Contacts of the helix formed by residues 76 - 93 (chain H) in PDB entry 5AN5
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 76 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H ASN* 1.3 63.5 + - - +
78H PHE* 3.0 16.0 - - - +
79H ASP* 3.0 23.7 + - - +
80H ILE* 3.1 18.2 + - - +
81I LEU* 5.9 0.2 - - - +
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Residues in contact with ASN 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-2B SER 5.5 3.8 - - - +
76B THR* 4.3 13.3 - - + +
77B ASN* 3.9 17.5 + - - +
80B ILE* 4.0 17.0 - - + +
76H THR* 1.3 74.6 - - - +
78H PHE* 1.3 59.8 + - + +
80H ILE* 3.4 20.6 + - - +
81H LEU* 3.0 33.7 + - + +
-3I GLY* 4.4 17.9 + - - +
-1I MET* 5.1 2.3 - - - +
0I ALA* 4.8 4.7 + - - +
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Residues in contact with PHE 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B THR* 6.2 1.3 - - + -
76H THR 3.0 8.6 - - - +
77H ASN* 1.3 79.3 - - + +
79H ASP* 1.3 60.3 + - - +
80H ILE 3.2 1.3 - - - -
81H LEU* 3.9 24.1 - - + +
82H LYS* 3.0 29.6 + - - +
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Residues in contact with ASP 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76H THR* 3.0 16.5 + - - +
78H PHE* 1.3 77.5 - - - +
80H ILE* 1.3 58.5 + - - +
82H LYS* 3.4 7.2 + - - +
83H ARG* 3.0 67.8 + - - +
81I LEU* 5.2 3.8 - - - +
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Residues in contact with ILE 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ILE* 3.7 31.2 - - + -
76H THR 3.1 14.6 + - - +
77H ASN* 3.5 25.1 - - - +
79H ASP* 1.3 77.4 - - + +
81H LEU* 1.3 57.7 + - - +
83H ARG* 3.2 3.1 + - - +
84H LEU* 2.9 35.9 + - + +
-1I MET* 6.1 0.4 - - + -
0I ALA* 4.3 14.1 - - + -
80I ILE* 3.8 19.7 - - + -
81I LEU* 4.0 25.6 - - + -
84I LEU* 3.9 21.2 - - + +
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Residues in contact with LEU 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B THR* 4.3 18.4 - - + -
79B ASP* 3.6 25.6 - - + +
80B ILE* 3.9 21.3 - - + -
83B ARG* 3.7 12.9 + - - +
77H ASN 3.0 22.2 + - - +
78H PHE* 3.4 29.4 + - + +
80H ILE* 1.3 74.4 - - - +
82H LYS* 1.3 58.5 + - - +
84H LEU* 3.2 8.3 + - + +
85H SER* 2.9 33.2 + - - +
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Residues in contact with LYS 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78H PHE 3.0 18.2 + - - +
79H ASP* 3.7 9.2 - - - +
81H LEU* 1.3 76.2 - - - +
83H ARG* 1.3 60.3 + - + +
85H SER* 3.3 6.2 + - - -
86H ASN* 3.0 44.5 + - - +
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Residues in contact with ARG 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H ASP* 3.0 49.7 + - - +
80H ILE 3.7 3.6 - - - +
82H LYS* 1.3 78.1 - - + +
84H LEU* 1.3 57.8 + - - +
86H ASN* 3.4 9.3 + - - +
87H LEU* 2.9 34.1 + - - +
81I LEU* 3.9 23.6 + - - +
84I LEU* 3.9 18.4 - - + +
85I SER* 3.4 30.1 + - - +
88I GLU* 2.8 44.3 + - - +
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Residues in contact with LEU 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ILE* 3.9 31.4 - - + +
83B ARG* 3.9 25.4 - - + +
84B LEU* 3.9 29.4 - - + +
87B LEU* 4.0 15.9 - - + -
80H ILE* 2.9 35.7 + - + +
81H LEU* 3.2 8.3 + - + +
83H ARG* 1.3 77.0 - - - +
85H SER* 1.3 62.2 + - - +
87H LEU* 3.2 3.9 + - + +
88H GLU* 2.9 29.1 + - - +
84I LEU* 3.9 20.6 - - + -
