Contacts of the helix formed by residues 5033 - 5054 (chain a) 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 PHE5033 (chain a).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5032a TRP* 1.3 80.4 - - - +
5034a GLY* 1.3 62.4 - - - +
5035a VAL 3.0 1.6 + - - -
5036a ILE* 3.0 15.9 + - - +
5037a MET* 3.2 9.1 + - - -
5125a CYS* 3.5 36.5 - - + +
5128a GLY* 3.0 40.2 - - - -
5129a ARG* 3.7 6.7 - - - +
5131a TRP* 4.0 13.7 - + - -
5132a GLU* 3.3 13.9 + - - +
5495c CLA 3.9 63.3 - - + -
5019i PHE* 3.4 32.1 - + - -
5023i PHE* 4.4 1.6 - + - -
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Residues in contact with GLY5034 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5030a VAL* 4.6 1.1 - - - -
5031a GLY* 3.6 19.5 - - - +
5032a TRP 3.2 0.8 - - - -
5033a PHE* 1.3 80.1 - - - +
5035a VAL* 1.3 53.6 + - - +
5036a ILE 3.0 1.1 - - - -
5037a MET* 3.7 13.2 - - - -
5038a ILE* 2.8 44.6 + - - +
5129a ARG* 4.0 15.3 - - - +
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Residues in contact with VAL5035 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5017a PHE* 5.4 0.2 - - + -
5021a VAL* 4.5 8.5 - - + -
5030a VAL* 4.5 4.7 - - + -
5031a GLY 3.4 15.5 + - - +
5032a TRP* 3.3 27.3 + - + +
5033a PHE 3.0 1.0 + - - -
5034a GLY* 1.3 75.3 - - - +
5036a ILE* 1.3 64.0 + - + +
5039a PRO* 3.2 13.8 - - - +
5566a BCR 3.7 32.0 - - + +
5015i PHE* 3.3 30.2 - - + +
5018i LEU* 4.2 23.8 - - + -
5019i PHE 4.7 3.4 - - - +
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Residues in contact with ILE5036 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5032a TRP 4.5 2.2 - - - +
5033a PHE 3.5 7.6 - - - +
5034a GLY 3.0 0.2 - - - -
5035a VAL* 1.3 89.6 - - + +
5037a MET* 1.3 68.1 + - - +
5038a ILE 3.0 1.3 - - - -
5039a PRO* 2.8 12.7 - - - +
5040a THR* 2.9 30.9 + - - +
5121a LEU* 4.6 9.4 - - + +
5125a CYS* 3.9 15.0 - - - -
5563a CLA 3.6 24.0 - - + -
5495c CLA 3.6 39.5 - - + -
5015i PHE* 4.9 6.3 - - + +
5016i VAL* 5.4 2.2 - - + -
5019i PHE* 3.9 24.7 - - + -
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Residues in contact with MET5037 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5033a PHE 3.2 2.2 + - - -
5034a GLY* 3.8 9.4 - - - -
5036a ILE* 1.3 80.5 - - - +
5038a ILE* 1.3 71.0 + - + +
5041a LEU* 3.0 49.4 + - + +
5122a GLY* 3.6 24.5 - - - +
5125a CYS* 3.8 15.6 - - + +
5126a TYR* 3.3 41.7 - - + -
5129a ARG* 3.8 39.5 - - - +
5361d MGE 4.4 15.7 - - + -
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Residues in contact with ILE5038 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212a SQD 6.2 2.0 - - + -
5030a VAL* 4.0 23.8 - - + -
5034a GLY 2.8 24.5 + - - +
5037a MET* 1.3 90.5 - - + +
5039a PRO* 1.3 63.9 - - + +
5041a LEU* 4.6 1.4 - - - +
5042a LEU* 3.0 37.1 + - + +
5129a ARG* 5.8 1.6 - - - +
5566a BCR 3.3 52.0 - - + -
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Residues in contact with PRO5039 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5035a VAL 3.2 14.4 - - - +
5036a ILE 2.8 18.8 - - - +
5038a ILE* 1.3 86.2 - - + +
5040a THR* 1.3 63.8 + - - +
5042a LEU* 3.2 2.3 + - - +
5043a ALA* 3.0 25.2 + - - +
5563a CLA 3.4 29.1 - - + +
5566a BCR 3.9 33.9 - - + +
5015i PHE* 3.4 30.1 - - + -
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Residues in contact with THR5040 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5036a ILE* 2.9 31.2 + - - +
