Contacts of the helix formed by residues 4639 - 4661 (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 PRO4639 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4635H GLY 3.4 19.5 - - - +
4636H TYR* 3.5 14.8 - - + +
4638H GLU* 1.3 94.3 - - + +
4640H ALA* 1.3 59.3 + - - +
4641H LEU* 3.2 1.6 + - + -
4642H ARG* 3.5 8.9 + - + +
4643H CYS* 3.4 19.6 + - - +
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Residues in contact with ALA4640 (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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4574H ILE* 5.9 7.8 - - + +
4636H TYR 3.5 17.1 + - - +
4637H MET* 3.4 12.1 + - - +
4638H GLU 3.1 2.0 - - - -
4639H PRO* 1.3 77.5 - - - +
4641H LEU* 1.3 59.9 + - - +
4642H ARG 3.3 0.2 - - - -
4643H CYS* 3.9 4.3 - - - -
4644H LEU* 3.1 48.8 + - + +
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Residues in contact with LEU4641 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4571H ILE* 5.7 3.1 - - - +
4574H ILE* 5.9 10.1 - - + +
4575H LEU* 6.4 2.0 - - + -
4629H PHE* 6.3 3.1 - - + -
4630H LEU* 5.9 7.4 - - + +
4637H MET 4.1 4.2 + - - +
4638H GLU* 3.3 22.1 + - - +
4639H PRO 3.2 1.6 - - - -
4640H ALA* 1.3 79.4 - - - +
4642H ARG* 1.3 62.3 + - + +
4644H LEU* 5.5 0.2 - - - -
4645H SER* 2.5 34.0 + - - -
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Residues in contact with ARG4642 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4639H PRO* 3.5 8.1 + - + +
4640H ALA 3.3 0.2 - - - -
4641H LEU* 1.3 90.5 - - + +
4643H CYS* 1.3 62.1 + - - +
4645H SER* 3.4 4.7 - - - -
4646H LEU* 3.3 29.1 - - + +
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Residues in contact with CYS4643 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4639H PRO 3.4 15.7 + - - +
4640H ALA* 3.6 4.7 + - - +
4641H LEU 3.4 0.2 - - - -
4642H ARG* 1.3 78.7 - - - +
4644H LEU* 1.3 77.5 + - + +
4645H SER 3.3 0.8 + - - -
4646H LEU* 3.6 4.6 + - - +
4647H LEU* 3.6 22.5 + - - +
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Residues in contact with LEU4644 (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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4567H LEU* 3.7 33.4 - - + +
4570H ALA* 4.7 22.9 - - + +
4571H ILE* 5.0 18.5 - - + +
4640H ALA* 3.1 36.0 + - + +
4641H LEU* 5.5 0.2 - - - -
4643H CYS* 1.3 91.0 - - - +
4645H SER* 1.3 63.9 + - - +
4647H LEU* 3.7 8.7 + - + +
4648H HIS* 3.4 22.2 + - - +
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Residues in contact with SER4645 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4571H ILE* 4.8 14.7 - - - +
4641H LEU 2.5 27.2 + - - -
4642H ARG* 3.4 11.4 + - - -
4644H LEU* 1.3 77.4 - - - +
4646H LEU* 1.3 68.4 + - - +
4648H HIS* 3.8 4.5 + - - +
4649H THR* 3.3 24.6 + - - +
4800H GLY 5.8 2.0 - - - -
4801H HIS* 3.9 16.4 + - - -
4807H PHE* 5.0 12.6 - - - -
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Residues in contact with LEU4646 (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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4642H ARG* 3.3 23.3 - - + +
4643H CYS 3.6 4.3 + - - +
4644H LEU 3.4 0.4 - - - -
4645H SER* 1.3 80.4 - - - +
4647H LEU* 1.3 63.6 + - - +
4649H THR* 2.6 23.2 + - - +
4650H LEU* 3.2 26.4 + - + +
4801H HIS* 3.6 27.6 - - + +
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Residues in contact with LEU4647 (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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4563H LEU* 4.8 6.5 - - + -
4567H LEU* 3.7 34.1 - - + -
4643H CYS* 3.6 19.2 + - - +
