Contacts of the helix formed by residues 921 - 938 (chain H) 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 921 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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918H GLU* 2.8 29.4 + - + +
920H SER* 1.3 78.9 + - - +
922H GLU* 1.3 66.0 + - - +
923H ASN* 2.8 24.3 + - - +
924H ASP* 3.0 19.5 + - + +
925H ARG* 3.0 22.2 + - - +
984K LEU* 5.0 3.1 - - - -
985K ALA* 3.3 11.6 - - - +
1071K ILE 3.0 27.1 + - - -
1072K TRP* 3.5 20.2 - - + +
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Residues in contact with GLU 922 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881H ARG* 4.3 22.6 + - - +
920H SER 3.6 5.7 + - - +
921H ASN* 1.3 70.9 + - - +
923H ASN* 1.3 67.3 + - - +
925H ARG* 3.2 28.1 + - - +
926H LEU* 3.0 23.3 + - - +
982K PRO* 4.1 16.2 - - + +
983K GLN* 3.4 19.9 + - - +
984K LEU* 2.7 35.8 + - - +
985K ALA* 2.9 27.3 + - - +
986K LYS* 3.6 3.5 + - - +
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Residues in contact with ASN 923 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921H ASN* 2.8 11.2 + - - +
922H GLU* 1.3 81.8 + - - +
924H ASP* 1.3 66.5 + - - +
926H LEU* 3.1 11.3 + - - +
927H LEU* 3.0 22.4 + - - +
985K ALA* 3.8 13.4 - - - +
986K LYS* 5.5 1.6 - - - +
1072K TRP 2.9 24.7 - - - +
1073K LYS* 3.1 26.2 - - - +
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Residues in contact with ASP 924 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908H LYS* 3.2 43.8 + - - +
916H GLY 4.8 1.0 - - - +
917H ILE* 2.4 47.3 - - + +
918H GLU* 4.1 6.8 - - - +
921H ASN* 3.0 25.7 + - + +
923H ASN* 1.3 77.0 - - - +
925H ARG* 1.3 63.6 + - - +
927H LEU* 3.2 8.8 + - - +
928H VAL* 3.0 28.3 + - - +
1071K ILE 5.1 0.3 - - - +
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Residues in contact with ARG 925 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786H TYR* 5.5 0.6 + - - -
805H ASN 3.8 6.7 - - - -
806H ILE* 4.1 9.7 - - + +
807H PRO* 3.1 27.2 - - - +
810H GLU* 2.7 50.6 + - - +
881H ARG* 4.8 0.2 - - - +
918H GLU 5.3 0.2 + - - -
919H TRP* 2.9 49.7 + - + +
920H SER* 4.0 8.3 + - - +
921H ASN 3.0 6.7 + - - -
922H GLU* 3.2 39.7 + - - +
924H ASP* 1.3 77.6 - - - +
926H LEU* 1.3 61.3 + - - +
928H VAL* 3.2 9.6 + - - +
929H CYS* 3.0 26.0 + - - -
982K PRO* 5.5 7.7 - - - +
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Residues in contact with LEU 926 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881H ARG* 6.3 0.7 - - - +
884H PHE* 4.4 13.9 - - + -
885H LEU* 4.5 22.7 - - + +
888H GLU* 4.0 43.5 - - + +
889H ALA* 5.2 1.8 - - + +
922H GLU 3.0 13.1 + - - +
923H ASN* 3.5 13.9 - - - +
925H ARG* 1.3 73.0 - - - +
927H LEU* 1.3 61.9 + - - +
929H CYS* 3.0 12.3 + - + +
930H GLN* 2.8 46.9 + - + +
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Residues in contact with LEU 927 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901H PHE* 4.2 24.2 - - + +
904H GLU* 3.9 32.3 - - - +
905H PHE* 3.7 37.7 - - + +
