Contacts of the helix formed by residues 709 - 724 (chain B) in PDB entry 3HZJ
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 PRO 709 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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707B LYS 4.4 0.4 - - - +
708B PHE* 1.4 94.4 - - + +
710B LEU* 1.3 66.2 + - - +
711B CYS* 4.2 6.5 - - - -
712B MSE 3.1 6.3 + - + +
713B VAL* 3.0 18.0 + - - +
760B PRO* 3.2 30.5 - - + +
763B TYR* 3.2 31.2 - - + +
764B ARG* 3.6 17.5 - - + +
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Residues in contact with LEU 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B PHE* 5.2 13.7 - - + -
589B HIS* 4.1 29.2 - - + -
629B VAL* 4.7 8.1 - - + -
632B LEU* 4.1 14.8 - - + -
708B PHE 3.7 1.6 + - - -
709B PRO* 1.3 69.8 - - - +
711B CYS* 1.3 65.9 + - - +
713B VAL* 2.9 24.7 + - + +
714B PHE* 2.9 45.0 + - + -
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Residues in contact with CYS 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B ARG* 5.4 0.3 + - - -
709B PRO* 4.2 4.0 - - - -
710B LEU* 1.3 77.7 - - - +
712B MSE 1.3 72.0 + - - +
714B PHE* 3.8 14.0 - - - +
715B HIS* 3.2 27.5 + - - -
763B TYR 3.4 23.3 - - - -
764B ARG 3.4 20.0 - - - -
765B ALA 4.2 11.2 - - - -
766B GLU* 4.2 18.6 - - + +
769B ALA* 4.5 2.0 - - - -
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Residues in contact with MSE 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704B PHE* 5.0 1.6 - - - -
708B PHE* 3.2 46.4 - - + -
709B PRO* 3.1 12.5 + - + +
710B LEU 2.9 0.8 + - - -
711B CYS* 1.3 79.7 - - - +
713B VAL* 1.3 65.5 + - - +
715B HIS* 2.9 17.5 + - - +
716B ILE* 3.2 28.4 + - - +
731B VAL* 5.5 0.7 - - - -
735B LEU* 4.1 4.0 - - + -
763B TYR* 3.2 52.3 - - + +
769B ALA* 4.0 17.0 - - + -
772B LEU* 3.4 19.1 - - + -
773B MSE 4.2 8.9 - - + +
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Residues in contact with VAL 713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629B VAL* 4.0 19.5 - - + -
703B LEU 4.8 1.1 - - - +
704B PHE* 3.6 31.2 - - + +
705B THR* 3.8 19.7 - - + -
708B PHE* 3.6 14.1 - - + +
709B PRO 3.0 8.9 + - - +
710B LEU* 2.9 34.3 + - + +
712B MSE 1.3 72.6 - - - +
714B PHE* 1.3 73.2 + - + +
716B ILE* 3.1 12.2 + - + +
717B ILE* 3.0 26.7 + - - +
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Residues in contact with PHE 714 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B GLU* 3.8 15.9 - - - -
544B ARG* 3.6 21.1 + - - +
548B TRP* 3.9 7.8 - - - -
629B VAL* 3.6 29.6 - - + -
632B LEU* 3.8 25.4 - - + -
633B HIS* 3.4 34.8 - + + -
710B LEU* 2.9 48.7 + - + +
711B CYS* 3.8 11.2 - - - +
713B VAL* 1.3 77.5 - - + +
715B HIS* 1.3 60.3 + - - +
717B ILE* 3.4 1.5 + - - -
718B ASP* 3.2 27.2 + - - +
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Residues in contact with HIS 715 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B VAL 5.4 0.6 + - - -
536B LYS 5.1 2.0 + - - -
537B SER 4.1 7.6 - - - -
538B GLY* 3.8 29.5 + - - -
544B ARG* 4.0 11.8 + - - -
711B CYS 3.2 23.3 + - - -
712B MSE 2.9 8.7 + - - +
714B PHE* 1.3 75.4 - - - +
716B ILE* 1.3 65.6 + - - +
718B ASP* 3.3 10.8 + - - +
719B LEU* 3.2 26.2 + - - +
766B GLU* 2.7 34.6 + - - -
769B ALA* 4.1 12.1 - - + -
770B ARG* 4.6 13.1 + - + -
773B MSE 3.5 29.5 - - + +
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Residues in contact with ILE 716 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703B LEU* 3.9 15.5 - - + +
704B PHE* 3.2 44.4 - - + -
712B MSE 3.2 18.6 + - - +
713B VAL* 3.1 13.8 + - - +
715B HIS* 1.3 77.9 - - - +
717B ILE* 1.3 63.6 + - + +
719B LEU* 4.1 2.6 - - - +
720B LEU* 2.8 29.3 + - + +
727B ILE* 5.1 5.0 - - + +
728B ILE* 4.4 20.2 - - + -
731B VAL* 4.4 8.1 - - + -
773B MSE 3.7 25.1 - - + -
