5 0.2 - - - +
5028d VAL* 5.3 5.2 - - + +
5030d VAL* 4.8 9.4 - - + -
5007e GLU* 5.2 1.6 - - - +
5017f THR* 1.3 82.1 + - - +
5019f ARG* 1.3 78.0 + - + +
5021f VAL* 2.9 31.0 + - + +
5022f ALA* 3.2 7.0 + - - +
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Residues in contact with ARG5019 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5484c UNK 5.3 0.9 - - + -
5027d PHE* 3.4 49.4 - - + -
5028d VAL* 5.0 7.4 - - + +
5006e GLY 5.5 0.2 + - - -
5007e GLU* 3.6 26.2 + - - +
5008e ARG* 2.7 35.1 + - - +
5009e PRO* 4.9 0.8 - - - +
5010e PHE* 3.0 37.3 - - - +
5017f THR* 3.1 5.1 + - - +
5018f VAL* 1.3 87.3 - - + +
5020f TRP* 1.3 54.1 + - - +
5022f ALA* 3.2 7.1 + - - +
5023f VAL* 2.8 43.5 + - + +
5051f HEM 2.7 38.6 + - - -
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Residues in contact with TRP5020 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5015f ILE 4.2 7.9 - - - +
5016f PHE* 3.8 36.1 - + + -
5017f THR* 2.9 28.1 + - + +
5019f ARG* 1.3 79.0 - - - +
5021f VAL* 1.3 78.6 + - + +
5023f VAL* 4.5 2.7 - - - -
5024f HIS* 3.0 65.3 + + + +
5051f HEM 3.0 81.4 - + + +
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Residues in contact with VAL5021 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5017f THR 3.6 13.5 - - - +
5018f VAL* 2.9 17.1 + - + +
5020f TRP* 1.3 94.8 - - + +
5022f ALA* 1.3 56.0 + - - +
5024f HIS* 4.0 2.6 - - - +
5025f THR* 2.7 43.7 + - + +
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Residues in contact with ALA5022 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5484c UNK 3.8 20.4 - - + -
5485c UNK 5.2 4.0 - - + -
5028d VAL* 5.4 7.0 - - + -
5018f VAL 3.2 6.3 + - - +
5019f ARG* 3.2 12.5 + - + +
5021f VAL* 1.3 75.3 - - - +
5023f VAL* 1.3 55.2 + - - +
5024f HIS 2.6 17.5 + - - -
5025f THR* 2.8 26.8 + - - -
5026f LEU* 3.5 7.0 + - - +
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Residues in contact with VAL5023 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5484c UNK 3.9 27.1 - - + +
5010e PHE* 3.9 20.6 - - + -
5019f ARG* 2.8 38.3 + - + +
5020f TRP* 4.1 6.5 - - - +
5022f ALA* 1.3 70.1 - - - +
5024f HIS* 1.3 60.8 + - - +
5026f LEU* 4.4 3.4 - - - +
5027f ALA* 3.0 24.5 + - + +
5051f HEM 4.3 32.3 - - + +
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Residues in contact with HIS5024 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5020f TRP* 3.0 52.3 + + + +
5021f VAL* 4.0 3.8 - - - +
5022f ALA 2.6 6.5 + - - -
5023f VAL* 1.3 79.8 + - - +
5025f THR* 1.3 59.8 + - + +
5026f LEU 3.0 2.5 - - - -
5027f ALA* 4.0 2.9 - - - -
5028f VAL* 2.8 45.9 + - + +
5051f HEM 2.3 92.0 + + + -
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Residues in contact with THR5025 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5042d TYR* 2.6 49.3 + - + +
5021f VAL* 2.7 34.7 + - + +
5022f ALA* 2.8 21.9 + - - -
5024f HIS* 1.3 76.2 - - - +
5026f LEU* 1.3 62.1 + - - +
5028f VAL* 5.3 0.4 - - - -
5029f PRO* 2.9 16.7 - - - +
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Residues in contact with LEU5026 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5564a PQ9 5.8 6.5 - - + -
5484c UNK 5.1 7.2 - - + -
5485c UNK 5.0 16.4 - - + -
5042d TYR* 3.3 35.2 - - + -
5045d LEU* 5.0 6.5 - - + -
5357d BCR 4.5 8.1 - - + +
5359d MGE 3.9 32.3 - - + -
5022f ALA 3.5 7.9 + - - +
5023f VAL* 4.9 2.5 - - - +
5024f HIS 3.0 0.2 - - - -
