Contacts of the helix formed by residues 5002 - 5025 (chain i) 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 GLU5002 (chain i).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5001i MET* 1.3 76.4 - - - +
5003i THR* 1.3 71.4 + - - +
5004i LEU 3.0 1.1 - - - -
5005i LYS* 2.9 32.4 + - - +
5006i ILE* 2.9 26.7 + - + +
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Residues in contact with THR5003 (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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5001i MET 4.4 6.9 + - - -
5002i GLU* 1.3 83.5 + - - +
5004i LEU* 1.3 56.1 - - - -
5006i ILE* 3.4 13.8 + - + +
5007i THR* 3.0 37.0 + - - +
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Residues in contact with LEU5004 (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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5096a ILE* 3.7 35.9 - - + -
5097a TRP* 4.5 8.1 - - + +
5563a CLA 4.4 8.5 - - + -
5487c UNK 3.8 40.8 - - + -
5001i MET* 3.8 22.1 - - + +
5002i GLU 3.0 0.4 - - - -
5003i THR* 1.3 76.6 - - - +
5005i LYS* 1.3 63.4 + - - +
5007i THR* 4.4 8.7 - - + -
5008i VAL* 3.0 47.2 + - + +
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Residues in contact with LYS5005 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5097a TRP* 3.6 40.3 - - + +
5001i MET 3.7 3.0 + - - +
5002i GLU* 2.9 26.1 + - - +
5004i LEU* 1.3 79.4 - - - +
5006i ILE* 1.3 69.5 + - + +
5008i VAL* 3.4 2.3 + - - +
5009i TYR* 3.1 44.6 + - + +
5201i MGE 2.9 38.1 + - - +
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Residues in contact with ILE5006 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5002i GLU* 2.9 28.2 + - + +
5003i THR* 3.6 17.3 - - + +
5005i LYS* 1.3 76.9 - - + +
5007i THR* 1.3 69.9 + - - +
5009i TYR* 2.9 19.0 + - - +
5010i ILE* 2.9 32.3 + - + +
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Residues in contact with THR5007 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5563a CLA 5.5 6.7 - - + -
5003i THR* 3.0 21.2 + - - +
5004i LEU* 3.8 11.6 - - + -
5006i ILE* 1.3 83.8 - - - +
5008i VAL* 1.3 62.8 + - + +
5010i ILE* 2.9 7.4 + - - +
5011i VAL* 2.8 46.5 + - + +
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Residues in contact with VAL5008 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5097a TRP* 3.7 31.9 - - + -
5563a CLA 3.8 53.4 - - + +
5004i LEU* 3.0 27.0 + - + +
5005i LYS 3.8 0.9 - - - +
5006i ILE 3.2 0.2 - - - -
5007i THR* 1.3 80.6 - - + +
5009i TYR* 1.3 53.5 + - + +
5011i VAL* 3.2 7.4 + - - +
5012i VAL* 2.6 55.9 + - + +
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Residues in contact with TYR5009 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5097a TRP* 3.9 10.9 - + - -
5563a CLA 3.1 78.8 + - + -
5005i LYS* 3.1 37.9 + - - +
5006i ILE* 2.9 13.7 + - - +
5008i VAL* 1.3 73.5 - - + +
5010i ILE* 1.3 58.1 + - + +
5012i VAL* 3.6 4.1 - - + +
5013i THR* 2.7 43.3 + - - -
5201i MGE 3.3 42.8 + - - -
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Residues in contact with ILE5010 (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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5006i ILE* 2.9 34.0 + - + +
5007i THR* 3.2 8.3 - - - +
5009i TYR* 1.3 78.8 - - + +
5011i VAL* 1.3 61.0 + - + +
5013i THR* 3.1 5.8 + - - -
5014i PHE* 2.9 29.8 + - + +
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Residues in contact with VAL5011 (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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5563a CLA 4.0 42.8 - - + +