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Residues in contact with SER 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ARG* 2.9 25.0 + - - +
81H LEU 2.9 17.2 + - - -
82H LYS* 3.3 6.7 + - - -
84H LEU* 1.3 74.8 - - - +
86H ASN* 1.3 61.6 + - - +
88H GLU* 3.4 5.4 + - - +
89H LYS* 2.9 29.6 + - - +
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Residues in contact with ASN 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H LYS* 3.0 33.4 + - - +
83H ARG* 3.6 8.7 - - - +
85H SER* 1.3 77.9 - - - +
87H LEU* 1.3 65.4 + - - +
89H LYS* 3.4 5.7 + - - +
90H HIS* 3.0 24.3 + - - +
92I PHE* 4.2 11.9 - - + -
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Residues in contact with LEU 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 4.1 15.7 - - + -
83H ARG 2.9 18.4 + - - +
84H LEU* 3.6 5.2 - - - +
86H ASN* 1.3 75.3 - - - +
88H GLU* 1.3 59.0 + - - +
90H HIS* 3.2 1.9 + - - +
91H VAL* 2.9 35.3 + - + +
84I LEU* 3.7 30.3 - - + -
87I LEU* 4.2 20.4 - - + +
88I GLU* 3.9 25.4 - - + +
91I VAL* 3.8 28.9 - - + -
92I PHE* 3.8 25.1 - - + -
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Residues in contact with GLU 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ARG* 2.9 60.8 + - - +
87B LEU* 4.0 23.0 - - + +
78C PHE* 6.1 3.6 - - + -
78D PHE* 5.4 3.9 - - + -
84H LEU 2.9 14.2 + - - +
85H SER* 3.7 4.8 - - - +
87H LEU* 1.3 76.8 - - - +
89H LYS* 1.3 55.9 + - - +
92H PHE* 2.9 45.6 + - + +
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Residues in contact with LYS 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D PHE* 5.8 3.1 - - - -
85H SER 2.9 17.4 + - - +
86H ASN* 3.8 7.0 - - - +
88H GLU* 1.3 77.7 - - - +
90H HIS* 1.3 58.6 + - - +
93H GLY* 2.8 36.3 + - - +
95H LYS* 4.6 1.6 + - - -
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Residues in contact with HIS 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C LYS* 5.4 0.9 + - - -
86H ASN 3.0 18.4 + - - +
87H LEU 3.7 3.4 - - - +
89H LYS* 1.3 79.7 - - - +
91H VAL* 1.3 62.5 + - - +
95H LYS* 2.9 42.6 + - - +
91I VAL* 3.4 35.1 + - + -
92I PHE* 3.4 36.3 + + + -
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Residues in contact with VAL 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 4.6 9.2 - - + -
90B HIS* 3.9 17.0 - - + +
91B VAL* 4.9 3.8 - - + -
82C LYS* 5.8 1.4 - - - -
85C SER* 4.8 6.6 + - - -
89C LYS* 4.8 10.7 + - - -
87H LEU* 2.9 21.9 + - + +
88H GLU* 4.8 0.2 - - - -
90H HIS* 1.3 79.6 - - - +
92H PHE* 1.3 96.2 + - + +
93H GLY 4.7 1.6 - - - +
95H LYS* 5.4 0.5 - - - -
91I VAL* 3.7 32.5 - - + -
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Residues in contact with PHE 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 4.3 10.3 - - + -
90B HIS* 3.6 27.6 - + - -
78C PHE* 3.5 65.7 - + - -
81C LEU* 3.6 49.1 - - + +
82C LYS* 4.0 8.3 - - + -
85C SER* 4.8 3.4 - - - -
78D PHE* 3.8 18.2 - - + -
83D ARG* 4.7 5.0 + - - -
88H GLU* 2.9 28.8 + - + +
91H VAL* 1.3 87.3 - - + +
93H GLY* 1.3 66.8 + - - +
94H SER* 3.7 1.2 + - - -
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Residues in contact with GLY 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C SER* 4.3 6.6 + - - -
78D PHE* 4.1 14.9 - - - -
88H GLU 3.9 0.8 + - - -
89H LYS* 2.8 34.8 + - - +
91H VAL 4.7 0.7 - - - +
92H PHE* 1.3 76.3 + - - +
94H SER* 1.3 66.3 + - - -
95H LYS* 3.4 15.1 + - - +
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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