4644H LEU* 3.7 6.0 + - + +
4646H LEU* 1.3 78.4 - - - +
4648H HIS* 1.3 63.5 + - - +
4649H THR 3.2 0.7 + - - -
4650H LEU* 3.3 6.7 + - + +
4651H VAL* 3.2 37.8 + - + +
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Residues in contact with HIS4648 (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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4564H ALA* 4.9 12.6 - - - -
4567H LEU* 4.2 22.4 - - + +
4568H ALA* 5.0 7.5 - - - +
4571H ILE* 5.9 8.7 - - + -
4644H LEU 3.4 16.2 + - - +
4645H SER* 4.1 6.5 - - - +
4646H LEU 3.3 0.4 - - - -
4647H LEU* 1.3 78.0 - - - +
4649H THR* 1.3 63.8 + - - +
4651H VAL* 3.3 18.3 - - + +
4652H ALA* 3.6 10.7 + - - +
4793H TYR* 2.4 43.2 + + - -
4797H SER* 4.3 10.3 + - - -
4807H PHE* 5.6 4.5 - + + -
4810H HIS* 3.3 34.7 + + - +
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Residues in contact with THR4649 (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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4645H SER 3.3 7.8 + - - +
4646H LEU* 2.6 30.7 + - - +
4648H HIS* 1.3 80.6 - - - +
4650H LEU* 1.3 68.3 + - - +
4652H ALA* 3.5 5.2 + - - +
4653H PHE* 3.2 23.7 + - - +
4797H SER* 3.6 32.4 - - - +
4798H LEU* 5.3 6.1 - - + -
4801H HIS* 3.5 26.3 + - + +
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Residues in contact with LEU4650 (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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4646H LEU* 3.2 38.3 + - + +
4647H LEU* 3.3 7.8 + - + +
4649H THR* 1.3 82.5 - - - +
4651H VAL* 1.3 65.3 + - + +
4653H PHE* 3.5 10.2 + - + +
4654H LEU* 3.2 24.4 + - - +
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Residues in contact with VAL4651 (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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4560H LEU* 3.3 49.8 - - + +
4563H LEU* 4.3 24.9 - - + +
4564H ALA* 5.2 8.7 - - + +
4567H LEU* 5.5 1.1 - - + -
4647H LEU* 3.2 35.2 + - + +
4648H HIS* 3.3 23.1 - - + +
4650H LEU* 1.3 77.4 - - + +
4652H ALA* 1.3 60.0 + - + +
4654H LEU* 4.0 2.5 - - - -
4655H CYS* 3.5 5.7 + - - +
4793H TYR* 6.6 0.2 - - + -
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Residues in contact with ALA4652 (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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4648H HIS 3.6 15.0 - - - +
4649H THR* 3.5 5.5 + - - +
4650H LEU 3.2 0.6 - - - -
4651H VAL* 1.3 82.0 - - + +
4653H PHE* 1.3 62.1 + - - +
4655H CYS* 3.4 11.8 + - - +
4656H ILE* 3.3 19.2 + - - +
4793H TYR* 4.3 21.3 - - + -
4794H MET* 4.9 8.8 - - + +
4797H SER* 4.1 18.6 - - - +
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Residues in contact with PHE4653 (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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4649H THR 3.2 16.8 + - - +
4650H LEU* 4.0 11.7 - - + +
4651H VAL 3.5 0.2 - - - -
4652H ALA* 1.3 76.6 - - - +
4654H LEU* 1.3 65.2 + - - +
4656H ILE* 3.4 33.7 + - + +
4657H ILE* 3.8 8.2 + - + +
4794H MET* 5.8 0.9 - - + -
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Residues in contact with LEU4654 (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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4549H PHE* 5.4 13.5 - - + -
4553H LEU* 4.5 9.5 - - + +
4560H LEU* 3.8 19.8 - - + +
4650H LEU 3.2 17.3 + - - +
4651H VAL* 4.2 1.8 - - - +
4652H ALA 3.3 0.4 - - - -
4653H PHE* 1.3 77.3 - - - +
4655H CYS* 1.3 60.3 + - - +
4656H ILE 3.2 0.2 - - - -
4657H ILE* 3.4 6.8 + - - +
4658H GLY* 3.0 24.3 + - - -
