Contacts of the helix formed by residues 649 - 668 (chain 5) in PDB entry 5U8T
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 THR 649 (chain 5).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4113 PRO* 4.4 7.2 - - + +
4123 SER* 3.0 20.2 - - - +
5513 ASP* 4.2 6.3 - - - +
5485 SER* 3.4 32.5 + - - -
6265 PHE* 3.5 7.8 - - - -
6305 ARG* 3.3 16.3 + - - +
6475 PRO 4.2 1.6 - - - +
6485 ILE* 1.3 88.6 - - - +
6505 ILE* 1.3 61.5 + - - +
6515 ARG* 2.8 21.5 + - - +
6525 GLN* 2.9 28.7 + - + +
6535 LEU 3.9 0.3 + - - -
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Residues in contact with ILE 650 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4123 SER* 3.1 29.5 + - - +
4133 THR* 5.2 0.2 - - - -
5513 ASP* 4.4 6.5 + - - +
5613 ILE* 3.9 35.0 - - + -
5653 VAL* 5.6 7.6 - - + +
10013 ANP 3.3 36.9 - - + +
6265 PHE* 4.9 2.2 - - + -
6305 ARG* 3.2 20.2 - - - +
6495 THR* 1.3 72.9 - - - +
6515 ARG* 1.3 62.9 + - - +
6525 GLN 3.2 1.8 - - - -
6535 LEU* 4.1 10.1 + - + +
6545 GLU* 3.6 18.5 + - - +
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Residues in contact with ARG 651 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4123 SER* 3.8 16.8 - - - +
10013 ANP 2.4 80.3 + - - +
4075 ARG* 3.8 16.8 - - - +
4985 GLU* 3.2 39.8 + - - +
4995 GLN* 4.6 0.4 - - - +
5485 SER* 3.7 19.1 + - - +
5495 ARG* 3.6 18.8 - - - +
5515 ASP* 4.1 1.3 - - - +
6495 THR* 2.8 9.9 + - - +
6505 ILE* 1.3 79.4 - - - +
6525 GLN* 1.3 59.2 + - - +
6545 GLU* 3.8 14.8 - - - +
6555 ALA* 2.9 26.9 + - - +
6585 ARG* 3.9 3.1 - - - +
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Residues in contact with GLN 652 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5475 LEU 3.7 7.8 - - - +
5485 SER* 3.6 20.9 + - - +
5505 PHE 4.3 4.6 - - - +
5515 ASP* 4.5 4.6 + - - -
5535 ILE* 4.6 4.7 - - - +
6265 PHE* 5.1 2.2 - - + -
6475 PRO 2.9 27.8 + - - +
6485 ILE* 4.4 8.9 - - + +
6495 THR* 2.9 39.7 + - - +
6505 ILE 3.2 0.6 - - - -
6515 ARG* 1.3 76.0 - - - +
6535 LEU* 1.3 64.4 + - - +
6555 ALA* 3.1 7.3 + - - +
6565 ILE* 2.9 30.9 + - + +
6845 PHE* 3.4 32.7 - - + -
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Residues in contact with LEU 653 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5583 ASP* 4.6 1.3 - - - +
5613 ILE* 5.5 4.7 - - + -
5623 SER* 4.4 25.6 - - - -
5653 VAL* 5.2 6.5 - - + -
5663 LEU* 4.3 8.1 - - + -
6225 LEU* 4.0 27.5 - - + +
6265 PHE* 3.3 54.8 - - + -
6495 THR 3.9 3.0 + - - -
6505 ILE* 4.2 8.7 - - - +
6525 GLN* 1.3 77.0 - - - +
6545 GLU* 1.3 59.3 + - - +
6565 ILE* 3.0 17.6 + - + +
6575 ILE* 2.9 37.2 + - + +
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Residues in contact with GLU 654 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5653 VAL* 5.0 9.2 - - + -
5693 HIS* 4.2 12.3 + - + -
10013 ANP 4.5 10.1 + - + +
4065 LEU* 4.0 35.0 - - + +
4075 ARG* 5.0 1.3 + - - +
6505 ILE 3.6 15.9 + - - +
6515 ARG* 3.8 13.7 - - - +
6525 GLN 3.2 0.2 - - - -
6535 LEU* 1.3 76.5 - - - +
6555 ALA* 1.3 64.4 + - - +
6575 ILE* 2.9 31.4 - - + +
6585 ARG* 2.6 66.0 + - - +
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Residues in contact with ALA 655 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4105 ILE* 4.1 2.4 - - - +
5515 ASP* 3.2 39.0 - - + +
6515 ARG 2.9 21.0 + - - +
6525 GLN* 3.1 11.6 + - - +
