Contacts of the helix formed by residues 70 - 91 (chain 1) in PDB entry 3J9X
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 GLY 70 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691 THR* 1.3 76.3 - - - +
711 PRO* 1.3 69.1 - - - +
731 ARG* 2.9 30.8 + - - +
903 ILE* 5.5 0.6 - - - +
993 MET* 5.3 0.4 - - - +
1114 PHE* 3.6 17.9 - - - -
3278 A 3.4 26.7 + - - +
3288 T 4.1 2.1 + - - -
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Residues in contact with PRO 71 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691 THR 4.4 0.4 - - - +
701 GLY* 1.3 82.2 - - - +
721 ASN* 1.3 65.2 + - - +
731 ARG 3.1 0.2 - - - -
741 ALA* 3.0 6.0 + - + +
751 ILE* 3.0 23.9 + - - +
714 PRO* 3.6 18.7 - - + +
744 ALA 4.8 0.4 - - - -
754 ILE* 3.6 38.6 - - + +
1074 TYR* 6.5 0.9 - - + -
1114 PHE* 4.6 6.1 - - + -
3278 A 3.7 30.5 - - + +
3288 T 3.6 26.7 - - - +
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Residues in contact with ASN 72 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681 ILE* 3.5 15.3 - - + -
691 THR* 3.3 13.4 + - - +
701 GLY 3.0 0.8 - - - -
711 PRO* 1.3 74.3 - - - +
731 ARG* 1.3 65.7 + - - +
751 ILE* 3.3 18.2 + - + +
761 TYR* 3.1 26.3 - - + -
724 ASN* 3.1 24.8 - - - +
754 ILE* 3.5 10.4 - - - +
1114 PHE* 3.2 26.3 + - - +
1124 ASN* 4.6 10.9 + - - +
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Residues in contact with ARG 73 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601 SER* 2.7 44.9 + - - -
631 LEU* 3.5 19.3 - - + +
641 THR* 3.0 32.1 + - - +
681 ILE* 2.8 55.0 + - + +
691 THR* 3.9 7.9 - - - +
701 GLY 2.9 14.0 + - - +
721 ASN* 1.3 76.8 - - - +
741 ALA* 1.3 58.7 + - - +
761 TYR 3.1 2.9 + - - -
771 GLN* 2.8 32.7 + - - +
893 ARG 4.6 0.8 + - - -
903 ILE* 3.7 26.8 + - - +
3278 A 2.9 39.6 + - - +
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Residues in contact with ALA 74 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701 GLY 3.7 1.0 + - - -
711 PRO* 3.0 11.5 + - + +
731 ARG* 1.3 80.5 - - - +
751 ILE* 1.3 62.8 + - - +
771 GLN* 3.6 8.3 - - - +
781 GLY* 2.9 21.7 + - - -
714 PRO* 4.8 3.4 - - + -
237 A 4.1 25.7 - - + +
3268 T 4.3 6.0 - - - +
3278 A 3.8 38.3 + - + +
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Residues in contact with ILE 75 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711 PRO 3.0 14.4 + - - +
721 ASN* 3.4 22.9 - - + +
741 ALA* 1.3 77.5 - - - +
761 TYR* 1.3 71.3 + - + +
781 GLY* 3.3 0.7 + - - -
791 PHE* 3.2 16.8 + - - +
1071 TYR* 3.5 31.1 - - + -
1111 PHE* 4.8 10.3 - - + +
1131 ALA* 4.2 19.7 - - + -
714 PRO* 3.5 27.6 - - + +
724 ASN* 3.5 36.1 - - - +
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Residues in contact with TYR 76 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591 VAL* 4.3 5.9 - - - +
631 LEU* 3.6 33.9 - - + -
681 ILE* 4.0 18.9 - - + +
721 ASN* 3.1 26.9 + - + -
731 ARG 3.1 3.7 + - - +
751 ILE* 1.3 80.6 - - + +
771 GLN* 1.3 60.9 + - - +
791 PHE* 3.2 7.9 + - - +
801 GLY* 2.9 25.3 + - - -
1121 ASN 5.2 0.2 + - - -
1131 ALA* 4.0 8.6 - - + -
1141 ASN* 2.9 37.7 + - - +
1171 VAL* 3.7 28.7 - - + +
1181 LEU* 3.6 31.6 - - + -
1211 VAL* 4.4 9.1 - - + +
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Residues in contact with GLN 77 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551 VAL* 5.2 0.7 - - - +
