Contacts of the helix formed by residues 79 - 99 (chain 0) in PDB entry 5IY8
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 79 (chain 0).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710 MET 4.3 0.2 - - - +
720 GLU* 3.0 32.8 - - - +
730 ASP 3.2 10.1 - - - +
740 GLN* 4.0 1.8 - - - +
760 LEU 2.8 7.2 - - - +
770 LYS 1.9 31.1 + - - +
780 PRO* 1.3 83.5 + - - +
800 ARG* 1.4 68.5 + - - +
810 LEU* 3.6 10.8 - - - +
820 THR* 2.7 43.8 + - - -
830 CYS 3.0 14.0 + - - -
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Residues in contact with ARG 80 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700 THR* 2.9 41.6 + - - +
710 MET* 3.3 21.8 + - - +
730 ASP* 2.9 39.6 + - - +
750 ASP* 4.0 21.4 + - - +
760 LEU* 3.2 25.0 + - + +
790 ASN* 1.4 73.3 - - - +
810 LEU* 1.3 60.0 + - - +
840 THR* 2.8 33.0 + - + +
1720 SER* 3.3 26.2 + - - -
2010 LEU* 3.7 26.6 + - + +
2020 SER* 4.5 12.7 + - - -
532W PRO* 6.2 1.8 - - - +
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Residues in contact with LEU 81 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650 VAL* 5.3 4.5 - - + -
660 ASP 4.9 3.8 - - - +
670 GLY* 5.3 2.2 - - - -
710 MET* 3.1 22.3 + - + +
720 GLU* 5.2 0.2 - - - -
790 ASN* 3.2 9.6 - - - +
800 ARG* 1.3 73.2 - - - +
820 THR* 1.4 66.7 + - - +
840 THR* 3.2 5.8 + - - +
850 LEU* 3.0 58.2 + - + +
1340 ALA 4.7 0.9 - - - +
1350 VAL* 3.9 26.9 - - + +
1380 THR* 4.2 16.6 - - + +
1390 CYS* 3.8 34.5 - - + -
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Residues in contact with THR 82 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780 PRO* 3.9 24.2 - - + +
790 ASN* 2.7 32.9 + - - -
810 LEU* 1.4 77.7 - - - +
830 CYS* 1.4 61.3 + - - +
850 LEU* 4.2 1.2 - - - +
860 LYS* 3.2 34.6 + - + +
1350 VAL* 4.2 24.7 - - + +
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Residues in contact with CYS 83 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760 LEU* 3.6 43.5 - - + +
770 LYS* 3.8 10.3 + - + +
780 PRO* 5.4 0.7 - - - -
790 ASN 3.0 15.5 + - - +
820 THR* 1.4 75.5 - - - +
840 THR* 1.4 65.0 + - - +
860 LYS* 3.7 6.3 - - - +
870 LEU* 3.2 28.3 + - - +
2250 GLU* 3.4 36.6 - - - -
2280 TYR* 4.8 1.6 - - - -
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Residues in contact with THR 84 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650 VAL* 4.7 3.7 - - - +
710 MET* 3.3 31.8 - - + +
760 LEU* 4.1 16.8 - - + -
800 ARG* 2.8 31.2 + - + +
810 LEU* 3.2 8.3 + - - +
830 CYS* 1.4 72.1 - - - +
850 LEU* 1.4 55.3 + - - +
870 LEU 3.4 0.2 + - - -
880 LEU* 2.8 37.8 + - - +
1700 ILE* 4.4 4.7 - - + -
2010 LEU* 5.0 4.7 - - + -
2280 TYR* 3.3 36.8 - - + +
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Residues in contact with LEU 85 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650 VAL* 4.5 26.9 - - + -
810 LEU* 3.0 41.2 + - + +
820 THR 4.3 1.8 - - - +
840 THR* 1.4 74.4 - - - +
860 LYS* 1.3 58.1 + - - +
880 LEU* 3.2 6.8 + - + +
890 GLU* 3.0 36.8 + - - +
1170 LEU* 5.8 0.4 - - + -
1310 LEU* 3.7 37.6 - - + +
1340 ALA* 3.9 11.9 - - + -
1350 VAL* 3.6 41.3 - - + +
