Contacts of the helix formed by residues 4639 - 4661 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4635B GLY 3.4 19.3 - - - +
4636B TYR* 3.5 14.4 - - + +
4638B GLU* 1.3 93.9 - - + +
4640B ALA* 1.3 60.0 + - - +
4641B LEU 3.2 1.4 + - - -
4642B ARG* 3.5 8.5 + - + +
4643B CYS* 3.4 19.8 + - - +
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Residues in contact with ALA4640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4574B ILE* 5.9 7.9 - - + -
4636B TYR 3.5 17.6 + - - +
4637B MET* 3.4 11.6 + - - +
4638B GLU 3.1 2.0 - - - -
4639B PRO* 1.3 77.2 - - - +
4641B LEU* 1.3 60.5 + - - +
4642B ARG 3.3 0.2 - - - -
4643B CYS* 3.9 4.5 - - - -
4644B LEU* 3.1 48.0 + - + +
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Residues in contact with LEU4641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4571B ILE* 5.7 2.8 - - - +
4574B ILE* 5.9 9.8 - - + +
4575B LEU* 6.4 2.0 - - + -
4629B PHE* 6.3 2.9 - - + -
4630B LEU* 5.9 7.0 - - + +
4637B MET 4.1 3.8 + - - +
4638B GLU* 3.3 23.8 + - - +
4639B PRO 3.2 1.2 - - - -
4640B ALA* 1.3 79.2 - - - +
4642B ARG* 1.3 62.3 + - + +
4643B CYS 3.4 0.2 - - - -
4644B LEU* 5.5 0.2 - - - -
4645B SER* 2.5 33.6 + - - -
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Residues in contact with ARG4642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4639B PRO* 3.5 8.1 + - + +
4640B ALA 3.3 0.2 - - - -
4641B LEU* 1.3 90.6 - - + +
4643B CYS* 1.3 62.2 + - - +
4645B SER* 3.4 4.9 - - - -
4646B LEU* 3.3 29.1 - - + +
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Residues in contact with CYS4643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4639B PRO 3.4 15.3 + - - +
4640B ALA* 3.6 4.5 + - - +
4642B ARG* 1.3 78.3 - - - +
4644B LEU* 1.3 79.4 + - + +
4645B SER 3.3 0.6 + - - -
4646B LEU* 3.6 4.7 + - - +
4647B LEU* 3.6 23.5 + - - +
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Residues in contact with LEU4644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4567B LEU* 3.8 34.1 - - + +
4570B ALA* 4.7 22.7 - - + +
4571B ILE* 5.0 17.5 - - + +
4640B ALA* 3.1 36.8 + - + +
4641B LEU* 5.5 0.2 - - - -
4643B CYS* 1.3 91.2 - - - +
4645B SER* 1.3 62.9 + - - +
4646B LEU 3.4 0.2 - - - -
4647B LEU* 3.7 8.1 + - + +
4648B HIS* 3.4 22.5 + - - +
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Residues in contact with SER4645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4571B ILE* 4.8 16.3 - - - +
4641B LEU 2.5 28.2 + - - -
4642B ARG* 3.4 11.6 + - - -
4644B LEU* 1.3 78.1 - - - +
4646B LEU* 1.3 68.1 + - - +
4648B HIS* 3.8 4.7 + - - +
4649B THR* 3.3 24.6 + - - +
4800B GLY 5.8 2.0 - - - -
4801B HIS* 3.9 16.1 + - - -
4807B PHE* 5.0 11.4 - - - -
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Residues in contact with LEU4646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4642B ARG* 3.3 24.5 - - + +
4643B CYS 3.6 4.8 + - - +
4644B LEU 3.4 0.4 - - - -
4645B SER* 1.3 80.7 - - - +
4647B LEU* 1.3 63.0 + - - +
4649B THR* 2.6 22.5 + - - +
4650B LEU* 3.2 26.7 + - + +
4801B HIS* 3.6 27.4 - - + +
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Residues in contact with LEU4647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4563B LEU* 4.8 6.7 - - + -
