Contacts of the helix formed by residues 70 - 91 (chain 4) 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 4).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1111 PHE* 3.5 19.4 - - - -
902 ILE* 5.6 0.4 - - - +
992 MET* 5.3 0.2 - - - +
694 THR* 1.3 76.3 - - - +
714 PRO* 1.3 66.3 - - - +
724 ASN 3.0 0.2 - - - -
734 ARG* 2.9 36.5 + - - +
227 T 3.5 25.7 + - - +
237 A 4.4 2.0 + - - -
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Residues in contact with PRO 71 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711 PRO* 3.6 18.9 - - + +
741 ALA* 4.8 2.9 - - + -
751 ILE* 3.5 37.7 - - + +
1071 TYR* 6.5 0.4 - - + -
1111 PHE* 4.6 7.2 - - + -
694 THR 4.4 0.2 - - - +
704 GLY* 1.3 82.4 - - - +
724 ASN* 1.3 64.4 + - - +
734 ARG 3.1 0.7 - - - -
744 ALA* 3.1 4.8 + - - +
754 ILE* 3.0 24.8 + - - +
227 T 3.6 23.1 - - + +
237 A 3.9 32.3 - - - +
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Residues in contact with ASN 72 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721 ASN* 3.1 24.8 - - - +
751 ILE* 3.5 11.7 - - - +
1111 PHE 3.3 25.3 + - - -
1121 ASN* 4.8 8.1 + - - +
684 ILE* 3.5 16.4 - - + -
694 THR 3.3 14.3 + - - +
704 GLY 3.0 0.8 - - - -
714 PRO* 1.3 75.4 - - - +
734 ARG* 1.3 65.5 + - - +
754 ILE* 3.3 18.6 + - + +
764 TYR* 3.0 25.9 - - + -
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Residues in contact with ARG 73 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892 ARG 4.6 1.0 + - - -
902 ILE* 3.7 26.8 + - - +
604 SER* 2.7 46.7 + - - -
634 LEU* 3.5 16.7 - - + +
644 THR* 2.9 32.3 + - - +
684 ILE* 2.8 56.2 + - + +
694 THR* 3.8 7.6 - - - +
704 GLY 2.9 15.8 + - - +
724 ASN* 1.3 76.2 - - - +
744 ALA* 1.3 59.1 + - - +
764 TYR* 3.0 4.9 + - - -
774 GLN* 2.8 30.1 + - - +
227 T 3.0 35.2 + - - +
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Residues in contact with ALA 74 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711 PRO* 4.8 3.8 - - + -
704 GLY 3.6 0.6 + - - -
714 PRO 3.1 8.8 + - - +
734 ARG* 1.3 77.8 - - - +
754 ILE* 1.3 65.7 + - - +
774 GLN* 3.6 10.1 - - - +
784 GLY* 2.9 21.8 + - - -
217 A 4.1 16.7 - - + +
227 T 3.0 41.4 + - + +
3278 A 4.7 5.2 - - + -
3288 T 4.4 5.7 - - - +
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Residues in contact with ILE 75 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711 PRO* 3.6 26.7 - - + +
721 ASN* 3.5 36.1 - - - +
714 PRO 3.0 14.6 + - - +
724 ASN* 3.4 22.9 - - - +
744 ALA* 1.3 77.9 - - - +
764 TYR* 1.3 67.5 + - + +
784 GLY* 3.4 0.7 + - - -
794 PHE* 3.1 21.5 + - - +
1074 TYR* 3.5 30.8 - - + -
1114 PHE* 4.6 11.0 - - + +
1124 ASN 5.9 0.7 - - - +
1134 ALA* 4.1 20.0 - - + -
3288 T 5.8 0.2 - - - -
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Residues in contact with TYR 76 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594 VAL* 4.4 3.1 - - - +
634 LEU* 3.6 28.9 - - + -
684 ILE* 4.0 18.0 - - + +
724 ASN* 3.0 28.0 - - + -
734 ARG 3.0 5.6 + - - +
754 ILE* 1.3 81.4 - - + +
774 GLN* 1.3 60.7 + - - +
794 PHE* 3.3 6.0 + - - +
804 GLY* 2.8 26.9 + - - -
1124 ASN 5.0 0.3 + - - -
1134 ALA* 4.0 8.8 - - + -
1144 ASN* 2.9 38.9 + - - +
1174 VAL* 3.7 30.5 - - + +
1184 LEU* 3.7 30.7 - - + -
1214 VAL* 4.2 11.8 - - + +