5037a MET 4.1 0.9 - - - -
5039a PRO* 1.3 80.4 - - - +
5041a LEU* 1.3 61.8 + - - +
5043a ALA* 3.2 2.6 + - - +
5044a ALA* 3.1 20.6 + - - +
5118a HIS* 2.6 55.6 - - + +
5121a LEU* 3.7 8.2 - - + +
5122a GLY* 3.5 16.4 - - - +
5563a CLA 3.6 17.6 - - - +
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Residues in contact with LEU5041 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5037a MET* 3.0 47.5 + - + +
5038a ILE* 4.6 2.0 - - - +
5040a THR* 1.3 77.2 - - - +
5042a LEU* 1.3 53.3 + - + +
5044a ALA* 3.9 2.4 - - - +
5045a THR* 2.6 41.5 + - - +
5119a PHE* 4.4 14.4 - - + +
5122a GLY* 4.2 15.5 - - - -
5123a ALA 4.5 2.5 - - - +
5561a PHO 3.5 68.6 - - + +
5361d MGE 5.5 3.1 - - + -
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Residues in contact with LEU5042 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5038a ILE* 3.0 25.3 + - + +
5039a PRO 3.2 4.6 + - - +
5040a THR 3.2 1.0 - - - -
5041a LEU* 1.3 79.3 - - + +
5043a ALA* 1.3 60.6 + - - +
5045a THR* 3.4 12.8 - - + -
5046a ILE* 2.9 39.2 + - + +
5566a BCR 3.7 50.7 - - + -
104t BCR 5.8 12.8 - - + -
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Residues in contact with ALA5043 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5039a PRO 3.0 16.2 + - - +
5040a THR 3.5 3.8 - - - +
5042a LEU* 1.3 75.5 - - - +
5044a ALA* 1.3 69.9 + - - +
5046a ILE* 3.4 1.2 + - - +
5047a CYS* 2.9 24.6 + - - +
5114a LEU* 5.7 1.3 - - + -
5118a HIS* 3.6 22.2 - - + +
5563a CLA 4.8 4.5 - - - +
5566a BCR 3.3 40.6 - - + +
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Residues in contact with ALA5044 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5040a THR 3.1 8.8 + - - +
5041a LEU* 3.9 1.6 - - - +
5043a ALA* 1.3 79.8 - - - +
5045a THR* 1.3 66.8 + - - +
5047a CYS* 3.6 2.6 - - - +
5048a PHE* 2.8 25.2 + - - +
5114a LEU* 5.2 0.7 - - - -
5115a ILE* 3.8 22.2 - - + +
5118a HIS* 3.7 25.4 - - + +
5119a PHE* 3.9 4.5 - - - +
5561a PHO 3.6 20.4 - - + -
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Residues in contact with THR5045 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5041a LEU* 2.6 33.5 + - + +
5042a LEU* 3.4 24.2 - - + +
5044a ALA* 1.3 73.5 - - - +
5046a ILE* 1.3 68.1 + - + +
5048a PHE* 3.8 4.8 - - - +
5049a VAL* 3.2 27.5 + - - +
5559a CLA 3.3 30.4 - - - +
5561a PHO 3.7 23.8 - - + +
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Residues in contact with ILE5046 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528B BCR 5.0 17.3 - - + -
5042a LEU* 2.9 28.1 + - + +
5043a ALA 4.0 1.8 - - - +
5044a ALA 2.9 1.8 + - - -
5045a THR* 1.3 83.2 - - + +
5047a CYS* 1.3 66.7 + - - +
5049a VAL* 3.5 5.3 + - - +
5050a ILE* 3.3 36.7 + - + +
5566a BCR 4.0 38.8 - - + -
5568a LMT 5.8 1.6 - - + -
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Residues in contact with CYS5047 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5043a ALA 2.9 17.2 + - - +
5044a ALA 2.9 3.0 + - - +
5046a ILE* 1.3 74.2 - - - +
5048a PHE* 1.3 60.7 + - - +
5050a ILE* 3.3 2.7 + - - +
5051a ALA* 2.8 33.3 + - - +
5111a PRO* 4.5 14.1 - - - -
5114a LEU* 3.2 34.5 - - + -
5115a ILE* 3.8 17.5 - - + -
5566a BCR 3.8 33.1 - - + +
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Residues in contact with PHE5048 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5044a ALA 2.8 14.8 + - - +