6545 GLU* 1.3 76.9 + - - +
6565 ILE* 1.3 62.7 + - + +
6585 ARG* 3.2 25.7 + - - +
6595 ILE* 3.4 18.7 + - + +
6845 PHE* 6.2 0.4 - - + -
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Residues in contact with ILE 656 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6225 LEU* 4.9 10.3 - - + -
6265 PHE* 5.5 2.5 - - + -
6295 ILE* 4.6 17.0 - - + -
6525 GLN* 2.9 17.6 + - + +
6535 LEU* 3.4 15.3 - - + +
6555 ALA* 1.3 73.3 - - + +
6575 ILE* 1.3 64.0 + - - +
6595 ILE* 3.4 17.3 + - + +
6605 THR* 3.2 16.8 + - + +
6805 ALA* 4.4 13.7 - - + +
6815 ILE* 4.6 18.4 - - + -
6845 PHE* 3.5 52.3 - - + -
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Residues in contact with ILE 657 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5653 VAL* 4.1 10.3 - - + -
5663 LEU* 3.5 26.7 - - + -
5693 HIS* 3.8 32.8 - - + +
3965 SER* 4.3 0.7 - - - +
6145 LEU* 4.7 6.5 - - + -
6225 LEU* 3.7 20.4 - - + +
6535 LEU* 2.9 18.8 + - + +
6545 GLU* 2.9 24.4 + - - +
6565 ILE* 1.3 75.9 - - - +
6585 ARG* 1.3 53.2 + - - +
6605 THR* 2.5 41.7 + - - +
6615 GLU* 2.6 27.5 - - - +
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Residues in contact with ARG 658 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3955 GLY* 3.8 2.4 - - - -
3965 SER* 3.2 19.3 - - - +
4065 LEU* 6.2 0.2 - - + -
4075 ARG* 3.0 64.2 - - - +
4095 ASP* 3.2 19.8 - - - +
4105 ILE* 3.3 17.5 - - + +
5515 ASP* 2.9 31.5 + - - -
6515 ARG* 3.6 4.9 + - - +
6545 GLU* 2.6 52.6 + - - +
6555 ALA* 3.2 17.6 + - - +
6575 ILE* 1.3 75.3 - - + +
6595 ILE* 1.3 56.4 + - - +
6615 GLU* 3.3 9.8 + - - +
6625 SER* 2.9 27.7 + - - -
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Residues in contact with ILE 659 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3905 CYS* 4.5 8.3 - - + -
4105 ILE* 3.9 7.6 - - + -
5515 ASP* 5.5 0.9 - - + -
5525 MET* 3.6 38.1 - - + -
6555 ALA* 3.4 19.1 - - + +
6565 ILE* 3.5 24.5 - - + +
6575 ILE 3.1 0.8 - - - -
6585 ARG* 1.3 72.0 - - - +
6605 THR* 1.3 60.0 + - - +
6625 SER* 2.2 33.1 + - - +
6635 LEU* 3.0 14.8 + - + +
6805 ALA* 3.6 22.0 - - + +
6835 LEU* 4.2 18.8 - - + -
6845 PHE* 4.6 13.0 - - + -
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Residues in contact with THR 660 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6145 LEU* 3.6 15.7 - - + +
6225 LEU* 4.7 4.5 - - + -
6565 ILE* 3.2 13.9 - - + +
6575 ILE* 2.5 27.3 + - - +
6595 ILE* 1.3 78.4 - - - +
6615 GLU* 1.3 73.2 + - - +
6635 LEU* 3.4 2.8 + - - +
6645 ALA* 2.9 31.7 + - - +
6765 HIS* 4.9 2.6 + - - -
6775 VAL* 3.4 44.4 - - + +
6805 ALA* 4.4 10.3 - - + +
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Residues in contact with GLU 661 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5693 HIS* 4.8 9.2 + - - +
3945 GLY 4.3 0.5 - - - +
3955 GLY* 4.4 2.0 - - - -
3965 SER* 3.0 43.9 + - - +
6125 PRO* 3.0 45.2 - - + +
6135 ARG* 4.1 8.2 - - - +
6145 LEU* 4.1 15.4 + - - +
6575 ILE* 2.6 37.2 - - - +
6585 ARG* 3.3 2.3 - - - -
6605 THR* 1.3 92.9 + - - +
6625 SER* 1.3 57.1 + - - +
6645 ALA* 3.8 8.1 - - - -
6655 LYS* 2.9 22.3 + - - +
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Residues in contact with SER 662 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3905 CYS* 3.0 44.4 - - - +
3935 MET* 4.3 3.6 - - - +
3945 GLY 3.9 11.2 - - - -