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Residues in contact with GLN 77 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554 VAL* 5.4 0.7 - - - +
564 ASN* 3.4 23.9 + - - +
594 VAL* 3.3 21.2 - - - +
604 SER* 3.5 26.3 - - - +
634 LEU* 4.0 1.9 - - + +
734 ARG 2.8 20.6 + - - +
744 ALA* 3.6 9.4 - - - +
764 TYR* 1.3 77.6 - - - +
784 GLY* 1.3 55.8 + - - +
804 GLY* 3.3 0.5 + - - -
814 LEU* 2.9 43.0 + - + +
217 A 3.4 34.3 + - + +
227 T 3.1 21.9 + - - +
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Residues in contact with GLY 78 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744 ALA 2.9 15.6 + - - -
754 ILE* 3.8 2.0 - - - -
774 GLN* 1.3 77.0 - - - +
794 PHE* 1.3 60.4 + - - +
814 LEU* 3.8 5.3 - - - +
824 LYS* 3.0 24.9 + - - +
1074 TYR* 3.5 13.1 + - - -
217 A 5.4 0.8 + - - -
3288 T 5.1 3.6 - - - -
3298 A 4.1 24.7 - - - +
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Residues in contact with PHE 79 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754 ILE 3.1 14.3 + - - +
764 TYR 3.5 8.1 - - - +
784 GLY* 1.3 75.5 - - - +
804 GLY* 1.3 64.3 + - - +
824 LYS* 3.1 5.5 + - - +
834 VAL* 2.9 33.2 + - + +
1004 ILE* 5.1 1.8 - - + -
1034 LEU* 3.7 23.6 - - + -
1044 LYS* 3.8 23.6 - - + -
1074 TYR* 3.5 35.2 + + + -
1184 LEU* 3.3 52.9 - - + -
1214 VAL* 3.8 16.8 - - + -
1224 VAL* 3.7 23.8 - - + -
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Residues in contact with GLY 80 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554 VAL* 4.5 5.8 - - - -
594 VAL* 5.0 2.2 - - - -
764 TYR 2.8 16.7 + - - -
774 GLN 3.8 0.7 - - - -
794 PHE* 1.3 74.2 - - - +
814 LEU* 1.3 62.2 - - - +
834 VAL* 3.1 2.6 + - - -
844 ALA* 3.0 19.4 + - - +
1214 VAL* 3.5 26.5 - - - -
1254 ILE* 3.1 17.7 - - - +
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Residues in contact with LEU 81 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524 PHE* 3.5 43.6 - - + +
554 VAL* 4.5 6.0 - - + +
564 ASN* 3.4 31.0 - - - +
774 GLN* 2.9 29.6 + - + +
784 GLY* 3.8 4.7 - - - +
804 GLY* 1.3 75.2 - - - +
824 LYS* 1.3 57.2 + - - +
844 ALA* 3.2 3.7 + - - -
854 ARG 2.9 23.6 + - - -
207 T 5.5 1.8 - - - +
217 A 5.6 3.6 - - - +
3298 A 4.1 19.3 - - + +
3308 T 3.4 36.7 - - - +
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Residues in contact with LYS 82 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1063 TYR* 2.8 33.8 + - - -
784 GLY 3.0 17.5 + - - +
794 PHE* 3.5 5.2 - - - +
814 LEU* 1.3 73.7 - - - +
834 VAL* 1.3 64.8 + - - +
854 ARG* 3.3 11.4 + - - +
864 ALA* 3.1 22.3 + - - +
994 MET* 5.9 2.6 - - - -
1034 LEU* 3.5 36.1 - - + +
1064 TYR* 5.0 5.8 - - - -
1074 TYR* 4.6 3.8 - - + -
117 A 4.9 0.2 + - - -
127 T 3.2 13.9 + - - -
3298 A 3.7 26.4 + - - +
3308 T 3.3 29.0 + - - +
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Residues in contact with VAL 83 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794 PHE* 2.9 42.5 + - + +
804 GLY* 3.3 8.5 - - - +
824 LYS* 1.3 76.4 - - - +
844 ALA* 1.3 61.7 + - - +
864 ALA* 3.3 8.3 + - - +
874 LEU* 3.0 19.9 + - + +
964 LEU* 4.5 2.5 - - + +
1004 ILE* 4.3 27.6 - - + -
1034 LEU* 3.7 19.3 - - + -
1224 VAL* 4.6 8.1 - - + -
1254 ILE* 3.9 26.0 - - + -
1264 THR* 4.5 5.6 - - + -
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Residues in contact with ALA 84 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514 LYS 5.7 0.4 - - - +