4567B LEU* 3.7 33.0 - - + -
4643B CYS* 3.6 17.1 + - - +
4644B LEU* 4.2 6.3 - - + +
4645B SER 3.5 0.2 - - - -
4646B LEU* 1.3 79.1 - - - +
4648B HIS* 1.3 62.8 + - - +
4649B THR 3.2 0.9 + - - -
4650B LEU* 3.3 7.2 + - + +
4651B VAL* 3.2 37.4 + - + +
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Residues in contact with HIS4648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4563B LEU 5.2 0.2 - - - -
4564B ALA* 4.8 12.1 + - + -
4567B LEU* 4.2 23.5 - - + +
4568B ALA* 5.0 7.9 - - - +
4571B ILE* 5.9 9.2 - - + -
4644B LEU 3.4 15.6 + - - +
4645B SER* 4.1 6.3 - - - +
4646B LEU 3.3 0.4 - - - -
4647B LEU* 1.3 78.8 - - - +
4649B THR* 1.3 62.4 + - - +
4651B VAL* 3.3 19.4 - - + +
4652B ALA* 3.6 10.9 + - - +
4793B TYR* 2.4 42.5 + + - -
4797B SER* 4.3 10.0 + - - -
4807B PHE* 5.6 4.3 - + + -
4810B HIS* 3.3 35.9 + + - +
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Residues in contact with THR4649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4645B SER 3.3 8.0 + - - +
4646B LEU* 2.6 31.2 + - - +
4648B HIS* 1.3 80.8 - - - +
4650B LEU* 1.3 67.9 + - - +
4652B ALA* 3.5 5.0 + - - +
4653B PHE* 3.2 23.4 + - - +
4797B SER* 3.6 33.6 - - - +
4798B LEU* 5.3 5.6 - - + -
4801B HIS* 3.5 25.9 + - + +
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Residues in contact with LEU4650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4646B LEU* 3.2 38.7 + - + +
4647B LEU* 3.3 6.7 + - + +
4649B THR* 1.3 82.4 - - - +
4651B VAL* 1.3 65.8 + - + +
4653B PHE* 3.5 10.4 + - + +
4654B LEU* 3.2 24.4 + - - +
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Residues in contact with VAL4651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4560B LEU* 3.3 50.1 - - + +
4563B LEU* 4.3 25.8 - - + -
4564B ALA* 5.2 8.1 - - + +
4567B LEU* 5.5 0.9 - - + -
4647B LEU* 3.2 37.2 + - + +
4648B HIS* 3.3 22.9 - - + +
4650B LEU* 1.3 78.9 - - + +
4652B ALA* 1.3 60.0 + - + +
4654B LEU* 4.0 2.2 - - - -
4655B CYS* 3.5 5.5 + - - +
4793B TYR* 6.6 0.2 - - + -
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Residues in contact with ALA4652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4648B HIS 3.6 15.0 - - - +
4649B THR 3.5 5.7 + - - +
4650B LEU 3.2 0.4 - - - -
4651B VAL* 1.3 81.4 - - + +
4653B PHE* 1.3 63.3 + - - +
4655B CYS* 3.4 11.9 + - - +
4656B ILE* 3.3 18.6 + - - +
4793B TYR* 4.3 21.8 - - + -
4794B MET* 4.9 9.9 - - + +
4797B SER* 4.1 18.2 - - - +
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Residues in contact with PHE4653 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4649B THR 3.2 17.2 + - - +
4650B LEU* 4.0 11.7 - - + +
4652B ALA* 1.3 76.8 - - - +
4654B LEU* 1.3 64.4 + - - +
4656B ILE* 3.4 31.9 + - + +
4657B ILE* 3.8 8.4 + - + +
4794B MET* 5.7 1.5 - - + +
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Residues in contact with LEU4654 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4549B PHE* 5.4 14.4 - - + -
4553B LEU* 4.5 8.8 - - + +
4560B LEU* 3.8 19.1 - - + +
4650B LEU 3.2 17.2 + - - +
4651B VAL* 4.2 1.6 - - - +
4652B ALA 3.3 0.2 - - - -
4653B PHE* 1.3 77.5 - - - +
4655B CYS* 1.3 60.2 + - - +
4656B ILE 3.4 0.2 + - - -
4657B ILE* 3.4 7.1 + - - +