908H LYS* 4.1 19.7 - - + -
917H ILE* 6.6 0.2 - - + -
923H ASN 3.0 12.9 + - - +
924H ASP* 3.5 10.3 - - - +
926H LEU* 1.3 76.0 - - - +
928H VAL* 1.3 64.0 + - + +
930H GLN* 3.2 15.4 + - - +
931H VAL* 2.9 34.6 + - + +
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Residues in contact with VAL 928 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802H LEU* 4.5 11.7 - - + -
806H ILE* 4.4 10.5 - - + -
905H PHE* 4.3 8.1 - - + -
917H ILE* 4.0 24.0 - - + -
919H TRP* 4.0 33.7 - - + -
924H ASP 3.0 18.7 + - - +
925H ARG 3.5 7.2 - - - +
927H LEU* 1.3 75.7 - - + +
929H CYS* 1.3 64.1 + - - +
931H VAL* 3.2 7.3 + - - +
932H CYS* 3.0 21.8 + - + +
1003H TYR* 4.8 3.7 - - + +
1008H LEU* 4.2 21.8 - - + -
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Residues in contact with CYS 929 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806H ILE* 4.0 34.3 - - - -
810H GLU* 4.7 13.7 - - - -
811H LEU* 4.7 1.6 - - - -
814H LEU* 3.3 32.2 - - + +
889H ALA* 6.0 0.9 - - + -
925H ARG 3.0 16.6 + - - +
926H LEU* 3.0 18.5 + - + +
928H VAL* 1.3 77.3 - - - +
930H GLN* 1.3 63.4 + - + +
932H CYS* 3.2 20.5 - - - +
933H ILE 3.2 7.4 + - - -
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Residues in contact with GLN 930 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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888H GLU* 3.1 42.8 + - - +
889H ALA* 4.5 4.9 - - - +
892H ALA* 3.9 15.1 - - + +
901H PHE* 3.8 32.3 - - + -
926H LEU* 2.8 39.7 + - + +
927H LEU* 3.6 15.3 - - - +
929H CYS* 1.3 73.4 - - + +
931H VAL* 1.3 65.3 + - - +
932H CYS 3.0 2.0 - - - -
933H ILE* 3.1 11.0 - - - +
934H LYS* 2.9 28.1 + - - +
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Residues in contact with VAL 931 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901H PHE* 4.7 10.5 - - + +
902H LEU* 6.0 0.4 - - - -
905H PHE* 3.5 41.7 - - + -
927H LEU* 2.9 26.8 + - + +
928H VAL 3.2 5.1 + - - +
930H GLN* 1.3 76.7 - - + +
932H CYS* 1.3 57.2 + - - +
934H LYS* 3.3 8.9 - - + +
935H LEU* 3.1 26.0 + - - +
999H LEU* 4.2 21.2 - - + +
1002H SER* 6.5 0.2 - - - -
1003H TYR* 3.6 29.6 - - + -
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Residues in contact with CYS 932 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749H VAL* 4.2 11.0 - - - -
752H LEU* 3.8 19.2 - - - +
753H THR* 3.6 29.8 - - - -
802H LEU* 5.1 0.4 - - - -
814H LEU* 4.3 4.3 - - + -
928H VAL* 3.0 14.8 + - + +
929H CYS* 3.2 14.8 - - - +
930H GLN 3.0 1.0 - - - -
931H VAL* 1.3 73.7 - - - +
933H ILE* 1.3 67.4 + - - +
934H LYS 3.0 0.7 - - - -
935H LEU* 2.9 8.3 + - - +
936H ALA* 2.8 21.8 + - - +
1003H TYR* 3.8 22.7 - - - +
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Residues in contact with ILE 933 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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745H VAL* 4.6 5.5 - - + +
749H VAL* 3.8 23.8 - - + +
814H LEU* 4.0 14.4 - - + +
817H ALA* 5.2 0.9 - - + -
818H ALA* 4.6 21.1 - - + +
821H HIS* 5.8 2.7 - - + -
