Contacts of the helix formed by residues 4127 - 4149 (chain H) in PDB entry 6X34
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 PHE4127 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3999H ALA* 6.0 7.0 - - + -
4005H ILE* 4.8 21.1 - - + -
4060H PHE* 3.5 58.6 - + + -
4063H LEU* 5.4 4.0 - - + -
4123H PHE 5.2 7.2 - - - -
4124H ALA 5.2 8.1 - - - -
4126H ARG* 1.3 90.3 - - + +
4128H GLN* 1.3 64.8 + - - +
4129H GLU* 3.3 7.4 - - - -
4130H PRO* 3.4 17.8 - - + +
4131H ALA* 3.7 17.0 + - + +
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Residues in contact with GLN4128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4064H LYS* 6.1 4.3 - - + +
4125H ASN* 5.2 18.8 - - + +
4126H ARG 3.7 2.0 - - - +
4127H PHE* 1.3 77.5 - - - +
4129H GLU* 1.3 69.0 + - + +
4131H ALA* 4.1 4.8 - - - +
4132H ARG* 3.3 23.0 + - - +
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Residues in contact with GLU4129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4126H ARG* 3.9 14.4 - - - +
4128H GLN* 1.3 85.6 + - + +
4130H PRO* 1.3 75.7 - - + +
4132H ARG* 3.3 17.5 + - - +
4133H ASP* 4.0 4.9 + - - +
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Residues in contact with PRO4130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4009H LYS* 4.8 23.8 - - + +
4012H LEU* 3.5 28.1 - - + +
4013H ASP* 5.2 6.1 - - - +
4016H LYS* 6.0 0.7 - - - +
4127H PHE* 3.4 20.4 - - + +
4129H GLU* 1.3 102.8 - - + +
4131H ALA* 1.3 59.7 + - - +
4132H ARG 3.3 0.3 + - - -
4133H ASP* 3.6 10.9 + - + +
4134H ILE* 3.4 15.6 + - - +
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Residues in contact with ALA4131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4012H LEU* 4.0 3.5 - - + +
4057H PHE* 4.9 16.6 - - + -
4060H PHE* 6.4 2.7 - - + -
4127H PHE* 3.7 20.5 + - + +
4128H GLN* 4.1 5.4 - - - +
4129H GLU 3.3 0.8 - - - -
4130H PRO* 1.3 77.2 - - - +
4132H ARG* 1.3 59.3 + - - +
4133H ASP 3.4 0.2 - - - -
4134H ILE* 3.7 10.0 - - + +
4135H GLY* 2.8 28.1 + - - -
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Residues in contact with ARG4132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4128H GLN 3.3 17.7 + - - +
4129H GLU* 3.3 8.9 + - - +
4130H PRO 3.2 1.2 - - - -
4131H ALA* 1.3 75.9 - - - +
4133H ASP* 1.3 64.2 + - - +
4135H GLY* 4.1 0.2 - - - -
4136H PHE* 3.4 21.5 + - - +
4168H TYR* 6.3 4.3 - - + -
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Residues in contact with ASP4133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4016H LYS* 3.7 38.3 + - + +
4129H GLU 4.0 4.1 + - - +
4130H PRO* 3.6 8.5 + - + +
4131H ALA 3.4 0.2 - - - -
4132H ARG* 1.3 77.1 - - - +
4134H ILE* 1.3 65.1 + - - +
4136H PHE* 3.4 6.6 + - - +
4137H ASN* 3.2 25.1 + - - +
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Residues in contact with ILE4134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4012H LEU* 3.7 20.4 - - + -
4015H GLN* 4.7 7.6 - - + +
4016H LYS* 4.5 23.5 - - + +
4019H VAL* 4.6 9.9 - - + -
4057H PHE* 3.6 37.2 - - + -
4130H PRO 3.4 18.1 + - - +
4131H ALA* 3.7 7.2 - - - -
4133H ASP* 1.3 78.2 + - - +
4135H GLY* 1.3 68.3 + - - +
4137H ASN* 3.0 22.8 + - + -
4138H VAL* 3.0 28.9 + - + +