4658B GLY* 3.0 24.1 + - - -
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Residues in contact with CYS4655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4557B PHE* 5.1 11.4 - - - -
4560B LEU* 3.5 13.6 - - + +
4561B ARG* 4.3 20.2 - - - +
4651B VAL 3.5 12.2 + - - +
4652B ALA* 3.4 12.3 + - - +
4653B PHE 3.3 0.8 - - - -
4654B LEU* 1.3 75.8 - - - +
4656B ILE* 1.3 61.2 + - + +
4658B GLY* 3.8 2.2 - - - +
4659B TYR* 2.8 37.1 + - - +
4790B LEU* 3.8 30.9 - - + +
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Residues in contact with ILE4656 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4652B ALA 3.3 18.6 - - - +
4653B PHE* 3.7 32.8 - - + +
4654B LEU 3.2 0.6 - - - -
4655B CYS* 1.3 79.1 - - + +
4657B ILE* 1.3 61.0 + - - +
4659B TYR* 3.5 5.1 + - - +
4660B ASN* 3.3 19.4 + - - +
4787B PHE* 4.4 27.6 - - + -
4790B LEU* 5.3 10.8 - - + +
4791B GLY* 5.9 4.3 - - - -
4794B MET* 3.9 23.1 - - + -
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Residues in contact with ILE4657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4549B PHE* 5.0 17.0 - - + -
4550B LEU* 5.5 11.9 - - + +
4553B LEU* 5.1 2.7 - - + -
4653B PHE* 3.8 9.4 + - + +
4654B LEU* 3.4 7.9 + - - +
4655B CYS 3.4 0.2 - - - -
4656B ILE* 1.3 75.9 - - - +
4658B GLY* 1.3 65.6 + - - +
4660B ASN* 3.2 20.4 + - - +
4661B CYS* 3.9 10.9 + - - -
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Residues in contact with GLY4658 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4550B LEU 5.4 0.9 - - - -
4553B LEU* 4.1 28.4 - - - +
4554B SER* 4.2 9.4 - - - -
4557B PHE* 4.9 7.0 - - - -
4654B LEU 3.0 15.5 + - - -
4655B CYS* 3.9 2.2 - - - -
4657B ILE* 1.3 78.7 - - - +
4659B TYR* 1.3 61.1 + - - +
4660B ASN 3.4 0.2 + - - -
4661B CYS* 3.4 7.8 + - - -
4662B LEU* 3.4 17.8 + - - +
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Residues in contact with TYR4659 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4557B PHE* 5.4 1.0 - - - +
4655B CYS* 2.8 24.8 + - - +
4656B ILE* 3.9 5.8 - - - +
4658B GLY* 1.3 74.3 - - - +
4660B ASN* 1.3 64.8 + - - +
4661B CYS 3.2 1.1 + - - -
4662B LEU* 3.3 22.3 + - + -
4663B LYS* 3.4 33.6 + - + +
4664B VAL* 3.2 27.1 - - + +
4667B VAL* 5.2 5.3 - - + +
4786B SER* 3.4 33.3 + - - -
4787B PHE* 4.0 30.5 - + + -
4790B LEU* 4.9 23.6 - - + -
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Residues in contact with ASN4660 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4656B ILE 3.3 12.5 + - - +
4657B ILE* 3.2 15.8 + - - +
4658B GLY 3.2 1.0 - - - -
4659B TYR* 1.3 77.9 - - - +
4661B CYS* 1.3 65.1 + - - +
4664B VAL* 3.5 22.9 - - - +
4665B PRO* 3.3 18.4 - - - +
4778B PHE* 6.3 1.6 - - - -
4781B ILE* 6.2 1.2 - - - +
4787B PHE* 5.9 5.5 - - + -
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Residues in contact with CYS4661 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4550B LEU* 4.2 36.8 - - + +
4554B SER* 4.4 16.4 - - - +
4657B ILE 4.0 12.1 - - - -
4658B GLY* 3.4 7.1 + - - +
4659B TYR 3.2 0.6 - - - -
4660B ASN* 1.3 88.2 - - - +
4662B LEU* 1.3 58.7 + - - +
4665B PRO* 4.2 12.7 - - - +
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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