5025f THR* 1.3 85.2 - - - +
5027f ALA* 1.3 58.2 + - - +
5028f VAL 3.5 0.4 - - - -
5029f PRO* 3.7 1.5 - - - +
5030f THR* 2.6 36.2 + - - -
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Residues in contact with ALA5027 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5359d MGE 5.8 0.7 - - - -
5023f VAL* 3.0 21.8 + - + +
5024f HIS* 3.2 5.8 + - - +
5026f LEU* 1.3 78.2 - - - +
5028f VAL* 1.3 64.8 + - - +
5030f THR* 3.6 3.7 + - - -
5031f ILE* 3.3 30.7 + - - +
5051f HEM 3.3 42.6 - - + -
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Residues in contact with VAL5028 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5030e LEU* 3.4 34.2 - - + +
5024f HIS* 2.8 40.8 + - + +
5025f THR* 5.3 0.2 - - - -
5027f ALA* 1.3 71.7 - - - +
5029f PRO* 1.3 75.1 - - + +
5032f PHE* 3.1 20.2 + - + +
5051f HEM 4.2 26.5 - - + -
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Residues in contact with PRO5029 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5042d TYR* 3.7 9.4 - - - +
5357d BCR 3.5 32.8 - - + -
5025f THR* 2.9 32.5 - - - +
5026f LEU 3.7 1.6 - - - -
5028f VAL* 1.3 97.6 - - + +
5030f THR* 1.3 68.6 + - - +
5032f PHE* 3.0 9.2 + - + +
5033f PHE* 2.9 29.7 + - + -
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Residues in contact with THR5030 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5357d BCR 3.6 35.1 - - + +
5359d MGE 3.5 20.0 - - + +
5026f LEU 2.6 23.3 + - - -
5027f ALA* 3.7 5.8 - - - -
5028f VAL 3.3 0.2 - - - -
5029f PRO* 1.3 77.0 - - - +
5031f ILE* 1.3 61.6 + - + +
5033f PHE* 2.6 26.5 + - - +
5034f LEU* 2.7 37.9 + - + -
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Residues in contact with ILE5031 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5027e ILE* 3.5 39.5 - - + +
5030e LEU* 3.8 4.9 - - + -
5031e PHE* 3.7 21.9 - - + +
5027f ALA 3.3 18.2 + - - +
5028f VAL 4.0 2.7 - - - +
5030f THR* 1.3 80.9 - - + +
5032f PHE* 1.3 64.2 + - - +
5034f LEU* 3.7 20.3 - - + +
5035f GLY* 2.9 21.3 + - - -
5051f HEM 3.4 29.2 - - + -
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Residues in contact with PHE5032 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5054d PHE* 4.9 2.9 - + - -
5030e LEU* 4.0 21.5 - - + +
5033e ALA* 3.9 12.1 - - + -
5034e GLY* 3.2 40.6 - - - -
5037e PHE* 3.7 40.8 - + + -
5028f VAL* 3.1 14.5 + - + +
5029f PRO* 3.0 13.2 + - + +
5030f THR 3.0 0.4 - - - -
5031f ILE* 1.3 76.0 - - - +
5033f PHE* 1.3 82.2 + + - +
5035f GLY* 3.5 0.5 + - - -
5036f ALA* 3.1 21.5 + - - +
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Residues in contact with PHE5033 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5049d LEU 3.4 24.2 - - - -
5050d THR* 4.0 13.5 - - + -
5053d THR* 4.0 23.3 - - + -
5054d PHE* 3.9 18.8 - + - -
5357d BCR 3.5 57.2 - - + -
5029f PRO* 2.9 20.2 + - + +
5030f THR 2.6 13.3 + - - +
5032f PHE* 1.3 89.3 - + - +
5034f LEU* 1.3 52.4 + - - +
5035f GLY 2.9 4.5 - - - -
5036f ALA* 2.7 9.7 + - - -
5037f ILE* 2.6 40.9 + - + +
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Residues in contact with LEU5034 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5357d BCR 4.0 31.2 - - + -
5031e PHE* 3.4 8.3 - - + -
5030f THR* 2.7 41.5 + - + +
5031f ILE* 3.8 18.8 - - + +
5033f PHE* 1.3 73.3 - - - +
5035f GLY* 1.3 57.4 + - - +
5037f ILE* 4.5 4.7 - - + -
5038f ALA* 3.0 28.8 + - - +
5024j ILE* 3.2 33.8 - - + +