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Residues in contact with GLY4135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4057H PHE* 5.0 9.6 - - - -
4131H ALA 2.8 21.9 + - - -
4132H ARG* 4.1 0.7 - - - -
4134H ILE* 1.3 80.4 - - - +
4136H PHE* 1.3 59.8 + - - +
4138H VAL* 4.0 3.7 + - - +
4139H ALA* 3.6 17.7 + - - +
4165H ILE* 4.9 10.6 - - - +
4168H TYR* 6.6 0.4 - - - -
4169H PHE* 4.6 4.2 - - - +
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Residues in contact with PHE4136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4132H ARG 3.4 16.1 + - - +
4133H ASP* 4.0 4.3 - - - +
4135H GLY* 1.3 75.3 - - - +
4137H ASN* 1.3 63.2 + - - +
4138H VAL 3.4 0.2 - - - -
4139H ALA* 3.5 7.8 + - - +
4140H VAL* 3.2 30.6 + - + +
4169H PHE* 4.5 11.4 - - + -
4172H TYR* 5.8 5.8 - - + +
4191H GLU* 5.2 14.4 - - + -
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Residues in contact with ASN4137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4016H LYS* 3.3 30.7 + - - +
4019H VAL* 4.1 14.6 - - + +
4020H VAL* 4.3 6.9 - - - +
4023H LEU* 3.3 29.1 - - - +
4133H ASP* 3.2 21.1 + - - +
4134H ILE* 3.0 19.7 + - + +
4136H PHE* 1.3 76.0 - - - +
4138H VAL* 1.3 64.5 + - - +
4140H VAL* 3.2 18.9 - - - +
4141H LEU* 3.2 17.0 - - - +
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Residues in contact with VAL4138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4019H VAL* 6.0 0.2 - - + -
4057H PHE* 5.0 9.4 - - + -
4134H ILE* 3.0 35.1 + - + +
4135H GLY* 4.5 4.3 - - - +
4137H ASN* 1.3 76.4 - - + +
4139H ALA* 1.3 60.7 + - - +
4140H VAL 3.4 0.2 - - - -
4141H LEU* 3.4 20.8 - - + +
4142H LEU* 3.1 26.2 + - + +
4162H ALA* 5.7 9.9 - - + -
4165H ILE* 5.8 8.1 - - + -
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Residues in contact with ALA4139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4135H GLY 3.6 14.0 + - - +
4136H PHE 3.5 8.7 + - - +
4137H ASN 3.2 1.0 - - - -
4138H VAL* 1.3 79.7 - - - +
4140H VAL* 1.3 62.2 + - + +
4142H LEU* 3.5 4.5 + - - +
4143H THR* 3.3 23.2 + - - +
4165H ILE* 4.5 10.7 - - + +
4166H LEU* 4.6 13.8 - - + +
4169H PHE* 3.8 24.2 - - + -
4173H LEU* 4.6 9.4 - - + +
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Residues in contact with VAL4140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4023H LEU* 4.3 15.4 - - + +
4136H PHE* 3.2 16.1 + - + +
4137H ASN* 3.2 26.9 - - - +
4139H ALA* 1.3 78.8 - - + +
4141H LEU* 1.3 60.7 + - - +
4143H THR* 3.3 19.1 - - - +
4144H ASN* 3.4 13.3 - - - +
4173H LEU* 4.2 18.6 - - + -
4189H TYR* 4.0 38.5 - - + +
4190H PHE 4.7 8.1 - - - +
4191H GLU* 5.5 1.6 - - + +
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Residues in contact with LEU4141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4019H VAL* 4.3 27.8 - - + +
4022H LEU* 5.6 7.0 - - + -
4023H LEU* 3.7 22.0 - - + -
4137H ASN* 3.2 20.5 + - - +
4138H VAL* 3.4 27.1 - - + +
4140H VAL* 1.3 79.9 - - - +
4142H LEU* 1.3 70.8 + - + +
4144H ASN* 3.2 11.0 + - - +
4145H LEU* 3.1 25.8 + - + +
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Residues in contact with LEU4142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4138H VAL* 3.1 22.6 + - + +
4139H ALA* 4.0 5.8 - - - +
4140H VAL 3.4 0.2 - - - -
4141H LEU* 1.3 83.4 - - + +
4143H THR* 1.3 50.4 + - - +
4145H LEU* 3.3 17.3 - - - +
4146H SER* 2.5 27.2 + - - -
