Contacts of the helix formed by residues 738 - 753 (chain G) in PDB entry 1SOJ
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 ASN 738 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731G TYR* 3.5 12.6 - - - -
732G ARG 3.7 19.7 - - - +
733G ASP* 5.4 1.3 - - - +
734G ILE 3.0 22.4 + - - +
735G PRO 3.7 8.9 + - - -
736G TYR 2.8 22.1 + - - +
737G HIS* 1.3 75.0 - - - +
739G ARG* 1.3 67.5 + - + +
740G ILE* 2.8 42.0 + - - +
741G HIS* 3.0 21.5 + - - +
742G ALA 3.2 8.7 + - - -
951G TRP* 5.1 3.5 - - - -
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Residues in contact with ARG 739 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692G SER 4.6 0.4 - - - -
693G GLY* 3.5 40.8 + - - -
695G ILE* 4.2 12.3 - - + -
696G LEU* 4.3 12.3 - - + +
728G GLU* 2.7 31.7 + - - +
729G ASN* 3.2 22.6 + - - +
731G TYR* 3.4 38.5 + - + +
732G ARG 5.6 1.2 + - - -
733G ASP* 5.9 3.0 + - - +
738G ASN* 1.3 74.6 - - + +
740G ILE* 1.3 61.2 + - + +
742G ALA* 3.4 5.3 + - - +
743G THR* 2.7 37.8 + - - -
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Residues in contact with ILE 740 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681G ILE* 3.5 26.0 - - + +
682G PHE* 4.4 17.3 - - + -
685G VAL* 3.8 35.2 - - + -
692G SER* 5.7 1.3 - - - +
695G ILE* 4.8 8.3 - - + -
738G ASN* 2.8 25.7 + - - +
739G ARG* 1.3 78.1 - - + +
741G HIS* 1.3 63.4 + - - +
743G THR* 3.3 7.4 + - - -
744G ASP* 2.9 19.6 + - - +
951G TRP* 3.8 15.5 - - + -
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Residues in contact with HIS 741 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736G TYR* 3.2 53.9 + + + +
737G HIS* 4.0 12.3 - - - -
738G ASN* 3.0 11.5 + - - +
740G ILE* 1.3 76.6 - - - +
742G ALA* 1.3 64.5 + - - +
744G ASP* 3.0 9.4 + - - +
745G VAL* 2.8 40.2 + - + +
821G HIS* 3.3 5.0 + + - -
822G ASP* 3.0 15.7 - - + -
937G ASP* 3.2 11.2 - - - -
951G TRP* 3.8 16.4 - - + -
2135G MG 1.9 32.1 - - - -
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Residues in contact with ALA 742 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696G LEU* 4.3 8.5 - - + -
731G TYR* 3.6 39.3 - - + +
738G ASN 3.2 3.0 + - - +
739G ARG 3.6 8.5 - - - +
741G HIS* 1.3 78.2 - - - +
743G THR* 1.3 64.2 + - - +
745G VAL* 3.2 2.8 + - - +
746G LEU* 2.9 23.6 + - - +
818G ALA 4.1 7.0 - - - +
819G ALA 3.9 9.4 - - - +
821G HIS* 4.3 13.9 - - + -
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Residues in contact with THR 743 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679G PHE* 5.3 4.0 - - + -
681G ILE* 3.9 15.7 - - + -
695G ILE* 4.0 10.4 - - + +
696G LEU* 3.4 30.0 + - + +
699G VAL* 3.6 39.5 - - + -
739G ARG 2.7 19.7 + - - -
740G ILE* 3.5 8.7 - - - -
741G HIS 3.2 0.2 - - - -
742G ALA* 1.3 75.6 - - - +
744G ASP* 1.3 56.7 + - - +
746G LEU* 3.0 5.9 + - - +
747G HIS* 2.9 27.8 + - + +
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Residues in contact with ASP 744 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679G PHE* 5.7 2.0 - - - -
681G ILE* 3.7 14.4 - - + +
740G ILE 2.9 13.5 + - - +
741G HIS* 3.3 11.6 + - - +
743G THR* 1.3 75.2 - - - +
745G VAL* 1.3 65.2 + - + +
747G HIS* 3.2 11.5 + - - +
748G ALA* 3.0 21.5 + - - +
939G ASN* 3.5 21.6 + - - +
943G LYS* 3.3 21.8 + - - -
951G TRP* 3.3 38.9 + - + -
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Residues in contact with VAL 745 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741G HIS* 2.8 51.0 + - + +
742G ALA 3.7 6.1 - - - +
744G ASP* 1.3 73.1 - - + +
746G LEU* 1.3 61.9 + - - +
748G ALA* 3.4 2.9 + - - +
749G VAL* 3.2 21.3 + - - +
818G ALA* 4.2 13.0 - - + +
821G HIS* 3.5 24.2 - - + +
933G ILE* 4.5 8.5 - - + -
936G ALA* 3.8 34.6 - - + +
937G ASP* 3.7 9.6 - - + +
939G ASN* 5.2 1.1 - - - +
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Residues in contact with LEU 746 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696G LEU* 4.2 12.1 - - + -
