Contacts of the helix formed by residues 82 - 92 (chain 7) in PDB entry 5U8T
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 LEU 82 (chain 7).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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807 ILE 3.8 0.4 + - - -
817 ASP* 1.3 69.7 - - - +
837 ASP* 1.3 64.9 + - - +
857 ILE* 3.1 25.5 + - + +
867 LEU 2.9 18.7 + - - -
1037 VAL* 3.6 18.6 - - + +
1067 ILE* 4.0 26.5 - - + -
1077 GLN* 5.3 4.0 - - - +
2047 PHE* 4.5 10.1 - - + -
2057 LYS 3.1 28.8 + - - +
2067 PRO* 4.0 12.3 - - + -
2077 LEU* 3.4 32.2 - - + +
2217 SER 5.9 1.6 - - - +
2227 SER 6.3 0.7 - - - +
2387 LEU* 3.9 24.2 - - + -
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Residues in contact with ASP 83 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817 ASP* 3.4 15.7 - - + +
827 LEU* 1.3 75.9 - - - +
847 ASP* 1.3 58.0 + - - +
867 LEU* 3.1 9.9 + - - +
877 GLN* 2.9 31.2 + - + +
2057 LYS* 4.1 16.3 + - - +
2067 PRO 3.6 6.0 - - - +
2077 LEU* 3.3 28.9 - - - +
2097 GLN* 3.9 17.8 - - - +
2117 CYS* 5.0 9.6 - - - -
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Residues in contact with ASP 84 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247 PHE* 3.6 2.1 - - - -
287 PHE* 2.9 44.4 - - - -
317 ASP* 4.9 10.3 - - - +
627 LYS* 6.0 0.2 - - - +
637 TYR* 2.4 44.9 + - - +
817 ASP* 3.2 19.2 + - - +
827 LEU 3.4 0.2 - - - -
837 ASP* 1.3 75.1 - - - +
857 ILE* 1.3 61.9 + - - +
867 LEU 3.2 0.2 - - - -
877 GLN* 3.7 7.1 - - - +
887 TYR* 2.8 25.5 + - - +
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Residues in contact with ILE 85 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247 PHE* 3.4 22.2 - - + -
807 ILE* 4.6 10.1 - - + -
817 ASP 3.1 19.3 - - - +
827 LEU* 3.1 22.4 + - + +
847 ASP* 1.3 78.3 - - - +
867 LEU* 1.3 57.3 + - - +
887 TYR* 3.8 1.2 - - - +
897 GLN* 3.0 30.5 + - - +
1027 LEU* 3.4 39.8 - - + +
1037 VAL* 3.5 11.0 - - + +
1067 ILE* 3.5 28.0 - - + -
1177 PHE* 5.9 2.9 - - + -
2047 PHE* 4.8 2.5 - - + -
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Residues in contact with LEU 86 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827 LEU 2.9 11.3 + - - +
837 ASP* 3.1 10.7 + - - +
857 ILE* 1.3 75.1 - - - +
877 GLN* 1.3 61.7 + - - +
897 GLN* 3.1 19.0 + - + +
907 ASN* 2.9 38.1 + - - +
1037 VAL* 4.2 5.5 - - + +
2077 LEU* 4.5 13.7 - - + -
2117 CYS* 3.3 31.2 - - - +
2127 ALA* 4.7 9.9 - - - +
2147 ARG* 3.9 20.4 - - + +
2167 ARG* 5.1 19.1 - - + -
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Residues in contact with GLN 87 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287 PHE* 4.5 11.5 - - + -
307 GLN* 5.2 14.3 + - + +
317 ASP* 5.9 2.2 - - - +
837 ASP* 2.9 27.1 + - + +
847 ASP* 3.9 12.3 - - - +
857 ILE 3.5 0.2 - - - -
867 LEU* 1.3 73.2 - - - +
887 TYR* 1.3 58.4 + - - +
907 ASN* 3.0 14.1 - - + +
917 GLU* 3.0 22.3 + - - +
2117 CYS* 3.8 18.6 - - - +
2147 ARG* 2.5 33.5 + - - +
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Residues in contact with TYR 88 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207 GLU* 3.7 17.3 + - + +
237 ASP* 3.1 45.3 + - - +
247 PHE* 3.1 41.2 + + + -
277 THR 4.0 7.4 - - - -
287 PHE* 4.1 19.3 - + + -
637 TYR* 6.2 0.2 - - + -
847 ASP* 2.8 27.2 + - - +
857 ILE 3.9 0.2 - - - +
877 GLN* 1.3 74.5 - - - +
897 GLN* 1.3 62.7 + - - +
907 ASN 3.1 0.2 - - - -
917 GLU* 3.0 14.4 + - + +
927 LYS* 2.8 66.7 + - + +
1027 LEU* 4.4 7.2 - - + -
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Residues in contact with GLN 89 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207 GLU* 4.6 4.7 - - - +
857 ILE* 3.0 23.8 + - - +
867 LEU* 3.1 18.5 + - + +
887 TYR* 1.3 73.0 - - - +
907 ASN* 1.3 61.9 + - - +
917 GLU 3.2 0.9 - - - -
927 LYS* 3.4 10.1 - - + -
937 PHE* 2.9 33.5 + - + +
997 ALA* 4.9 4.4 - - + +
1007 ASP 3.3 9.6 - - - +
1017 ASP* 3.6 5.7 + - - +
1027 LEU* 3.0 56.2 + - + +
1037 VAL* 4.4 7.3 - - - +
2167 ARG* 5.9 4.6 - - - +
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Residues in contact with ASN 90 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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867 LEU* 2.9 19.9 + - - +
877 GLN* 3.0 17.9 + - + +
897 GLN* 1.3 80.0 + - - +
917 GLU* 1.3 56.8 + - - +
947 LEU* 3.2 37.2 + - + +
957 GLN* 3.1 25.6 - - - +
2147 ARG* 2.6 60.3 + - - +
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Residues in contact with GLU 91 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287 PHE* 4.9 12.1 - - + -
307 GLN* 5.2 9.9 + - - +
877 GLN 3.0 10.9 + - - +
887 TYR* 3.0 23.1 + - + +
907 ASN* 1.3 76.9 - - - +
927 LYS* 1.3 61.8 + - + +
957 GLN* 2.8 30.7 - - - +
967 GLY 3.9 5.5 - - - +
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Residues in contact with LYS 92 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207 GLU* 4.6 4.9 - - - +
237 ASP* 5.0 9.3 + - - +
887 TYR* 2.8 62.8 + - + +
897 GLN* 3.2 11.3 + - + -
917 GLU* 1.3 84.1 - - + +
937 PHE* 1.3 55.8 + - - +
957 GLN 3.4 4.3 - - - -
967 GLY 5.1 0.9 - - - -
977 THR* 2.6 34.2 + - - +
997 ALA* 3.1 35.5 + - + -
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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
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Atomic class I II III IV V VI VII VIII
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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