Contacts of the helix formed by residues 743 - 759 (chain B) in PDB entry 6MZL
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 SER 743 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740B ASN 4.5 1.0 + - - -
741B PHE 3.1 6.4 + - - -
742B MET* 1.3 77.6 - - - +
744B PHE* 1.3 58.8 + - - +
745B GLN* 3.1 7.4 - - - -
746B SER* 2.3 67.1 + - - -
747B TYR* 3.2 2.5 + - - +
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Residues in contact with PHE 744 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B ILE* 3.6 44.0 - - + -
339B THR* 5.4 11.0 - - + -
692B TYR* 4.6 14.2 - - + +
741B PHE* 5.5 0.2 - - + -
742B MET* 3.9 15.2 + - - -
743B SER* 1.3 72.0 - - - +
745B GLN* 1.3 65.1 + - - +
747B TYR* 3.6 18.9 - + + +
748B PHE* 3.5 28.5 + - + +
789B PHE* 3.9 24.9 - + - -
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Residues in contact with GLN 745 (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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688B GLU 4.1 14.6 - - - +
689B GLN* 3.7 35.8 + - - +
690B CYS 5.5 0.4 - - - +
692B TYR* 3.5 38.2 + - + +
695B ARG* 5.2 2.3 + - - +
743B SER* 3.1 3.8 + - - +
744B PHE* 1.3 78.8 - - - +
746B SER* 1.3 63.3 + - - +
747B TYR 3.2 0.5 + - - -
748B PHE* 3.5 3.5 + - - +
749B LEU* 3.0 24.4 + - - +
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Residues in contact with SER 746 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727B PHE* 4.6 17.3 - - - -
740B ASN 3.5 17.5 + - - -
741B PHE* 4.9 0.2 - - - -
743B SER* 2.3 44.9 + - - -
745B GLN* 1.3 76.5 - - - +
747B TYR* 1.3 57.8 + - - +
749B LEU* 4.1 8.3 - - - -
750B GLN* 2.8 35.1 + - - +
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Residues in contact with TYR 747 (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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336B ILE* 3.7 37.3 - - + +
337B ASP* 3.4 30.9 + - - -
741B PHE* 3.4 49.4 - + + -
743B SER 3.2 1.7 + - - +
744B PHE* 3.7 27.8 - + + +
745B GLN 3.1 1.0 - - - -
746B SER* 1.3 81.6 + - - +
748B PHE* 1.3 80.6 + + - +
750B GLN* 4.1 1.6 - - - +
751B LYS* 3.0 32.4 + - + +
789B PHE 6.1 0.9 - - - -
792B ASN 5.7 0.3 + - - -
793B TYR* 3.6 23.0 + - - +
794B TYR* 5.2 8.4 - + + -
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Residues in contact with PHE 748 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B ILE* 5.5 2.9 - - + -
337B ASP* 3.3 27.1 - - - -
340B PRO* 5.7 9.2 - - + -
390B GLU* 4.7 1.1 - - - -
692B TYR* 3.6 44.0 - + + -
693B ARG* 4.0 25.1 - - - -
696B MET* 4.5 22.9 - - + -
744B PHE* 3.5 9.1 + - + -
745B GLN 3.5 6.3 + - - +
747B TYR* 1.3 98.3 - + - +
749B LEU* 1.3 58.3 + - - +
751B LYS* 3.2 11.8 + - + +
752B THR* 2.9 35.1 + - - -
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Residues in contact with LEU 749 (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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686B GLU* 4.6 9.6 - - + +
692B TYR 5.4 1.1 - - - +
695B ARG* 4.0 32.3 - - + +
696B MET* 5.2 2.2 - - + +
699B CYS* 4.6 7.6 - - - -
726B MET* 3.7 30.7 - - + -
727B PHE* 4.6 8.5 - - + -
745B GLN 3.0 18.9 + - - +
746B SER* 3.8 7.6 - - - +
747B TYR 3.2 0.2 - - - -
748B PHE* 1.3 77.4 - - - +
750B GLN* 1.3 58.6 + - - +
752B THR* 3.2 4.3 + - - -
753B MET* 3.0 62.1 + - + +
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Residues in contact with GLN 750 (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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723B PHE* 4.8 13.0 - - + -
727B PHE* 3.3 45.6 - - + -
736B VAL* 4.6 4.2 - - - +
740B ASN* 3.5 39.3 + - - +
741B PHE* 4.2 12.0 - - + -
746B SER* 2.8 17.1 + - - +
747B TYR* 4.2 2.2 - - - +
749B LEU* 1.3 76.1 - - - +
751B LYS* 1.3 62.1 + - - +
754B PRO* 3.3 18.5 - - - +
794B TYR* 3.1 42.3 + - + +
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Residues in contact with LYS 751 (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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337B ASP* 2.3 40.0 + - - +
696B MET* 6.5 0.9 - - + -
747B TYR* 3.0 32.7 + - + +
748B PHE* 3.2 15.6 + - + +
750B GLN* 1.3 77.1 - - - +
752B THR* 1.3 64.5 + - - +
754B PRO* 4.4 4.2 - - - +
755B VAL* 4.8 0.9 - - - +
793B TYR* 3.6 28.0 - - + +
794B TYR* 3.9 13.6 - - + -
797B GLU* 3.3 49.3 + - + +
798B MET* 5.3 0.3 + - - +
