Contacts of the helix formed by residues 738 - 753 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731K TYR* 3.5 12.9 - - - -
732K ARG 3.7 19.7 - - - +
733K ASP* 5.4 1.1 - - - +
734K ILE 3.1 21.9 + - - +
735K PRO 3.8 8.5 + - - -
736K TYR* 2.8 21.1 + - - +
737K HIS* 1.3 74.2 - - - +
739K ARG* 1.3 67.4 + - + +
740K ILE* 2.8 42.5 + - - +
741K HIS* 2.9 20.8 + - - +
742K ALA 3.2 9.2 + - - -
951K TRP* 5.1 3.3 - - - -
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Residues in contact with ARG 739 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692K SER 4.7 0.4 - - - -
693K GLY* 3.5 39.8 + - - -
695K ILE* 4.3 12.3 - - + -
696K LEU* 4.4 13.4 - - + +
728K GLU* 2.7 31.4 + - - +
729K ASN* 3.1 23.0 + - - +
731K TYR* 3.4 38.2 + - + +
732K ARG 5.6 1.8 + - - -
733K ASP* 5.9 2.6 + - - +
738K ASN* 1.3 73.6 - - + +
740K ILE* 1.3 64.0 + - + +
742K ALA* 3.3 6.1 + - - +
743K THR* 2.8 33.7 + - - -
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Residues in contact with ILE 740 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681K ILE* 3.5 26.2 - - + +
682K PHE* 4.4 16.8 - - + -
685K VAL* 3.9 35.2 - - + -
692K SER* 5.6 1.8 - - - +
695K ILE* 4.8 8.1 - - + -
738K ASN* 2.8 25.9 + - - +
739K ARG* 1.3 77.9 - - + +
741K HIS* 1.3 63.4 + - - +
743K THR* 3.3 6.9 + - - -
744K ASP* 2.9 19.6 + - - +
951K TRP* 3.8 15.3 - - + -
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Residues in contact with HIS 741 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736K TYR* 3.2 53.7 + + - +
737K HIS* 4.0 11.9 - - - -
738K ASN* 2.9 11.7 + - - +
740K ILE* 1.3 77.1 - - - +
742K ALA* 1.3 58.9 + - - +
744K ASP* 3.0 8.6 + - - +
745K VAL* 2.8 45.4 + - + +
821K HIS* 3.3 4.8 + + - -
822K ASP* 2.8 17.2 + - + -
937K ASP* 3.2 15.0 - - - -
939K ASN* 6.1 0.2 - - - -
951K TRP* 3.7 16.0 - - + -
2143K MG 1.8 34.0 - - - -
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Residues in contact with ALA 742 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696K LEU* 4.2 8.5 - - + -
731K TYR* 3.5 40.2 - - + +
738K ASN 3.2 2.8 + - - +
739K ARG 3.6 7.9 - - - +
741K HIS* 1.3 78.2 - - - +
743K THR* 1.3 64.2 + - - +
745K VAL* 3.2 2.9 + - - +
746K LEU* 2.8 23.6 + - - +
818K ALA 4.0 10.9 - - - +
819K ALA 3.9 10.1 - - - +
821K HIS* 4.3 9.6 - - + -
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Residues in contact with THR 743 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679K PHE* 5.3 4.0 - - + -
681K ILE* 3.9 15.5 - - + -
695K ILE* 3.9 10.6 - - + +
696K LEU* 3.4 31.3 + - - +
699K VAL* 3.6 39.3 - - + -
739K ARG 2.8 20.1 + - - -
740K ILE* 3.5 8.7 - - - -
742K ALA* 1.3 76.5 - - - +
744K ASP* 1.3 56.9 + - - +
746K LEU* 3.0 6.0 + - - +
747K HIS* 2.9 27.6 + - + +
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Residues in contact with ASP 744 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679K PHE* 5.7 1.6 - - - -
681K ILE* 3.7 14.9 - - + +
740K ILE 2.9 13.7 + - - +
741K HIS* 3.0 11.4 + - - +
743K THR* 1.3 76.1 - - - +
745K VAL* 1.3 64.1 + - + +
746K LEU 3.2 0.2 + - - -
747K HIS* 3.2 11.5 + - - +
748K ALA* 2.9 21.7 + - - +
939K ASN* 3.5 20.4 + - - +
940K GLY* 5.9 0.2 - - - -
943K LYS* 3.2 22.3 + - - -
951K TRP* 3.2 38.3 + - + -
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Residues in contact with VAL 745 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741K HIS* 2.8 49.6 + - + +
742K ALA 3.7 6.1 - - - +
744K ASP* 1.3 72.9 - - + +
746K LEU* 1.3 62.2 + - - +
748K ALA* 3.3 3.2 + - - +
749K VAL* 3.1 21.4 + - - +
818K ALA* 4.2 13.5 - - + +
821K HIS* 3.5 24.9 - - + +
933K ILE* 4.6 8.1 - - + -
936K ALA* 3.8 20.0 - - + +
937K ASP* 3.7 24.7 - - + +
939K ASN* 5.1 1.3 - - - +
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Residues in contact with LEU 746 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696K LEU* 4.2 12.3 - - + -
699K VAL* 3.7 24.0 - - + -