561 ASN* 3.1 42.4 + - - +
591 VAL* 3.3 24.2 - - - +
601 SER* 3.4 11.5 - - - +
631 LEU* 4.0 3.3 - - + +
731 ARG 2.8 24.9 + - - +
741 ALA* 3.6 7.2 - - - +
751 ILE 3.3 0.2 - - - -
761 TYR* 1.3 76.5 - - - +
781 GLY* 1.3 56.1 + - - +
801 GLY* 3.2 1.4 + - - -
811 LEU* 2.9 38.2 + - + +
3268 T 3.2 31.6 + - + +
3278 A 3.2 20.6 + - - +
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Residues in contact with GLY 78 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741 ALA 2.9 15.1 + - - -
751 ILE 3.8 4.3 - - - -
761 TYR 3.2 0.2 - - - -
771 GLN* 1.3 76.9 - - - +
791 PHE* 1.3 60.4 + - - +
811 LEU* 3.3 6.3 + - - +
821 LYS* 3.0 23.9 + - - +
1071 TYR* 3.5 10.7 + - - -
237 A 5.6 1.1 - - - -
247 T 3.7 31.1 + - - +
3268 T 5.3 0.2 + - - -
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Residues in contact with PHE 79 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751 ILE 3.2 13.6 + - - +
761 TYR 3.4 7.2 - - - +
781 GLY* 1.3 75.1 - - - +
801 GLY* 1.3 65.1 + - - +
821 LYS* 3.2 6.0 + - - +
831 VAL* 3.1 28.7 + - + +
1001 ILE* 5.0 0.9 - - + -
1031 LEU* 3.6 31.2 - - + -
1041 LYS* 3.8 28.7 - - + -
1071 TYR* 3.5 27.6 + + + -
1181 LEU* 3.3 48.9 - - + -
1211 VAL* 3.8 16.4 - - + -
1221 VAL* 3.6 24.9 - - + -
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Residues in contact with GLY 80 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551 VAL* 4.1 6.3 - - - -
591 VAL* 4.7 2.0 - - - -
761 TYR 2.9 12.8 + - - -
771 GLN 3.2 3.1 + - - -
791 PHE* 1.3 76.4 - - - +
811 LEU* 1.3 62.3 - - - +
831 VAL* 3.1 2.9 + - - -
841 ALA* 3.1 19.4 + - - +
1211 VAL* 3.6 13.7 - - - -
1251 ILE* 3.2 30.4 - - - +
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Residues in contact with LEU 81 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521 PHE* 3.7 37.4 - - + +
551 VAL* 4.3 7.1 - - + +
561 ASN* 3.3 30.3 - - - +
771 GLN* 2.9 25.5 + - + +
781 GLY* 3.6 4.5 - - - +
801 GLY* 1.3 74.1 - - - +
821 LYS* 1.3 58.0 + - - +
841 ALA* 3.3 6.7 + - - +
851 ARG* 2.9 28.1 + - - +
247 T 3.6 24.5 - - + +
257 A 3.4 30.2 - - + +
3258 A 4.9 6.7 - - + -
3268 T 5.2 2.2 - - - +
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Residues in contact with LYS 82 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781 GLY 3.0 13.4 + - - +
791 PHE* 3.2 10.3 + - - +
811 LEU* 1.3 74.7 - - - +
831 VAL* 1.3 65.4 + - - +
851 ARG* 3.2 10.1 + - - +
861 ALA* 3.1 24.5 + - + +
991 MET* 4.7 16.8 - - + -
1031 LEU* 3.5 28.6 - - + +
1061 TYR* 5.5 3.8 - - - -
1071 TYR* 5.2 1.1 - - + -
1062 TYR* 2.7 38.0 + - - -
1112 PHE* 6.1 0.2 - - - -
247 T 4.0 13.5 + - - +
257 A 2.9 31.5 + - - +
3168 T 5.6 1.8 - - - -
3178 A 3.8 14.0 + - - -
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Residues in contact with VAL 83 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791 PHE* 3.1 34.3 + - + +
801 GLY* 3.1 9.2 + - - +
821 LYS* 1.3 75.9 - - - +
841 ALA* 1.3 63.0 + - - +
861 ALA* 3.4 6.4 + - - +
871 LEU* 3.0 21.7 + - + +
961 LEU* 4.3 4.1 - - + +
991 MET* 6.3 0.7 - - - -
1001 ILE* 4.3 20.0 - - + -
1031 LEU* 3.6 18.2 - - + -
1221 VAL* 4.5 8.1 - - + -
1251 ILE* 3.7 27.6 - - + -
1261 THR* 4.3 15.0 - - + -
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Residues in contact with ALA 84 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511 LYS 5.5 0.7 - - - +