5007i THR* 2.8 34.2 + - + +
5008i VAL* 3.4 10.5 - - - +
5010i ILE* 1.3 78.0 - - + +
5012i VAL* 1.3 65.1 + - - +
5013i THR 3.4 0.3 + - - -
5014i PHE* 3.4 8.9 + - - +
5015i PHE* 2.8 44.3 - - + -
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Residues in contact with VAL5012 (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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5563a CLA 3.8 61.4 - - + +
5495c CLA 3.7 29.4 - - + -
5008i VAL* 2.6 41.1 + - + +
5009i TYR* 3.9 5.4 - - - +
5011i VAL* 1.3 72.5 - - + +
5013i THR* 1.3 58.6 + - - +
5015i PHE* 3.5 2.6 + - - +
5016i VAL* 2.9 41.8 + - + +
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Residues in contact with THR5013 (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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5563a CLA 3.4 35.5 - - + +
5009i TYR 2.7 28.2 + - - -
5010i ILE* 3.5 6.1 - - - -
5012i VAL* 1.3 71.5 - - - +
5014i PHE* 1.3 67.2 + - - +
5016i VAL* 3.8 6.4 - - + +
5017i LEU* 2.8 51.0 + - + +
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Residues in contact with PHE5014 (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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5017a PHE* 6.1 2.5 - + - -
5566a BCR 4.1 19.3 - - + -
5010i ILE* 2.9 13.6 + - + +
5011i VAL* 3.6 10.1 - - - +
5013i THR* 1.3 79.0 - - - +
5015i PHE* 1.3 85.8 + + - +
5017i LEU* 3.3 13.2 - - + +
5018i LEU* 3.1 66.1 + - + +
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Residues in contact with PHE5015 (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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5035a VAL* 3.3 30.2 - - + +
5036a ILE* 4.9 4.8 - - + +
5039a PRO* 3.4 24.2 - - + -
5563a CLA 3.7 35.0 - - + -
5566a BCR 3.4 41.5 - - + -
5011i VAL* 2.8 41.0 + - + -
5012i VAL 4.0 2.9 - - - +
5013i THR 3.2 0.4 - - - -
5014i PHE* 1.3 92.6 - + - +
5016i VAL* 1.3 66.8 + - - +
5017i LEU 3.0 2.2 + - - -
5018i LEU* 3.2 7.0 + - + +
5019i PHE* 3.0 23.6 + - - +
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Residues in contact with VAL5016 (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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5036a ILE* 5.4 1.1 - - + -
5563a CLA 5.2 5.6 - - + -
5495c CLA 3.8 46.7 - - + -
5012i VAL* 2.9 32.4 + - + +
5013i THR* 3.2 7.6 + - + +
5015i PHE* 1.3 74.9 - - - +
5017i LEU* 1.3 63.4 + - + +
5019i PHE* 3.4 6.0 + - - +
5020i VAL* 2.8 40.9 + - + +
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Residues in contact with LEU5017 (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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5013i THR* 2.8 41.8 + - + +
5014i PHE* 3.3 13.7 - - + +
5016i VAL* 1.3 76.4 - - + +
5018i LEU* 1.3 72.5 + - + +
5019i PHE 2.8 1.7 + - - -
5020i VAL* 2.9 17.7 + - + -
5021i PHE* 3.1 40.5 + - + -
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Residues in contact with LEU5018 (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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5014a TRP* 3.7 29.0 - - + -
5017a PHE* 4.6 15.0 - - + -
5032a TRP* 3.4 15.4 - - + -
5035a VAL* 4.2 12.6 - - + -
5566a BCR 4.1 22.2 - - + -
5014i PHE* 3.1 52.6 + - + +
5015i PHE* 3.6 7.9 - - + +
5017i LEU* 1.3 79.2 - - + +
5019i PHE* 1.3 57.5 + - - +
5021i PHE* 3.6 1.9 + - + +
5022i GLY 2.9 26.9 + - - -