3955 GLY* 4.0 1.0 - - - -
4095 ASP* 3.4 15.0 - - - -
6585 ARG 2.9 8.2 + - - -
6595 ILE* 2.2 30.3 + - - -
6615 GLU* 1.3 73.1 - - - +
6635 LEU* 1.3 57.5 + - - +
6645 ALA 2.9 3.6 - - - -
6655 LYS* 2.7 24.9 + - - +
6665 LEU* 3.0 12.8 + - - +
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Residues in contact with LEU 663 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3675 TYR* 3.8 41.3 - - + +
3905 CYS* 4.4 5.8 - - + +
6595 ILE* 3.0 14.5 + - + +
6605 THR* 4.0 3.6 - - - +
6625 SER* 1.3 82.7 + - - +
6645 ALA* 1.3 56.4 + - - +
6665 LEU* 3.1 30.3 - - + +
6675 GLU* 3.9 1.2 + - - +
6765 HIS* 3.6 48.9 + - + +
6795 GLU* 4.5 6.7 - - + +
6805 ALA* 4.0 24.0 - - + +
6835 LEU* 5.0 4.3 - - + -
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Residues in contact with ALA 664 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6125 PRO* 4.3 8.5 - - + -
6135 ARG 5.6 0.7 - - - +
6605 THR 2.9 20.3 + - - +
6615 GLU* 3.8 9.9 - - - +
6635 LEU* 1.3 75.3 - - - +
6655 LYS* 1.3 57.7 + - - +
6665 LEU 3.0 4.7 - - - -
6675 GLU* 2.8 25.8 + - - +
6685 LEU 3.4 3.1 + - - -
6695 SER* 3.9 6.1 + - - +
6715 ILE 4.1 7.9 - - - +
6725 ALA* 4.0 13.9 - - + -
6765 HIS* 3.1 24.2 - - + +
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Residues in contact with LYS 665 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3935 MET* 3.2 21.0 - - + +
3945 GLY 3.5 22.7 - - - +
3955 GLY 4.9 3.8 - - - +
6065 CYS* 2.3 66.2 + - - +
6075 ARG* 4.2 7.9 - - - +
6095 LYS* 3.1 26.0 + - - +
6105 CYS 3.7 7.7 + - - -
6115 ALA* 4.3 3.8 - - - +
6125 PRO* 3.5 28.0 - - + +
6615 GLU 2.9 16.9 + - - +
6625 SER 2.7 11.6 + - - +
6645 ALA* 1.3 68.3 - - - +
6665 LEU* 1.3 65.0 + - - +
6685 LEU* 3.4 4.0 + - - +
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Residues in contact with LEU 666 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3615 SER* 5.0 2.1 - - - -
3665 LEU* 4.4 8.4 - - + +
3675 TYR* 3.3 41.5 - - + -
3705 LEU* 3.5 25.6 - - + -
3895 VAL* 3.6 20.2 - - + -
3905 CYS* 5.7 1.3 - - + -
3935 MET* 3.5 29.3 - - + +
6025 TYR* 2.7 22.4 + - - +
6065 CYS* 5.1 0.3 - - - -
6625 SER 3.0 11.3 + - - +
6635 LEU* 3.1 25.4 - - + +
6655 LYS* 1.3 79.1 - - - +
6675 GLU* 1.3 61.7 + - - +
6685 LEU* 3.1 5.1 + - - +
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Residues in contact with GLU 667 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3615 SER* 3.4 31.5 - - - +
3665 LEU* 6.1 0.4 - - - -
6635 LEU 3.9 0.2 + - - -
6645 ALA 2.8 16.2 + - - +
6665 LEU* 1.3 74.2 - - - +
6685 LEU* 1.3 67.9 + - - +
6695 SER* 2.8 26.9 + - - +
6715 ILE* 4.1 2.3 - - - +
6725 ALA* 4.9 0.2 - - - -
6735 GLN* 3.1 27.9 + - - +
6765 HIS* 2.7 37.7 + - - +
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Residues in contact with LEU 668 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3575 PHE* 4.4 19.7 - - + +
3585 LEU* 4.4 21.8 - - + -
3615 SER* 4.9 4.3 - - - -
6025 TYR* 6.1 4.0 - - + -
6055 TYR* 3.7 33.0 - - + +
6065 CYS* 3.6 22.7 - - + -
6095 LYS* 5.3 10.1 - - + -
6645 ALA 3.4 3.2 + - - -
6655 LYS* 3.4 8.6 + - - +
6665 LEU 3.1 7.5 + - - +
6675 GLU* 1.3 80.0 - - - +
6695 SER* 1.3 58.8 + - - +
6705 PRO* 3.9 5.9 - - - +
15A ARG* 4.8 13.9 + - - +
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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