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Residues in contact with LYS 86 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820 THR* 3.2 25.4 + - + +
830 CYS* 3.7 6.5 - - - +
850 LEU* 1.3 75.9 - - - +
870 LEU* 1.3 67.1 + - + +
890 GLU* 3.4 17.1 + - - +
900 TYR* 3.0 58.2 + - + +
2250 GLU* 6.0 2.2 - - - +
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Residues in contact with LEU 87 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830 CYS* 3.2 15.6 + - - +
860 LYS* 1.3 81.7 - - + +
880 LEU* 1.4 61.0 + - - +
900 TYR* 3.1 27.3 + - + +
910 PHE* 3.0 26.7 + - - +
2250 GLU* 3.3 53.6 - - + +
2280 TYR* 3.5 32.3 - - + -
2290 LYS* 3.7 32.1 - - + +
2320 LEU* 3.8 5.9 - - + +
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Residues in contact with LEU 88 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630 VAL* 4.1 21.1 - - + -
650 VAL* 4.6 17.5 - - + -
840 THR 2.8 20.1 + - - +
850 LEU* 3.2 8.0 + - + +
870 LEU* 1.4 76.4 - - - +
890 GLU* 1.4 54.6 + - - +
910 PHE* 3.2 16.3 + - + +
920 VAL* 3.0 31.2 + - - +
1310 LEU* 3.7 19.7 - - + -
1680 LEU* 4.7 0.4 - - + -
1700 ILE* 3.8 23.8 - - + -
2280 TYR* 3.3 23.3 - - - +
2320 LEU* 3.5 31.0 - - + -
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Residues in contact with GLU 89 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
850 LEU* 3.0 21.8 + - - +
860 LYS* 3.5 17.2 + - - +
870 LEU 3.2 0.2 - - - -
880 LEU* 1.4 70.1 - - - +
900 TYR* 1.3 73.8 + - + +
920 VAL* 3.4 8.2 + - - -
930 GLU* 3.4 20.6 + - - +
1280 ILE* 3.8 24.1 - - + +
1310 LEU* 3.5 29.8 - - + +
1320 LYS* 2.7 49.6 + - - +
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Residues in contact with TYR 90 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860 LYS* 3.0 49.7 - - + -
870 LEU* 3.1 34.4 + - + +
890 GLU* 1.3 86.0 - - + +
910 PHE* 1.3 60.1 + - - +
930 GLU* 3.5 6.2 + - - +
940 GLU* 3.1 29.2 + - + +
2290 LYS* 4.7 19.1 - - + -
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Residues in contact with PHE 91 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610 LEU* 3.8 19.5 - - + -
630 VAL* 4.3 17.9 - - + -
870 LEU 3.0 5.4 + - - +
880 LEU* 3.2 22.2 + - + +
900 TYR* 1.3 72.4 - - - +
920 VAL* 1.3 65.3 + - + +
940 GLU* 3.3 5.2 + - - +
950 TYR* 2.8 43.4 + + + +
1040 ILE* 4.6 7.6 - - + -
1680 LEU* 3.6 27.4 - - + -
2320 LEU* 3.6 52.7 - - + -
2330 THR* 6.3 2.2 - - - -
2350 HIS* 4.0 14.6 - - + -
2360 VAL* 3.7 15.9 - - + -
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Residues in contact with VAL 92 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630 VAL* 6.1 2.0 - - + -
880 LEU 3.0 19.5 + - - +
890 GLU* 3.4 6.5 + - - +
910 PHE* 1.3 84.6 - - + +
930 GLU* 1.3 61.0 + - - +
950 TYR* 3.9 2.5 - - - +
960 PHE* 2.9 50.9 + - + +
1040 ILE* 5.0 9.0 - - + -
1060 ILE* 5.3 2.2 - - + -
1240 PRO* 3.7 26.5 - - + +
1270 HIS* 3.9 19.5 - - + -
1280 ILE* 4.3 7.0 - - + -
1310 LEU* 3.8 20.4 - - + -
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Residues in contact with GLU 93 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890 GLU 3.4 7.4 + - - +