5028j PHE* 3.8 20.8 - - + -
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Residues in contact with GLY5035 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5031e PHE* 3.3 35.8 - - - -
5035e TRP* 3.6 16.8 - - - -
5031f ILE 2.9 11.0 + - - -
5032f PHE 3.8 0.9 - - - -
5033f PHE 2.9 1.0 - - - -
5034f LEU* 1.3 78.2 - - - +
5036f ALA* 1.3 62.9 + - - +
5038f ALA* 3.6 0.3 + - - +
5039f ALA* 3.2 21.3 + - - +
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Residues in contact with ALA5036 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5054d PHE* 3.9 23.1 - - + -
5034e GLY* 3.6 17.9 - - - +
5037e PHE* 5.0 1.8 - - + -
5038e VAL* 3.3 27.0 - - + +
5032f PHE* 3.1 14.7 + - + +
5033f PHE* 2.7 13.7 + - - +
5035f GLY* 1.3 70.2 - - - +
5037f ILE* 1.3 60.7 + - + +
5039f ALA* 3.0 21.8 + - - +
5040f MET* 3.2 7.8 + - - +
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Residues in contact with ILE5037 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5053d THR* 3.9 15.0 - - + +
5067d TYR* 3.5 33.2 - - + -
5357d BCR 3.7 30.5 - - + -
5359d MGE 3.9 18.6 - - - +
5033f PHE* 2.6 22.8 + - + +
5034f LEU* 4.3 1.3 - - - +
5036f ALA* 1.3 68.9 - - + +
5038f ALA* 1.3 61.4 + - - +
5039f ALA 3.0 5.4 + - - -
5040f MET* 3.2 24.2 + - + +
5041f GLN* 3.1 16.6 - - - +
5028j PHE* 3.1 30.5 - - + -
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Residues in contact with ALA5038 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5031e PHE* 3.7 22.9 - - + -
5035e TRP* 3.7 5.3 - - + -
5034f LEU 3.0 22.6 + - - +
5035f GLY 3.9 0.7 - - - +
5036f ALA 3.3 0.2 - - - -
5037f ILE* 1.3 77.3 - - - +
5039f ALA* 1.3 58.1 + - - +
5040f MET 3.4 0.2 - - - -
5041f GLN* 3.4 14.0 - - - +
5042f PHE* 3.4 17.7 - - - -
5024j ILE* 4.7 4.5 - - + -
5027j LEU* 3.5 21.0 - - + +
5028j PHE* 3.8 12.8 - - + -
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Residues in contact with ALA5039 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5035e TRP* 3.6 46.3 - - + +
5038e VAL* 4.0 10.6 - - + +
5039e SER* 4.9 1.6 - - - +
5035f GLY 3.2 13.1 + - - +
5036f ALA 3.0 13.6 + - - +
5038f ALA* 1.3 78.5 - - - +
5040f MET* 1.3 60.9 + - - +
5041f GLN 3.3 0.6 + - - -
5042f PHE* 3.5 16.5 + - - +
5043f ILE* 4.0 5.7 - - - +
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Residues in contact with MET5040 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5053d THR* 3.6 12.6 - - - +
5054d PHE* 3.6 22.9 - - + -
5067d TYR* 3.8 13.7 - - - -
5068d LEU* 3.4 50.0 - - + -
5359d MGE 3.7 18.6 + - - +
5038e VAL* 3.8 10.8 - - + -
5036f ALA 3.3 10.1 - - - +
5037f ILE* 3.2 19.5 + - + +
5039f ALA* 1.3 73.9 - - - +
5041f GLN* 1.3 52.9 + - - +
5042f PHE 2.5 18.8 + - - -
5043f ILE* 2.5 47.2 + - + +
5036j LEU* 5.5 1.4 + - - +
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Residues in contact with GLN5041 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5359d MGE 2.8 46.0 + - - +
5037f ILE* 3.1 11.3 - - - +
5038f ALA* 3.4 21.5 - - - +
5039f ALA 3.3 0.6 - - - -
5040f MET* 1.3 72.6 - - - +
5042f PHE* 1.3 70.1 + - + +
5043f ILE 4.8 1.3 - - - -
5027j LEU* 3.9 29.2 - - + +
5028j PHE* 3.0 27.2 + - + -
5030j TYR* 4.3 13.4 - - + -
5031j GLY* 3.3 15.4 - - - -
5034j ALA* 5.4 0.7 - - - +
5035j GLY* 4.5 12.8 - - - -
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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