699G VAL* 3.7 23.1 - - + -
700G MET* 3.1 52.5 - - + -
703G LEU* 3.6 14.4 - - + -
742G ALA 2.9 12.6 + - - +
743G THR 3.0 7.6 + - - +
745G VAL* 1.3 73.8 - - - +
747G HIS* 1.3 66.5 + - - +
749G VAL* 2.9 23.9 - - + +
750G TRP* 3.0 10.6 + - + +
815G TYR* 3.6 28.7 - - + +
818G ALA* 3.9 7.2 - - + +
819G ALA* 5.0 2.5 - - + +
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Residues in contact with HIS 747 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674G MET* 2.9 49.2 + - + -
676G ASN 3.5 9.1 + - - -
677G TRP* 3.8 18.8 - + - -
679G PHE* 3.5 37.8 - + + +
699G VAL* 5.4 1.6 - - + -
703G LEU* 4.6 3.6 - - - -
743G THR* 2.9 12.5 + - + +
744G ASP* 3.6 17.1 + - - +
746G LEU* 1.3 77.9 - - - +
748G ALA* 1.3 62.4 + - - +
750G TRP* 3.6 20.8 - + - -
751G TYR* 2.9 35.6 + - + +
943G LYS* 5.0 3.0 + - - -
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Residues in contact with ALA 748 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677G TRP* 4.4 19.1 - - + -
744G ASP* 3.0 14.5 + - - +
745G VAL 3.5 4.5 - - - +
747G HIS* 1.3 81.9 + - - +
749G VAL* 1.3 51.3 + - - +
751G TYR* 3.2 2.0 + - - +
752G LEU* 2.7 42.2 + - + +
936G ALA* 3.5 30.7 - - + +
939G ASN* 4.2 9.2 - - - +
943G LYS* 5.7 0.9 - - - -
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Residues in contact with VAL 749 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745G VAL 3.2 8.4 + - - +
746G LEU* 2.9 25.8 - - + +
748G ALA* 1.3 73.7 - - - +
750G TRP* 1.3 57.0 + - - +
752G LEU* 4.4 4.9 - - - -
753G THR* 2.6 38.3 + - - +
814G LEU* 4.1 25.1 - - + +
815G TYR* 4.1 15.9 - - + -
818G ALA* 3.8 12.3 - - + -
932G CYS* 4.1 4.9 - - - +
933G ILE* 3.7 25.8 - - + -
936G ALA* 3.5 21.8 - - + -
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Residues in contact with TRP 750 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671G ILE* 5.0 4.5 - - + -
674G MET* 3.2 38.8 - - + -
675G SER* 4.6 1.3 - - - -
703G LEU* 3.5 36.6 - - + +
706G ASP* 3.3 22.5 + - - -
707G THR* 4.0 15.2 + - - -
746G LEU* 3.0 16.7 + - + +
747G HIS* 3.6 22.0 - + - +
749G VAL* 1.3 80.4 - - - +
751G TYR* 1.3 77.5 + + + +
753G THR* 3.3 1.2 + - - -
754G THR* 3.0 40.0 + - - -
755G ARG* 3.0 37.7 - - - -
789G SER* 4.1 1.0 + - - -
791G SER* 3.7 9.9 - - - -
815G TYR* 3.7 22.7 - + + -
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Residues in contact with TYR 751 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674G MET 4.4 10.8 - - - -
675G SER 3.4 25.4 + - - -
677G TRP* 3.5 54.4 + + + +
747G HIS* 2.9 22.2 + - + +
748G ALA* 3.6 5.2 - - - +
750G TRP* 1.3 87.1 - + + +
752G LEU* 1.3 63.5 + - - +
754G THR* 4.5 0.9 - - - -
755G ARG* 3.2 56.3 + - + +
1010G PRO* 3.9 23.0 - - + +
1060G GLN* 4.5 5.5 + - - -
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Residues in contact with LEU 752 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677G TRP* 4.0 22.7 - - + -
748G ALA 2.7 28.1 + - - +
749G VAL 4.1 0.2 - - - +
751G TYR* 1.3 74.8 - - + +
753G THR* 1.3 58.9 + - - +
754G THR 3.5 0.4 + - - -
755G ARG 5.0 1.1 - - - +
757G VAL* 5.0 1.6 - - - +
802G LEU* 3.1 19.6 - - - +
932G CYS* 3.9 35.9 - - - +
935G LEU* 4.3 25.4 - - + -
936G ALA* 4.5 5.6 - - + -
1003G TYR* 4.1 9.8 + - + +
1008G LEU 4.4 4.0 - - - +
1009G LEU* 4.5 4.9 - - + -
1010G PRO* 3.7 34.0 - - + +
1061G LEU* 4.1 11.0 - - + -
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Residues in contact with THR 753 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749G VAL 2.6 23.0 + - - +
750G TRP 3.3 1.2 + - - -
751G TYR 3.2 0.2 - - - -
752G LEU* 1.3 81.0 - - - +
754G THR* 1.3 58.1 + - - +
755G ARG 5.1 0.2 - - - -
802G LEU* 3.8 25.6 + - + -
803G SER* 3.0 30.9 + - - -
806G ILE* 5.3 2.0 - - + -
811G LEU* 4.1 22.0 - - + +
814G LEU* 4.2 6.3 - - + -
815G TYR* 2.9 25.8 + - - -
932G CYS* 3.8 21.1 - - + -
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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