900 TYR* 3.8 8.9 - - - +
910 PHE 3.3 0.2 - - - -
920 VAL* 1.3 78.8 - - + +
940 GLU* 1.3 62.6 + - + +
960 PHE* 3.5 4.4 + - - +
970 ASP* 3.1 25.6 + - - +
1240 PRO* 5.2 7.7 - - + +
1280 ILE* 3.7 40.4 - - + +
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Residues in contact with GLU 94 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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900 TYR* 3.1 24.0 + - + +
910 PHE* 3.3 4.9 + - - +
930 GLU* 1.3 75.5 - - + +
950 TYR* 1.3 55.8 + - - +
970 ASP* 3.4 14.4 + - - +
980 GLN* 3.0 29.5 + - - +
2330 THR* 5.5 9.4 - - + -
2360 VAL* 3.7 20.0 - - + +
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Residues in contact with TYR 95 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590 ARG* 3.5 45.4 - - + +
610 LEU* 3.5 27.7 - - + +
910 PHE* 2.8 32.5 + + + +
920 VAL* 3.9 1.6 - - - +
940 GLU* 1.3 68.5 - - - +
960 PHE* 1.3 65.9 + + - +
980 GLN 3.3 0.3 + - - -
990 ASN* 2.7 57.7 + - + +
1020 SER* 3.3 24.7 - - - -
1030 GLN 3.4 17.0 + - - -
1040 ILE* 3.5 33.0 - - + -
2350 HIS 4.4 3.8 - - - -
2360 VAL* 3.9 16.3 - - + +
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Residues in contact with PHE 96 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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920 VAL* 2.9 27.7 + - + +
930 GLU* 4.1 3.1 - - - +
950 TYR* 1.3 82.7 - + - +
970 ASP* 1.3 56.7 + - - +
990 ASN 3.2 3.3 - - - -
1000 PRO* 3.1 36.9 - - - +
1020 SER* 3.4 33.4 - - - -
1030 GLN 4.3 0.2 - - - -
1040 ILE* 3.9 24.9 - - + -
1210 SER 3.9 20.2 - - - -
1220 GLY 3.3 27.6 - - - -
1230 ASN 4.4 0.2 - - - -
1240 PRO* 3.6 31.4 - - + -
1270 HIS* 3.8 20.9 - + - -
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Residues in contact with ASP 97 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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930 GLU 3.1 18.8 + - - +
940 GLU* 3.6 14.9 - - - +
960 PHE* 1.3 73.6 - - - +
980 GLN* 1.3 51.9 + - - +
1000 PRO* 3.4 1.3 - - - +
2073 CYS* 4.4 9.4 - - - +
2083 ASP* 2.0 73.7 - - - +
2113 GLY* 5.1 2.8 - - - -
2123 GLY 4.9 4.9 - - - +
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Residues in contact with GLN 98 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540 ARG* 2.9 49.7 + - - +
940 GLU 3.0 16.2 + - - +
970 ASP* 1.3 76.6 + - - +
990 ASN* 1.3 62.3 + - - +
1000 PRO* 3.2 1.9 - - - +
2360 VAL* 3.8 23.1 - - + +
2370 SER* 5.0 0.9 - - - -
2380 PRO* 3.9 25.8 - - + -
1853 GLN* 3.6 7.9 + - - -
2083 ASP 3.1 10.5 + - - +
2093 ILE* 2.5 46.8 + - - +
2113 GLY* 4.6 2.8 - - - +
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Residues in contact with ASN 99 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540 ARG 4.6 4.1 - - - +
550 LEU* 5.9 0.2 - - - -
590 ARG* 3.5 32.6 + - + +
950 TYR* 2.7 38.0 + - + +
960 PHE* 3.2 5.9 - - - +
980 GLN* 1.3 77.4 - - - +
1000 PRO* 1.3 62.6 - - - +
1010 ILE 3.0 6.3 + - - +
1020 SER* 2.6 42.9 + - - +
2360 VAL 2.8 25.5 + - - +
2380 PRO* 3.8 17.0 - - - +
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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