521 PHE* 3.6 21.1 - - + -
551 VAL* 4.0 21.1 - - + -
801 GLY 3.1 10.2 + - - +
811 LEU* 3.5 8.1 - - - +
831 VAL* 1.3 79.2 - - - +
851 ARG* 1.3 63.7 + - - +
871 LEU* 3.1 12.0 + - + +
881 ASN* 2.9 27.0 + - - +
1251 ILE* 4.5 7.2 - - + -
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Residues in contact with ARG 85 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521 PHE* 3.6 10.2 - - - -
811 LEU 2.9 13.8 + - - +
821 LYS* 3.4 14.8 - - - +
841 ALA* 1.3 77.0 - - - +
861 ALA* 1.3 63.0 - - - +
881 ASN* 3.1 5.9 + - - +
891 ARG* 3.0 53.2 + - - +
257 A 3.0 34.5 + - - +
267 T 3.1 34.2 + - - +
3168 T 3.8 34.4 + - - +
3178 A 3.9 21.3 + - - -
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Residues in contact with ALA 86 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821 LYS* 3.1 11.9 + - - +
831 VAL* 3.7 8.7 - - - +
851 ARG* 1.3 77.8 - - - +
871 LEU* 1.3 59.3 + - - +
891 ARG* 4.5 2.9 - - - +
901 ILE* 2.7 50.6 + - + +
961 LEU* 3.9 10.8 - - + -
991 MET* 3.8 33.4 - - + -
3168 T 5.4 3.1 - - - -
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Residues in contact with LEU 87 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831 VAL* 3.0 15.2 + - + +
841 ALA* 3.3 12.1 - - + +
861 ALA* 1.3 76.3 - - - +
881 ASN* 1.3 65.1 + - - +
911 GLY* 2.7 31.1 + - - +
921 SER* 3.6 33.0 - - - +
961 LEU* 3.8 23.0 - - + +
1251 ILE* 4.8 22.0 - - + +
1261 THR* 6.1 2.5 - - + -
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Residues in contact with ASN 88 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481 ASN* 4.9 5.4 + - - -
511 LYS* 3.9 29.9 + - - +
521 PHE* 3.3 34.9 - - + -
841 ALA* 2.9 12.7 + - - +
851 ARG* 3.1 8.2 + - - +
871 LEU* 1.3 86.1 - - - +
891 ARG* 1.3 63.2 + - + +
901 ILE 5.0 0.3 - - - -
911 GLY 4.8 0.7 + - - -
267 T 5.9 0.9 - - - +
7z SER* 3.8 17.8 + - - +
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Residues in contact with ARG 89 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851 ARG* 3.0 54.5 + - - +
861 ALA* 4.2 1.1 - - - +
881 ASN* 1.3 80.2 - - + +
901 ILE* 1.3 63.1 + - + +
267 T 3.8 18.8 + - - +
277 A 4.3 14.3 + - - -
3148 T 4.7 3.8 + - - -
3158 A 3.6 26.3 + - - +
3168 T 3.5 37.0 + - - +
60y SER* 4.7 1.9 + - - -
73y ARG* 4.6 4.0 + - - -
7z SER* 3.6 36.4 - - - +
8z ARG* 5.5 3.4 - - - +
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Residues in contact with ILE 90 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861 ALA* 2.7 28.4 + - + +
881 ASN 5.0 0.9 - - - -
891 ARG* 1.3 78.5 - - + +
911 GLY* 1.3 68.9 + - - +
951 ALA* 3.5 26.0 - - + +
961 LEU* 4.2 4.0 - - - +
991 MET* 3.7 31.4 - - + -
3158 A 5.4 0.9 - - - +
3168 T 4.4 10.1 - - - +
60y SER* 4.7 3.2 + - - -
64y THR* 2.6 35.7 + - - +
69y THR* 4.4 17.9 - - + -
70y GLY 5.5 0.4 - - - +
73y ARG* 3.7 20.0 + - - +
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Residues in contact with GLY 91 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861 ALA 3.6 0.4 + - - -
871 LEU* 2.7 30.9 + - - -
881 ASN 4.6 0.4 - - - -
901 ILE* 1.3 88.5 - - - +
921 SER* 1.3 67.8 + - - +
961 LEU* 3.6 10.6 - - - +
64y THR* 3.8 1.4 - - - +
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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