700K MET* 3.1 52.5 - - + +
703K LEU* 3.6 15.0 - - + -
742K ALA 2.8 12.6 + - - +
743K THR 3.0 7.8 + - - +
745K VAL* 1.3 74.2 - - - +
747K HIS* 1.3 67.8 + - - +
749K VAL* 2.9 25.7 - - + +
750K TRP* 3.0 9.9 + - + +
815K TYR* 3.6 28.0 - - + +
818K ALA* 3.9 7.1 - - + +
819K ALA* 5.0 2.5 - - + +
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Residues in contact with HIS 747 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674K MET* 2.9 47.2 + - + -
676K ASN 3.6 8.3 - - - -
677K TRP* 3.7 19.3 - + - -
679K PHE* 3.5 40.0 - + + +
699K VAL* 5.4 1.3 - - + -
703K LEU* 4.6 3.6 - - - -
743K THR* 2.9 14.8 + - + +
744K ASP* 3.6 17.0 + - - +
746K LEU* 1.3 75.7 - - - +
748K ALA* 1.3 60.0 + - - +
750K TRP* 3.5 21.5 + + - -
751K TYR* 2.9 35.4 + - + +
943K LYS* 5.0 3.0 + - - -
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Residues in contact with ALA 748 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677K TRP* 4.4 18.8 - - + -
744K ASP* 2.9 14.1 + - - +
745K VAL 3.5 4.9 - - - +
746K LEU 3.1 0.2 - - - -
747K HIS* 1.3 83.4 + - - +
749K VAL* 1.3 53.0 + - - +
751K TYR* 3.2 2.3 + - - +
752K LEU* 2.7 41.7 + - + +
936K ALA* 3.5 30.5 - - + +
939K ASN* 4.2 9.0 - - - +
943K LYS* 5.7 0.9 - - - -
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Residues in contact with VAL 749 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745K VAL 3.1 8.0 + - - +
746K LEU* 2.9 24.7 - - + +
748K ALA* 1.3 73.2 - - - +
750K TRP* 1.3 57.0 + - - +
752K LEU* 4.4 5.2 - - - -
753K THR* 2.6 38.3 + - - +
814K LEU* 4.1 24.0 - - + +
815K TYR* 3.9 16.6 - - + -
818K ALA* 3.8 13.2 - - + -
932K CYS* 4.0 5.4 - - - +
933K ILE* 3.7 26.0 - - + -
936K ALA* 3.5 21.5 - - + -
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Residues in contact with TRP 750 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671K ILE* 5.0 4.9 - - + -
674K MET* 3.2 39.3 - - + -
675K SER* 4.6 1.3 - - - -
703K LEU* 3.4 39.9 - - + +
706K ASP* 3.3 22.4 + - - -
707K THR* 4.0 14.7 + - - -
746K LEU* 3.0 15.6 + - + +
747K HIS* 3.6 21.5 - + - +
749K VAL* 1.3 80.6 - - - +
751K TYR* 1.3 76.4 + + + +
753K THR* 3.2 1.4 + - - -
754K THR* 3.0 41.0 + - - -
755K ARG* 3.0 37.5 - - - -
789K SER* 4.1 0.8 + - - -
791K SER* 3.7 10.3 - - - -
815K TYR* 3.7 23.3 - + + -
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Residues in contact with TYR 751 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674K MET 4.4 10.8 - - - -
675K SER 3.4 25.4 + - - -
677K TRP* 3.5 56.4 + + + +
747K HIS* 2.9 23.7 + - + +
748K ALA 3.6 2.9 - - - +
750K TRP* 1.3 88.2 - + + +
752K LEU* 1.3 63.0 + - - +
754K THR* 4.5 0.9 - - - -
755K ARG* 3.2 53.5 + - + +
1010K PRO* 3.9 24.0 - - + +
1060K GLN* 4.4 5.7 + - - -
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Residues in contact with LEU 752 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677K TRP* 4.0 22.7 - - + -
748K ALA 2.7 27.0 + - - +
749K VAL 4.1 0.7 - - - +
751K TYR* 1.3 73.7 - - + +
753K THR* 1.3 57.9 + - - +
754K THR 3.5 0.2 - - - -
755K ARG 5.0 1.1 - - - +
757K VAL* 5.0 1.6 - - - +
802K LEU* 3.1 19.4 - - - +
932K CYS* 3.9 35.7 - - - +
935K LEU* 4.3 25.6 - - + -
936K ALA* 4.5 5.8 - - + +
1003K TYR* 4.1 8.7 + - + +
1008K LEU 4.4 3.6 - - - +
1009K LEU* 4.4 4.3 - - + -
1010K PRO* 3.7 33.8 - - + +
1061K LEU* 4.1 12.3 - - + -
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Residues in contact with THR 753 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749K VAL 2.6 23.4 + - - +
750K TRP 3.2 1.0 + - - -
751K TYR 3.2 0.2 - - - -
752K LEU* 1.3 79.1 - - - +
754K THR* 1.3 59.3 + - - +
802K LEU* 3.8 28.6 + - + -
803K SER* 2.9 31.3 + - - -
806K ILE* 5.3 2.2 - - + -
811K LEU* 4.1 18.9 - - + +
814K LEU* 4.2 7.4 - - + -
815K TYR* 2.9 25.2 + - - -
932K CYS* 3.8 20.4 - - + -
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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