Contacts of the helix formed by residues 79 - 86 (chain L) in PDB entry 6AHU
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 THR 79 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75L HIS* 3.3 20.0 - - - +
76L GLU* 3.1 25.1 + - - +
77L LEU 3.6 0.2 - - - -
78L ILE* 1.3 81.2 - - + +
80L PRO* 1.3 72.0 - - + +
81L GLU* 3.9 6.4 + - - +
82L PHE* 3.4 6.4 + - - +
83L ILE* 3.2 20.2 + - - +
162L TYR* 4.0 0.7 - - - -
170L LYS* 5.7 8.3 - - - +
196L TYR* 3.3 17.2 + - - -
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Residues in contact with PRO 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79L THR* 1.3 86.0 - - + +
81L GLU* 1.3 60.7 + - - +
83L ILE* 3.9 11.1 - - + +
84L SER* 3.1 31.7 + - - +
88L LYS* 6.2 1.1 - - - +
157L LEU* 4.2 32.5 - - + -
162L TYR* 3.4 22.2 - - + +
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Residues in contact with GLU 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79L THR* 3.2 5.5 + - - +
80L PRO* 1.3 80.5 - - - +
82L PHE* 1.3 58.0 + - - +
84L SER* 3.7 3.7 + - - -
85L THR* 2.7 44.4 + - - -
196L TYR* 3.7 27.5 - - + +
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Residues in contact with PHE 82 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76L GLU 3.8 6.7 - - - +
77L LEU* 3.4 47.1 - - + +
79L THR* 3.2 15.5 + - - +
81L GLU* 1.3 77.1 - - - +
83L ILE* 1.3 64.9 + - - +
85L THR* 4.6 1.8 - - - +
86L PHE* 3.3 40.0 + + - +
87L ILE* 3.8 21.2 + - + -
92L CYS* 3.6 28.0 - - + -
109L LEU* 4.8 5.6 - - + -
181L LEU* 5.4 1.8 - - + -
193L MET* 5.8 0.9 - - + -
196L TYR* 3.4 33.6 + + - +
197L PHE* 3.7 23.3 - + - -
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Residues in contact with ILE 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77L LEU 4.6 5.4 - - - +
78L ILE* 4.0 16.8 - - - +
79L THR 3.2 19.2 + - - +
80L PRO* 3.7 8.3 + - + +
81L GLU 3.3 0.2 - - - -
82L PHE* 1.3 77.5 - - - +
84L SER* 1.3 54.4 + - - +
87L ILE* 3.1 37.2 + - + -
88L LYS* 2.6 59.5 + - + -
150L LEU* 4.5 27.1 - - + +
151L MET* 5.0 2.0 - - - -
153L LEU* 6.4 0.7 - - + -
154L SER* 4.7 10.1 - - - -
157L LEU* 5.6 5.4 - - + -
162L TYR* 5.1 6.7 - - + -
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Residues in contact with SER 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80L PRO* 3.1 20.4 + - - +
81L GLU* 4.3 4.7 - - - -
83L ILE* 1.3 76.7 - - - +
85L THR* 1.3 61.4 + - - +
88L LYS* 3.5 33.8 + - - +
89L LYS* 3.8 26.9 + - - +
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Residues in contact with THR 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81L GLU* 2.7 36.9 + - - +
82L PHE* 4.2 0.9 - - - -
83L ILE 3.2 0.4 - - - -
84L SER* 1.3 81.2 - - - +
86L PHE* 1.3 88.7 + - + +
89L LYS* 3.7 18.4 - - - +
183L TRP* 4.4 7.6 - - - -
189L GLU 5.7 0.3 - - - +
191L SER* 3.4 26.8 + - - +
196L TYR* 5.1 7.6 - - + -
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Residues in contact with PHE 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82L PHE* 3.3 39.2 + + + +
85L THR* 1.3 98.9 - - + +
87L ILE* 1.3 66.3 + - - +
88L LYS 3.6 0.7 - - - -
89L LYS 4.1 0.7 - - - -
90L GLY 3.4 13.5 + - - -
92L CYS* 3.8 22.5 + - + -
183L TRP* 3.1 57.1 + + + +
191L SER 4.0 14.8 - - - -
192L THR 4.1 6.1 - - - -
193L MET* 3.8 42.6 - - + -
196L TYR* 4.2 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
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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