Contacts of the helix formed by residues 736 - 753 (chain D) in PDB entry 3T6A
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 736 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587C THR 3.8 5.4 + - - -
588C LEU* 6.0 1.2 - - - +
589C PRO* 4.2 11.4 - - - +
717C MET* 4.2 2.0 - - - +
733D ASN 4.1 11.7 - - - -
734D ASP 2.7 12.5 + - - -
735D GLN* 1.3 73.9 - - - +
737D CYS* 1.3 64.3 + - - +
738D GLU* 3.2 18.9 + - - +
739D ILE* 3.3 21.1 + - - +
740D MET* 3.0 25.1 + - - +
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Residues in contact with CYS 737 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587C THR* 3.0 39.2 + - + +
713C LEU* 4.0 7.4 - - - -
717C MET* 3.6 30.1 - - - +
744C LEU* 4.3 10.5 - - + +
747C ALA* 3.8 25.6 - - + -
748C ARG* 5.4 4.9 - - + +
736D SER* 1.3 71.3 - - - +
738D GLU* 1.3 54.6 + - - +
740D MET* 3.8 6.2 - - - +
741D LEU* 2.7 38.6 + - - +
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Residues in contact with GLU 738 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587C THR 4.7 0.6 + - - -
748C ARG* 6.6 0.4 - - - -
695D ARG* 5.9 0.9 + - - -
736D SER* 3.0 10.4 + - - +
737D CYS* 1.3 79.2 - - - +
739D ILE* 1.3 65.6 + - + +
741D LEU* 3.5 8.9 + - + +
742D ASN* 3.0 41.3 + - - +
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Residues in contact with ILE 739 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692D HIS* 3.8 22.0 - - + +
693D GLU* 3.9 34.1 - - + +
730D TRP* 4.1 13.0 - - + -
733D ASN 4.3 11.9 - - - +
734D ASP* 4.5 12.1 - - - +
736D SER* 3.0 25.5 + - - +
738D GLU* 1.3 77.2 - - + +
740D MET* 1.3 66.4 + - - +
742D ASN* 3.1 14.4 + - - +
743D HIS* 3.2 24.0 + - + -
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Residues in contact with MET 740 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716C LEU* 3.8 29.2 - - + -
717C MET* 3.9 35.9 - - + +
744C LEU* 3.4 34.1 - - + -
716D LEU* 3.8 21.3 - - + +
730D TRP* 3.4 32.8 - - + -
735D GLN* 5.3 2.0 - - - -
736D SER 3.0 20.6 + - - +
737D CYS* 3.8 2.7 - - - +
739D ILE* 1.3 76.3 - - - +
741D LEU* 1.3 56.7 + - - +
743D HIS* 3.3 3.7 + - - +
744D LEU* 3.0 32.4 + - - +
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Residues in contact with LEU 741 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834B POG 5.0 9.9 - - - +
741C LEU* 3.4 32.3 - - + -
744C LEU* 3.7 15.1 - - + +
745C ALA* 3.8 17.7 - - + +
748C ARG* 3.6 48.9 - - + +
737D CYS 2.7 23.0 + - - +
738D GLU* 3.7 9.0 - - + +
740D MET* 1.3 73.8 - - - +
742D ASN* 1.3 63.6 + - - +
744D LEU* 4.6 0.7 - - - +
745D ALA* 2.9 28.0 + - + +
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Residues in contact with ASN 742 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834B POG 3.4 30.0 + - + +
693D GLU* 3.0 22.2 + - - +
694D GLY* 3.3 15.0 - - - +
695D ARG* 3.8 16.8 - - - +
738D GLU* 3.0 32.7 + - - +
739D ILE* 3.1 11.6 + - - +
741D LEU* 1.3 79.3 - - - +
743D HIS* 1.3 54.4 + - - +
745D ALA* 4.1 1.2 - - - +
746D THR* 2.7 38.3 + - - -
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Residues in contact with HIS 743 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691D LEU 3.5 12.3 - - - -
692D HIS 3.0 20.8 + - - -
694D GLY* 3.3 22.3 + - - -
696D GLU* 4.7 9.9 + - - -
709D LEU* 4.2 5.4 - - + +
712D PRO* 3.5 32.0 - - + +
713D LEU* 4.5 21.5 + - + +
716D LEU* 5.4 2.0 - - + -
730D TRP* 3.9 15.2 - + + -
739D ILE* 3.2 30.1 + - + -
740D MET* 3.3 7.4 + - - +
742D ASN* 1.3 78.7 - - - +
744D LEU* 1.3 53.6 + - + +
746D THR* 3.2 6.6 + - - -
747D ALA* 2.7 35.1 + - - +
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Residues in contact with LEU 744 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716C LEU* 5.0 0.7 - - + -
737C CYS* 4.0 20.1 - - + +
740C MET* 3.6 43.3 - - + -
741C LEU* 4.1 19.5 - - + +
744C LEU* 2.7 36.6 - - + -
713D LEU* 3.7 22.7 - - + -
716D LEU* 4.2 15.9 - - + -
740D MET 3.0 11.6 + - - +