4158H PHE 6.5 0.2 - - - -
4159H LEU* 5.5 13.6 - - + +
4162H ALA* 5.7 7.9 - - + -
4166H LEU* 6.0 7.4 - - + -
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Residues in contact with THR4143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4139H ALA 3.3 18.1 + - - +
4140H VAL* 3.3 16.6 - - - +
4142H LEU* 1.3 76.0 - - - +
4144H ASN* 1.3 61.5 + - - +
4146H SER* 3.5 7.6 + - - -
4147H GLU* 3.4 30.8 + - - +
4173H LEU* 4.4 16.4 - - + -
4189H TYR* 5.2 6.7 - - + -
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Residues in contact with ASN4144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4023H LEU* 5.7 7.9 - - + +
4026H LEU* 4.1 23.1 + - - +
4140H VAL 3.4 18.4 + - - +
4141H LEU* 3.2 9.9 + - - +
4143H THR* 1.3 78.4 - - - +
4145H LEU* 1.3 65.2 + - - +
4147H GLU* 3.7 1.4 + - - -
4148H HIS* 3.1 61.4 + - - -
4187H ARG* 4.8 12.0 - - - +
4189H TYR* 5.6 6.0 + - + +
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Residues in contact with LEU4145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4026H LEU* 5.5 5.4 - - + -
4036H ALA 5.8 1.3 - - - +
4039H MET* 4.2 25.1 - - + +
4040H VAL* 4.2 23.0 - - + +
4043H LEU* 4.3 27.6 - - + -
4141H LEU* 3.1 29.4 + - + +
4142H LEU* 3.3 23.1 - - - +
4144H ASN* 1.3 81.9 - - - +
4146H SER* 1.3 68.7 + - - +
4148H HIS* 4.1 5.4 - - - +
4149H VAL* 3.2 29.3 + - - +
4155H LEU* 5.5 6.5 - - + -
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Residues in contact with SER4146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4142H LEU 2.5 25.2 + - - -
4143H THR* 3.5 9.2 - - - -
4145H LEU* 1.3 84.0 - - - +
4147H GLU* 1.3 62.2 + - - +
4149H VAL* 3.3 23.6 - - - +
4155H LEU* 4.4 20.6 - - - -
4159H LEU* 5.5 7.3 - - - +
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Residues in contact with GLU4147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4031H VAL* 5.3 0.7 - - - +
4143H THR* 3.4 26.8 + - - +
4144H ASN* 4.2 3.0 - - - +
4145H LEU 3.4 0.2 - - - -
4146H SER* 1.3 79.6 + - - +
4148H HIS* 1.3 71.5 + - + +
4149H VAL 3.7 4.5 + - - +
4187H ARG* 2.6 49.3 + - - -
5026H PHE* 4.7 6.9 - - - +
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Residues in contact with HIS4148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4026H LEU* 3.5 36.1 - - + +
4027H GLU 5.9 0.9 - - - -
4029H ASN 5.9 3.1 - - - -
4030H VAL 5.6 0.4 + - - -
4031H VAL* 3.0 59.1 - - + +
4032H ASN* 5.3 0.2 - - - +
4036H ALA* 5.2 4.0 - - + +
4144H ASN* 3.1 48.3 + - - +
4145H LEU* 3.7 5.3 + - - +
4146H SER 3.4 0.8 - - - -
4147H GLU* 1.3 86.4 - - + +
4149H VAL* 1.3 66.0 + - + +
4150H PRO* 3.6 2.8 - - - +
4186H GLU* 6.1 2.6 - - + +
4187H ARG* 5.8 7.7 + - - +
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Residues in contact with VAL4149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4031H VAL 4.3 4.9 - - - +
4036H ALA* 5.0 8.1 - - + +
4037H ARG* 5.4 9.2 - - + -
4040H VAL* 3.8 26.0 - - + -
4145H LEU 3.2 19.7 + - - +
4146H SER* 3.3 22.7 - - - +
4147H GLU 3.7 4.9 - - - +
4148H HIS* 1.3 79.6 - - + +
4150H PRO* 1.3 72.2 - - + +
4151H HIS 4.6 1.6 - - - +
4152H ASP* 4.1 27.6 - - + +
4155H LEU* 4.6 4.7 - - + -
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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