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Residues in contact with PHE5019 (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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5032a TRP* 3.3 27.4 - - - +
5033a PHE* 3.4 32.8 - + - -
5035a VAL* 4.7 1.5 - - + +
5036a ILE* 3.9 24.0 - - + -
5495c CLA 4.2 43.1 - - + -
5506c BCR 5.0 10.5 - - + -
5015i PHE 3.0 12.3 + - - +
5016i VAL* 3.6 7.6 - - - +
5017i LEU 2.8 3.4 + - - -
5018i LEU* 1.3 76.4 - - - +
5020i VAL* 1.3 74.8 + - + +
5022i GLY* 3.9 0.9 - - - -
5023i PHE* 3.1 57.0 + + - -
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Residues in contact with VAL5020 (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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5495c CLA 6.0 0.4 - - + -
5496c CLA 4.0 22.2 - - + -
5506c BCR 3.4 43.0 - - + +
5016i VAL* 2.8 31.2 - - + +
5017i LEU* 2.9 11.3 + - + +
5019i PHE* 1.3 84.3 - - + +
5021i PHE* 1.3 64.1 + - + +
5023i PHE 3.5 0.2 + - - -
5024i LEU* 3.2 27.5 + - + +
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Residues in contact with PHE5021 (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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5014a TRP* 3.5 26.5 - + + -
5017i LEU* 3.1 49.2 + - + +
5018i LEU* 4.9 0.9 - - + -
5020i VAL* 1.3 76.1 - - + +
5022i GLY* 1.3 54.9 + - - +
5023i PHE 3.0 1.8 - - - -
5024i LEU* 2.6 45.9 + - + +
5025i SER* 2.7 21.3 + - - +
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Residues in contact with GLY5022 (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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5014a TRP* 3.8 1.4 - - - -
5032a TRP* 3.0 58.1 + - - -
5018i LEU 2.9 14.7 + - - -
5019i PHE 3.5 0.4 + - - -
5021i PHE* 1.3 73.5 - - - +
5023i PHE* 1.3 60.1 + - - +
5025i SER* 3.5 17.9 - - - -
5027i ASP* 3.8 4.9 - - - +
5030i ARG* 4.9 0.5 + - - -
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Residues in contact with PHE5023 (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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5032a TRP* 3.4 22.2 - + + -
5033a PHE* 4.4 6.5 - + - -
5131a TRP* 4.2 13.2 - + - -
5132a GLU* 3.9 11.0 - - - -
5262c ARG 5.0 0.7 - - - +
5263c ALA* 5.2 3.3 - - - +
5449c ARG* 5.6 0.2 - - - -
5495c CLA 2.8 36.6 - - + -
5506c BCR 3.6 26.6 - - + +
5019i PHE* 3.1 56.5 + + - -
5020i VAL 4.0 0.2 - - - +
5021i PHE 2.8 1.8 + - - -
5022i GLY* 1.3 72.8 - - - +
5024i LEU* 1.3 67.1 + - - +
5025i SER 3.0 2.5 + - - -
5026i GLY* 3.4 0.7 + - - -
5027i ASP* 2.9 56.3 + - + +
5028i PRO* 4.9 1.7 - - - +
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Residues in contact with LEU5024 (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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5259c TRP* 4.3 28.0 - - + +
5262c ARG* 4.0 12.3 + - - +
5263c ALA* 4.4 14.9 - - + +
5496c CLA 3.6 24.5 - - + -
5506c BCR 3.6 19.0 - - + +
5020i VAL* 3.2 23.0 + - + +
5021i PHE* 2.6 38.6 + - + +
5023i PHE* 1.3 69.9 - - - +
5025i SER* 1.3 50.7 + - - +
5026i GLY* 2.5 21.7 + - - -
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Residues in contact with SER5025 (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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5014a TRP* 3.3 30.0 + - - -
5018a CYS* 4.3 5.6 - - - -
5021i PHE* 2.7 14.8 + - - +
5022i GLY* 3.5 14.4 - - - -
5023i PHE 3.0 1.0 - - - -
5024i LEU* 1.3 72.3 - - - +
5026i GLY* 1.3 65.2 + - - +
5027i ASP 3.7 0.9 - - - -
5030i ARG* 3.0 24.2 + - - -
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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