5045a THR 3.8 2.5 - - - +
5047a CYS* 1.3 78.0 - - - +
5049a VAL* 1.3 69.6 + - + +
5051a ALA* 3.6 0.3 - - - +
5052a PHE* 2.9 48.2 + + + +
5082a VAL* 3.6 25.4 - - + -
5115a ILE* 3.1 21.4 - - + +
5174a LEU* 4.1 16.4 - - + -
5559a CLA 4.0 40.2 - - + -
5561a PHO 4.1 42.0 - - + -
5474c UNK 4.5 16.8 - - + -
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Residues in contact with VAL5049 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5045a THR* 3.2 20.9 + - - +
5046a ILE* 4.0 6.1 - - - +
5047a CYS 3.4 0.4 - - - -
5048a PHE* 1.3 83.5 - - + +
5050a ILE* 1.3 62.1 + - + +
5052a PHE* 4.1 3.7 - - - +
5053a ILE* 2.9 44.8 + - + +
5559a CLA 4.0 22.4 - - + -
5474c UNK 5.9 4.2 - - + +
5010t PHE* 4.0 29.6 - - + -
5217t LMT 4.4 14.1 - - + -
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Residues in contact with ILE5050 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5046a ILE* 3.3 26.9 + - + +
5047a CYS* 3.3 5.9 + - - +
5048a PHE 3.2 0.4 - - - -
5049a VAL* 1.3 78.3 - - + +
5051a ALA* 1.3 66.9 + - - +
5053a ILE* 3.1 4.7 + - + -
5054a ALA* 2.8 31.0 + - + +
5566a BCR 3.9 39.9 - - + -
5568a LMT 3.6 52.7 - - + -
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Residues in contact with ALA5051 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5047a CYS* 2.8 19.8 + - - +
5048a PHE* 3.6 3.8 - - - +
5050a ILE* 1.3 78.1 - - - +
5052a PHE* 1.3 62.1 + - - +
5054a ALA 3.0 12.6 - - - +
5055a ALA* 3.0 15.1 - - + +
5070a SER* 3.4 6.1 - - - -
5081a ALA 5.3 1.4 - - - +
5082a VAL* 4.0 19.2 - - + -
5111a PRO* 4.5 12.3 - - + -
5115a ILE* 4.4 5.6 - - + -
5566a BCR 3.5 22.4 - - + +
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Residues in contact with PHE5052 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5048a PHE* 2.9 43.8 + + + +
5049a VAL* 4.1 4.9 - - - +
5051a ALA* 1.3 78.2 - - - +
5053a ILE* 1.3 58.7 + - + +
5070a SER* 3.2 6.2 - - - +
5071a LEU* 3.0 50.5 + - + +
5077a ILE* 4.0 19.7 - - + -
5080a GLY* 3.6 33.2 - - - -
5081a ALA* 3.7 17.0 - - - -
5082a VAL* 4.3 4.2 - - + +
5174a LEU 4.4 3.1 - - - -
5175a GLY* 4.8 3.8 - - - -
5176a ILE 5.6 0.4 - - - -
5474c UNK 3.6 42.2 - - + -
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Residues in contact with ILE5053 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5049a VAL* 2.9 24.9 - - + +
5050a ILE* 3.1 6.1 + - - +
5052a PHE* 1.3 79.3 - - + +
5054a ALA* 1.3 60.5 + - + +
5070a SER* 3.9 0.4 - - - -
5071a LEU* 3.1 13.1 + - + +
5072a LEU* 2.9 35.5 + - + +
5474c UNK 5.8 5.4 - - + -
5003t THR* 4.4 12.8 - - + -
5007t VAL* 3.7 35.2 - - + -
5010t PHE* 6.1 2.5 - - + -
5217t LMT 3.8 34.5 - - + +
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Residues in contact with ALA5054 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5050a ILE* 2.8 22.3 + - + +
5051a ALA 3.5 1.5 - - - -
5053a ILE* 1.3 76.3 - - + +
5055a ALA* 1.3 68.9 + - - +
5070a SER* 3.8 2.5 - - - -
5072a LEU* 3.7 26.5 - - + -
5073a TYR* 5.2 2.9 - - + -
5566a BCR 3.3 18.6 - - + +
5568a LMT 4.1 22.7 - - + -
5489c UNK 5.4 2.9 - - + -
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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) + - + + + + + -
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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