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Residues in contact with CYS4655 (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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4557H PHE* 5.1 11.2 - - - -
4560H LEU* 3.5 14.8 - - + +
4561H ARG* 4.3 20.4 - - - +
4651H VAL 3.5 11.7 + - - +
4652H ALA* 3.4 13.1 + - - +
4653H PHE 3.3 0.4 - - - -
4654H LEU* 1.3 75.9 - - - +
4656H ILE* 1.3 61.8 + - + +
4658H GLY* 4.4 2.2 - - - +
4659H TYR* 2.8 36.5 + - - +
4790H LEU* 3.8 31.2 - - + -
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Residues in contact with ILE4656 (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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4652H ALA 3.3 18.8 - - - +
4653H PHE* 3.7 31.4 - - + +
4654H LEU 3.2 0.4 - - - -
4655H CYS* 1.3 78.6 - - + +
4657H ILE* 1.3 62.1 + - - +
4659H TYR* 3.5 5.9 + - - +
4660H ASN* 3.3 19.9 + - - +
4787H PHE* 4.4 27.2 - - + -
4790H LEU* 5.3 10.3 - - + +
4791H GLY* 5.9 4.9 - - - -
4794H MET* 3.9 23.6 - - + -
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Residues in contact with ILE4657 (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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4549H PHE* 5.0 17.0 - - + -
4550H LEU* 5.5 11.5 - - + +
4553H LEU* 5.1 2.9 - - + -
4653H PHE* 3.8 9.7 + - + +
4654H LEU* 3.4 9.0 + - - +
4656H ILE* 1.3 76.5 - - - +
4658H GLY* 1.3 65.8 + - - +
4660H ASN* 3.2 19.2 + - - +
4661H CYS* 3.9 11.3 + - - -
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Residues in contact with GLY4658 (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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4550H LEU 5.4 1.1 - - - -
4553H LEU* 4.1 28.6 - - - +
4554H SER* 4.2 9.6 - - - -
4557H PHE* 4.9 7.0 - - - -
4654H LEU 3.0 16.7 + - - -
4655H CYS* 3.8 2.7 - - - -
4656H ILE 3.3 0.2 - - - -
4657H ILE* 1.3 78.6 - - - +
4659H TYR* 1.3 59.7 + - - +
4660H ASN 3.4 0.5 + - - -
4661H CYS* 3.4 8.0 + - - -
4662H LEU* 3.4 17.3 + - - +
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Residues in contact with TYR4659 (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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4557H PHE* 5.4 0.8 - - - +
4655H CYS* 2.8 24.5 + - - +
4656H ILE* 3.9 7.0 - - - +
4657H ILE 3.3 0.2 - - - -
4658H GLY* 1.3 74.7 - - - +
4660H ASN* 1.3 63.9 + - - +
4661H CYS 3.2 0.7 + - - -
4662H LEU* 3.3 23.4 + - + -
4663H LYS* 3.4 32.9 + - + +
4664H VAL* 3.2 26.3 - - + +
4667H VAL* 5.2 5.0 - - + +
4786H SER* 3.4 32.3 + - - -
4787H PHE* 4.0 30.5 - + + -
4790H LEU* 4.9 22.0 - - + -
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Residues in contact with ASN4660 (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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4656H ILE 3.3 12.9 + - - +
4657H ILE* 3.2 15.8 + - - +
4658H GLY 3.2 1.0 - - - -
4659H TYR* 1.3 78.1 - - - +
4661H CYS* 1.3 64.7 + - - +
4664H VAL* 3.5 22.2 - - - +
4665H PRO* 3.3 18.9 - - - +
4778H PHE* 6.3 1.4 - - - -
4781H ILE* 6.2 1.2 - - - +
4787H PHE* 5.9 5.1 - - + -
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Residues in contact with CYS4661 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4550H LEU* 4.2 37.2 - - - +
4554H SER* 4.4 18.2 - - - +
4657H ILE 4.0 12.3 - - - -
4658H GLY* 3.4 6.2 + - - +
4659H TYR 3.2 0.6 - - - -
4660H ASN* 1.3 87.9 - - - +
4662H LEU* 1.3 59.6 + - - +
4665H PRO* 4.2 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
------------------------------------------------------------
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