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Residues in contact with THR 752 (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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696B MET* 3.2 60.9 - - + +
699B CYS* 4.4 7.2 - - + -
700B PHE* 4.4 15.7 - - + -
748B PHE 2.9 16.7 + - - -
749B LEU* 3.9 4.0 - - - -
750B GLN 3.2 0.2 - - - -
751B LYS* 1.3 81.8 - - - +
753B MET* 1.3 69.3 + - - +
754B PRO* 3.4 1.3 - - - +
755B VAL* 3.0 25.3 + - + +
756B ALA 4.0 1.0 + - - -
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Residues in contact with MET 753 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686B GLU* 5.6 2.0 - - - +
699B CYS* 3.5 26.9 - - - -
719B MET* 3.7 28.2 - - + +
722B LEU* 3.7 35.4 - - + -
723B PHE* 3.5 28.7 - - + -
726B MET* 5.1 2.7 - - - +
727B PHE* 4.9 3.6 - - - -
749B LEU* 3.0 42.6 + - + +
752B THR* 1.3 76.1 - - - +
754B PRO* 1.3 68.2 - - + +
756B ALA* 3.1 7.1 + - - +
757B MET* 3.0 24.1 + - - +
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Residues in contact with PRO 754 (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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723B PHE* 3.9 12.3 - - + -
750B GLN 3.3 20.6 - - - +
751B LYS 4.7 3.8 - - - +
752B THR 3.5 3.1 - - - +
753B MET* 1.3 91.1 - - + +
755B VAL* 1.3 57.7 + - + +
756B ALA 3.4 0.2 - - - -
757B MET* 3.5 14.2 - - + +
758B ALA* 2.8 27.9 + - - +
775B ILE* 3.6 13.1 - - + +
778B LEU* 4.2 22.0 - - + -
794B TYR* 5.5 1.8 - - + +
797B GLU 5.4 0.2 - - - +
798B MET* 4.4 21.1 - - + -
801B ALA* 3.6 8.4 - - + +
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Residues in contact with VAL 755 (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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700B PHE* 4.1 19.7 - - + -
751B LYS 4.8 1.3 - - - +
752B THR* 3.0 13.7 + - + +
754B PRO* 1.3 78.1 - - + +
756B ALA* 1.3 58.9 + - - +
758B ALA* 2.9 18.7 + - - +
759B LEU* 3.0 12.9 + - + +
797B GLU* 3.3 41.5 - - + +
800B ASP* 4.4 3.6 - - + +
801B ALA* 3.7 15.0 - - + +
804B ASN* 3.9 24.7 + - + +
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Residues in contact with ALA 756 (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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699B CYS* 3.3 48.0 - - + +
700B PHE* 3.6 11.4 - - + -
703B ALA* 4.0 1.8 - - + +
719B MET* 4.0 5.6 - - + -
752B THR 4.0 0.6 + - - -
753B MET* 3.1 6.2 + - - +
755B VAL* 1.3 79.4 - - - +
757B MET* 1.3 62.2 + - - +
759B LEU* 3.2 23.8 + - - +
760B LEU* 3.3 16.9 - - - +
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Residues in contact with MET 757 (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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718B ALA 4.0 3.4 - - - +
719B MET* 3.6 30.5 - - + +
720B LYS* 3.6 42.8 - - + +
723B PHE* 4.0 24.0 - - - -
753B MET* 3.0 15.2 + - - +
754B PRO* 3.5 16.8 - - + +
756B ALA* 1.3 77.7 - - - +
758B ALA* 1.3 56.5 + - - +
759B LEU 3.1 0.2 - - - -
760B LEU* 3.0 33.2 + - + +
768B PRO* 5.2 0.2 - - - +
771B VAL* 3.3 25.9 - - + +
774B PHE* 4.0 20.0 - - + -
775B ILE* 5.1 0.7 - - + -
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Residues in contact with ALA 758 (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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754B PRO 2.8 14.5 + - - +
755B VAL 2.9 9.4 + - - +
757B MET* 1.3 74.8 - - - +
759B LEU* 1.3 59.1 + - - +
760B LEU 3.3 0.7 - - - -
761B ARG* 3.2 12.3 + - - +
768B PRO* 4.8 7.4 - - - +
771B VAL* 3.9 8.7 - - + +
775B ILE* 4.0 8.7 - - + -
801B ALA* 3.3 32.5 - - + +
804B ASN 3.0 19.5 - - - +
805B SER* 4.5 5.7 - - - +
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Residues in contact with LEU 759 (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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700B PHE* 4.3 14.8 - - + -
703B ALA* 3.7 25.1 - - + -
707B ASN* 3.0 25.4 + - - +
755B VAL 3.0 11.8 + - - +
756B ALA* 3.4 16.2 - - - +
757B MET 3.1 0.4 - - - -
758B ALA* 1.3 79.6 - - - +
760B LEU* 1.3 59.3 + - - +
761B ARG* 3.0 17.3 + - - +
804B ASN* 3.3 42.2 - - - +
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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
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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