889H ALA* 2.8 46.4 - - + +
890H ILE* 6.3 0.2 - - - -
892H ALA* 3.9 11.2 - - + -
893H THR* 4.0 13.9 - - + -
929H CYS 3.2 10.3 + - - +
930H GLN* 3.1 20.4 - - - +
932H CYS* 1.3 74.6 - - - +
934H LYS* 1.3 52.9 + - - +
936H ALA* 4.1 0.7 - - - -
937H ASP* 2.6 37.9 + - - +
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Residues in contact with LYS 934 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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892H ALA* 3.1 30.5 + - + +
893H THR* 4.4 9.2 - - - -
894H ASP 5.5 0.4 - - - +
895H LEU* 4.6 10.5 - - + +
898H HIS* 3.1 60.1 + - - +
901H PHE* 3.9 18.1 - - + +
902H LEU 5.1 0.6 - - - +
930H GLN 2.9 24.9 + - - +
931H VAL* 3.3 12.6 - - - +
933H ILE* 1.3 81.2 - - - +
935H LEU* 1.3 60.4 + - - +
937H ASP* 3.5 8.9 + - + +
938H ILE* 3.4 22.0 + - - +
999H LEU* 3.9 14.2 - - + +
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Residues in contact with LEU 935 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677H TRP* 5.8 1.3 - - + -
752H LEU* 4.2 14.6 - - + -
931H VAL 3.1 12.9 + - - +
932H CYS* 2.9 9.2 + - - +
934H LYS* 1.3 73.4 - - - +
936H ALA* 1.3 66.8 + - - +
937H ASP 3.1 1.3 - - - -
938H ILE* 3.0 16.8 + - + +
939H ASN* 3.0 22.0 + - + -
942H ALA* 5.3 4.0 - - + -
996H VAL* 5.1 2.5 - - + -
999H LEU* 3.5 22.6 - - + +
1000H CYS* 3.7 31.2 - - - -
1003H TYR* 3.8 34.8 - - + -
1009H LEU* 4.5 8.7 - - + -
1061H LEU* 4.7 7.0 - - + -
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Residues in contact with ALA 936 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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745H VAL* 3.5 20.3 - - + +
748H ALA* 3.3 30.3 - - + -
749H VAL* 3.5 30.5 - - + +
752H LEU* 4.6 5.1 - - + +
932H CYS 2.8 12.5 + - - +
933H ILE 3.8 1.1 - - - +
935H LEU* 1.3 73.4 - - - +
937H ASP* 1.3 58.2 + - - +
939H ASN* 2.7 25.8 - - - +
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Residues in contact with ASP 937 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736H TYR* 4.1 2.1 + - - -
741H HIS* 2.9 19.9 + - - -
745H VAL* 3.9 7.2 - - + +
821H HIS* 2.7 14.9 + - + +
893H THR* 3.6 30.1 - - + +
895H LEU* 6.0 0.9 - - - +
933H ILE* 2.6 22.5 + - + +
934H LYS* 3.7 7.4 - - + +
936H ALA* 1.3 74.2 - - - +
938H ILE* 1.3 68.3 + - + +
939H ASN* 3.6 1.3 + - - +
2118H IBM 3.8 6.1 - - - +
2137H MG 2.0 32.8 - - - -
2138H MG 4.1 4.9 - - - -
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Residues in contact with ILE 938 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895H LEU* 4.7 15.9 - - + -
898H HIS* 4.7 2.7 - - + -
934H LYS* 3.4 18.8 - - - +
935H LEU* 3.0 9.7 + - + +
937H ASP* 1.3 88.4 - - + +
939H ASN* 1.3 58.7 + - - -
940H GLY 3.1 7.0 + - - -
941H PRO* 3.8 2.6 - - - +
991H PHE* 4.0 7.9 - - + -
995H ILE* 3.7 21.3 - - + -
996H VAL* 3.5 43.4 - - + +
999H LEU* 3.9 18.2 - - + -
2118H IBM 3.4 29.2 - - + +
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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