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Residues in contact with ILE 717 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B TRP* 3.6 29.2 - - + -
626B LEU* 3.7 26.0 - - + -
629B VAL* 4.1 19.7 - - + -
630B LEU* 4.3 9.0 - - + -
646B ILE* 4.9 4.5 - - + -
703B LEU* 4.4 7.2 - - + -
705B THR* 4.7 5.8 - - + -
713B VAL 3.0 16.4 + - - +
714B PHE 3.9 0.2 - - - +
715B HIS 3.2 0.2 - - - -
716B ILE* 1.3 84.6 - - + +
718B ASP* 1.3 66.7 + - - +
720B LEU* 4.1 14.6 - - + -
721B LEU* 3.0 51.3 + - + +
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Residues in contact with ASP 718 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B VAL* 3.7 22.4 - - + +
538B GLY* 4.3 0.5 - - - -
539B VAL* 3.3 25.6 + - + +
544B ARG* 2.7 34.6 + - - -
548B TRP* 2.6 37.4 + - - +
551B LEU* 4.1 4.1 - - - +
714B PHE 3.2 8.8 + - - +
715B HIS* 3.3 13.3 + - - +
717B ILE* 1.3 76.6 - - - +
719B LEU* 1.3 57.2 + - + +
721B LEU* 3.5 3.3 + - - +
722B CYS* 3.1 27.0 + - - +
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Residues in contact with LEU 719 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B VAL* 4.2 13.5 - - + +
536B LYS* 4.0 21.8 - - + +
715B HIS* 3.2 10.4 + - - +
716B ILE 4.1 2.0 - - - +
718B ASP* 1.3 75.9 - - - +
720B LEU* 1.3 67.4 + - - +
722B CYS* 4.3 3.4 - - + -
723B GLU* 2.8 42.7 + - - +
727B ILE* 3.6 29.2 - - + +
731B VAL* 5.7 0.2 - - + -
773B MSE 3.5 45.1 - - + -
776B ALA* 5.8 1.3 - - + -
777B CYS* 3.9 23.3 - - - -
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Residues in contact with LEU 720 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B ILE* 4.2 26.0 - - + -
650B TYR* 3.8 10.5 - - + -
703B LEU* 3.4 28.7 - - + -
716B ILE* 2.8 27.9 + - + +
717B ILE* 3.7 14.4 - - + +
719B LEU* 1.3 71.1 - - - +
721B LEU* 1.3 62.2 + - + +
724B GLY* 2.6 51.6 + - - +
725B LEU* 3.5 35.2 - - + +
727B ILE* 4.4 6.3 - - + +
728B ILE* 5.1 5.6 - - + -
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Residues in contact with LEU 721 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B TRP* 3.6 44.4 - - + +
551B LEU* 4.1 20.5 - - + +
630B LEU* 5.6 1.1 - - + -
642B VAL* 5.7 6.1 - - + +
645B LYS* 6.1 1.8 - - + -
646B ILE* 4.0 27.8 - - + -
650B TYR* 2.6 45.7 + - + +
717B ILE* 3.0 38.5 + - + +
718B ASP 3.8 2.9 - - - +
720B LEU* 1.3 82.4 - - + +
722B CYS* 1.3 62.4 + - - +
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Residues in contact with CYS 722 (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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532B SER* 3.4 37.5 - - - -
535B VAL* 3.8 23.6 - - + -
551B LEU* 4.3 20.1 - - + +
650B TYR* 5.5 0.2 - - - -
718B ASP 3.1 17.7 + - - +
719B LEU* 3.8 3.6 - - - +
720B LEU 3.1 0.2 - - - -
721B LEU* 1.3 80.8 - - - +
723B GLU* 1.3 70.5 + - + +
724B GLY 3.6 0.7 + - - -
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Residues in contact with GLU 723 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B SER* 4.7 13.8 - - - +
536B LYS* 6.1 0.9 - - - +
719B LEU* 2.8 30.7 + - - +
722B CYS* 1.3 87.7 - - + +
724B GLY* 1.3 61.4 + - - +
726B ASN* 5.0 4.5 + - - +
727B ILE* 3.2 31.3 + - + +
730B HIS* 6.0 0.3 - - - -
777B CYS* 4.4 9.1 - - - +
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Residues in contact with GLY 724 (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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650B TYR* 4.1 15.0 - - - -
720B LEU* 2.6 34.7 + - - +
721B LEU 4.4 0.4 + - - -
722B CYS 3.4 3.2 + - - -
723B GLU* 1.3 73.6 - - - +
725B LEU* 1.3 64.0 + - - -
726B ASN 3.4 1.3 - - - -
727B ILE* 3.4 18.5 - - - +
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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
------------------------------------------------------------
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