524 PHE* 3.6 20.4 - - + -
554 VAL* 4.2 19.5 - - + -
804 GLY 3.0 11.5 + - - +
814 LEU* 3.5 8.1 - - - +
834 VAL* 1.3 73.8 - - - +
854 ARG* 1.3 67.4 + - - +
874 LEU* 3.1 12.6 + - + +
884 ASN* 3.0 26.5 + - - +
1254 ILE* 4.4 10.8 - - + -
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Residues in contact with ARG 85 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524 PHE* 3.5 11.8 - - - -
814 LEU 2.9 13.5 + - - +
824 LYS* 3.3 20.2 - - - +
844 ALA* 1.3 75.9 - - - +
864 ALA* 1.3 63.6 + - - +
884 ASN* 3.0 5.8 + - - +
894 ARG* 3.0 44.3 + - - +
117 A 3.8 37.0 + - - -
127 T 2.9 33.3 + - - +
3308 T 3.0 37.6 + - - +
3318 A 3.4 30.3 + - - +
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Residues in contact with ALA 86 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824 LYS 3.1 8.7 + - - +
834 VAL* 3.6 9.4 - - - +
854 ARG* 1.3 78.8 - - - +
874 LEU* 1.3 58.5 + - - +
894 ARG* 4.5 2.9 - - - +
904 ILE* 2.7 47.3 + - + +
964 LEU* 3.8 17.3 - - + -
994 MET* 3.8 26.9 - - + -
1004 ILE* 6.0 0.4 - - + -
1034 LEU* 6.2 0.4 - - + -
117 A 5.6 2.5 - - - -
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Residues in contact with LEU 87 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834 VAL* 3.0 14.4 + - + +
844 ALA* 3.1 12.3 + - + +
864 ALA* 1.3 76.7 - - - +
884 ASN* 1.3 64.1 + - - +
914 GLY* 2.7 31.3 + - - +
924 SER* 3.6 29.4 - - - +
964 LEU* 3.6 23.9 - - + +
1254 ILE* 4.5 25.1 - - + +
1264 THR* 6.0 3.1 - - + -
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Residues in contact with ASN 88 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484 ASN* 4.9 6.0 + - - +
514 LYS* 3.8 31.1 + - - +
524 PHE* 3.4 34.1 - - - -
844 ALA* 3.0 13.2 + - - +
854 ARG* 3.5 7.6 - - - +
874 LEU* 1.3 86.9 - - - +
894 ARG* 1.3 64.3 + - + +
904 ILE 4.8 0.3 - - - -
914 GLY* 4.5 1.2 + - - -
75 SER* 4.6 13.3 - - - +
3318 A 5.4 1.7 + - - +
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Residues in contact with ARG 89 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854 ARG* 3.0 45.5 + - - +
864 ALA* 4.3 2.5 - - - +
884 ASN* 1.3 79.5 - - + +
904 ILE* 1.3 62.1 + - + +
75 SER* 4.1 33.0 - - - +
606 SER* 4.5 6.4 + - - -
736 ARG* 4.6 1.9 + - - -
97 A 4.6 10.3 + - - -
107 T 3.6 28.4 + - - +
117 A 3.3 31.7 + - - +
3318 A 4.1 17.3 + - - +
3328 T 4.3 15.8 + - - -
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Residues in contact with ILE 90 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864 ALA* 2.7 30.4 + - + +
884 ASN 4.8 0.7 - - - -
894 ARG* 1.3 77.6 - - - +
914 GLY* 1.3 67.7 + - - +
954 ALA* 3.6 26.5 - - + +
964 LEU* 4.0 5.2 - - + +
994 MET* 3.8 37.9 - - + -
606 SER* 4.9 1.9 + - - -
616 ALA* 5.8 0.5 - - - -
646 THR* 2.6 36.9 + - + +
696 THR* 4.4 10.5 - - + -
736 ARG* 3.7 19.6 + - - +
107 T 5.6 0.7 - - - +
117 A 4.5 10.3 - - - +
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Residues in contact with GLY 91 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864 ALA 3.6 0.2 + - - -
874 LEU* 2.7 31.0 + - - -
884 ASN 5.2 0.4 - - - -
904 ILE* 1.3 89.7 - - - +
924 SER* 1.3 68.8 + - - +
964 LEU* 3.4 9.4 - - - +
646 THR* 3.6 1.5 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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