741D LEU 4.3 0.4 - - - +
743D HIS* 1.3 72.7 - - - +
745D ALA* 1.3 58.9 + - - +
747D ALA* 3.2 4.6 + - - +
748D ARG* 3.0 26.2 + - - +
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Residues in contact with ALA 745 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834B POG 4.3 29.7 - - - +
741C LEU* 4.1 18.6 - - + +
741D LEU* 2.9 22.5 + - + +
742D ASN 4.1 2.0 - - - +
744D LEU* 1.3 75.7 - - - +
746D THR* 1.3 62.5 + - - +
748D ARG* 3.3 16.0 + - - +
749D PHE* 3.1 21.1 + - - +
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Residues in contact with THR 746 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834B POG 4.1 15.7 + - + +
694D GLY* 3.8 11.9 + - - -
696D GLU* 4.0 33.8 - - + +
697D SER* 4.3 15.7 + - - -
742D ASN 2.7 24.1 + - - -
743D HIS* 3.2 8.0 + - - +
745D ALA* 1.3 77.0 - - - +
747D ALA* 1.3 51.4 + - - +
749D PHE* 3.1 10.8 + - + +
750D MET* 2.7 38.1 + - + +
757D TYR* 5.6 3.1 - - - +
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Residues in contact with ALA 747 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737C CYS* 3.9 13.9 - - - -
587D THR* 3.9 6.5 - - + +
713D LEU* 3.4 38.8 - - + -
743D HIS 2.7 16.0 + - - +
744D LEU 3.2 8.7 + - - +
746D THR* 1.3 70.6 - - - +
748D ARG* 1.3 66.8 + - - +
750D MET* 3.6 10.2 - - - +
751D ALA* 3.0 24.6 + - - +
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Residues in contact with ARG 748 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748A ARG* 4.5 17.2 - - - +
834B POG 5.2 11.9 - - - +
737C CYS* 5.2 4.9 - - + +
741C LEU* 4.0 28.8 - - + +
587D THR* 5.7 0.9 - - - -
744D LEU 3.0 13.3 + - - +
745D ALA* 3.3 17.2 + - - +
747D ALA* 1.3 76.7 - - - +
749D PHE* 1.3 63.9 + - - +
751D ALA* 3.3 5.7 + - - +
752D GLU* 3.3 39.5 + - + +
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Residues in contact with PHE 749 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697B SER* 3.7 42.4 - - - -
698B THR* 4.3 6.5 - - + -
749B PHE* 4.6 20.0 - + - -
834B POG 3.8 52.3 - - + +
697D SER* 5.2 4.5 - - - -
745D ALA 3.1 9.1 + - - +
746D THR* 3.1 10.9 + - + +
748D ARG* 1.3 81.4 - - - +
750D MET* 1.3 57.9 + - - +
752D GLU* 3.2 6.3 + - - +
753D ALA* 2.8 42.6 + - + +
757D TYR* 4.5 12.6 - + - -
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Residues in contact with MET 750 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583D LEU* 3.4 33.9 - - + +
586D ILE* 3.5 19.7 - - + -
587D THR* 3.7 16.8 - - + -
708D PRO* 3.7 26.2 - - + -
710D LEU* 4.1 9.2 - - - -
713D LEU* 3.8 16.4 - - + -
746D THR* 2.7 23.3 + - + +
747D ALA* 3.3 4.5 + - - +
749D PHE* 1.3 72.4 - - - +
751D ALA* 1.3 56.0 + - - +
753D ALA* 3.4 0.7 - - - -
754D ALA* 2.9 29.8 + - - +
757D TYR* 3.6 33.0 - - + +
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Residues in contact with ALA 751 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583D LEU 4.3 1.6 - - - -
584D GLU* 3.9 36.3 - - + +
587D THR* 3.8 25.6 - - + +
747D ALA 3.0 11.4 + - - +
748D ARG* 3.6 9.6 - - - +
750D MET* 1.3 77.2 - - - +
752D GLU* 1.3 62.8 + - + +
754D ALA* 3.3 16.7 + - - +
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Residues in contact with GLU 752 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695B ARG* 3.5 23.8 + - - +
698B THR* 3.4 36.4 - - + +
834B POG 5.7 0.9 + - - -
748D ARG* 3.3 30.2 + - + +
749D PHE* 3.2 9.4 + - - +
751D ALA* 1.3 79.9 - - + +
753D ALA* 1.3 58.5 + - - +
754D ALA 3.5 0.7 + - - -
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Residues in contact with ALA 753 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B SER 3.9 21.1 - - - +
698B THR* 4.0 11.9 - - - +
749D PHE* 2.8 32.3 + - + +
750D MET 3.4 3.6 - - - +
752D GLU* 1.3 76.4 - - - +
754D ALA* 1.3 61.8 + - - +
755D ASP 2.9 5.4 + - - -
756D SER* 2.8 30.9 + - - +
757D TYR* 3.7 6.9 - - + -
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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