Contacts of the helix formed by residues 76 - 93 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0E ALA 1.3 66.6 - - - +
77E ASN* 1.3 65.1 + - - +
79E ASP* 3.1 7.8 + - - +
80E ILE* 3.0 35.3 + - - +
77G ASN* 5.7 2.5 - - - -
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Residues in contact with ASN 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0E ALA 3.3 0.4 - - - +
76E THR* 1.3 79.1 - - - +
78E PHE* 1.3 65.9 + - - +
80E ILE* 3.3 8.1 + - - +
81E LEU* 3.0 31.8 + - + +
-1F MET* 3.7 33.9 - - + +
77G ASN* 3.7 20.1 + - - -
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Residues in contact with PHE 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0E ALA 3.5 12.6 - - - +
76E THR 3.4 0.2 - - - -
77E ASN* 1.3 77.9 - - - +
79E ASP* 1.3 63.6 + - - +
81E LEU* 3.2 10.8 + - + +
82E LYS* 2.8 64.4 + - + +
98E ASP 6.0 2.5 - - - -
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Residues in contact with ASP 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0E ALA 3.0 14.5 - - - +
76E THR* 3.1 10.3 + - - +
78E PHE* 1.3 83.6 - - + +
80E ILE* 1.3 58.3 + - + +
82E LYS* 4.5 4.2 - - - +
83E ARG* 2.8 62.5 + - - +
81G LEU* 5.9 1.0 - - - +
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Residues in contact with ILE 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E THR* 3.0 20.9 + - - +
77E ASN* 3.6 9.9 - - - +
79E ASP* 1.3 76.6 - - + +
81E LEU* 1.3 62.3 + - + +
83E ARG* 3.8 2.9 - - - +
84E LEU* 3.0 29.7 + - + +
-1F MET* 4.0 22.0 - - + -
80F ILE* 5.1 4.9 - - + -
77G ASN* 3.6 40.2 - - + +
80G ILE* 3.8 24.9 - - + -
81G LEU* 3.7 27.4 - - + -
84G LEU* 3.9 12.8 - - + +
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Residues in contact with LEU 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E ASN* 3.0 25.0 + - + +
78E PHE* 3.8 7.6 - - + +
80E ILE* 1.3 77.5 - - + +
82E LYS* 1.3 58.3 + - - +
84E LEU* 3.5 8.4 + - + +
85E SER* 2.9 33.5 + - - +
-1F MET* 4.5 14.6 - - + -
80F ILE* 3.8 33.4 - - + -
83F ARG* 4.6 15.8 + - - +
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Residues in contact with LYS 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E PHE* 2.8 54.8 + - + +
79E ASP* 4.0 7.2 - - - +
81E LEU* 1.3 71.4 - - - +
83E ARG* 1.3 59.2 + - + +
85E SER* 3.3 3.2 + - - -
86E ASN* 2.8 50.9 + - - +
89E LYS* 5.2 2.6 - - - +
96E LEU* 3.6 27.5 - - + +
97E TYR 3.0 28.7 + - - -
98E ASP* 4.4 12.0 + - - +
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Residues in contact with ARG 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E ASP* 2.8 46.5 + - - +
80E ILE* 3.8 4.0 - - - +
82E LYS* 1.3 76.3 - - + +
84E LEU* 1.3 63.0 + - - +
86E ASN* 3.3 10.0 + - - +
87E LEU* 3.0 27.0 + - - +
81G LEU* 3.6 30.5 + - - +
84G LEU* 3.7 18.5 - - + +
85G SER* 3.2 31.3 + - - +
88G GLU* 2.9 45.0 + - - +
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Residues in contact with LEU 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E ILE* 3.0 19.0 + - + +
81E LEU* 3.6 9.9 - - + +
83E ARG* 1.3 76.1 - - - +
85E SER* 1.3 62.1 + - - +
87E LEU* 3.2 6.3 + - - +
88E GLU* 3.0 29.4 + - - +
80F ILE* 4.3 25.1 - - + -
83F ARG* 3.5 48.0 - - + +
84F LEU* 3.8 25.1 - - + -
87F LEU* 3.7 28.9 - - + -
84G LEU* 3.8 9.5 - - + +
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Residues in contact with SER 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E LEU* 2.9 24.7 + - - +
82E LYS* 3.7 7.4 - - - -
84E LEU* 1.3 78.0 - - - +
86E ASN* 1.3 57.9 + - - +
88E GLU* 3.3 11.8 + - - +
89E LYS* 2.8 31.2 + - - +
96E LEU* 3.8 26.0 - - - +
83F ARG* 3.5 12.8 + - - -
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Residues in contact with ASN 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E LYS* 2.8 39.5 + - - +
83E ARG* 3.7 9.6 - - - +
85E SER* 1.3 69.8 - - - +
87E LEU* 1.3 66.9 + - - +
89E LYS* 3.1 33.9 + - - +
90E HIS* 3.1 22.9 + - - +
96E LEU* 3.8 9.7 - - - +
92G PHE* 4.1 12.3 - - + -
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Residues in contact with LEU 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E ARG 3.0 19.4 + - - +
84E LEU* 3.2 6.7 + - - +
86E ASN* 1.3 77.2 - - - +
88E GLU* 1.3 61.4 + - - +
90E HIS* 3.3 2.8 + - - +
91E VAL* 2.9 31.5 + - + +
87F LEU* 4.0 15.3 - - + -
84G LEU* 3.8 23.6 - - + +
87G LEU* 3.8 49.4 - - + +
88G GLU* 4.2 11.4 - - + +
91G VAL* 4.2 13.7 - - + -
92G PHE* 3.8 27.6 - - + -
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Residues in contact with GLU 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E LEU* 3.0 13.8 + - - +
85E SER* 3.5 12.9 + - - +
87E LEU* 1.3 75.5 - - - +
89E LYS* 1.3 64.3 + - - +
91E VAL 4.6 0.2 - - - +
92E PHE* 2.9 41.6 + - + +
94E SER* 4.4 1.3 + - - -
83F ARG* 2.7 62.9 + - - +
87F LEU* 4.1 20.3 - - + +
-1J MET* 3.6 32.7 - - + +
78J PHE* 5.7 3.3 - - + -
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Residues in contact with LYS 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E LYS* 5.2 3.2 - - - +
85E SER 2.8 13.2 + - - +
86E ASN* 3.1 37.5 + - - +
87E LEU 3.3 0.2 - - - -
88E GLU* 1.3 76.6 - - - +
90E HIS* 1.3 60.4 + - + +
93E GLY* 2.9 25.1 + - - -
94E SER* 3.0 37.0 + - - +
95E LYS 5.3 0.2 - - - +
96E LEU* 3.7 35.9 + - + +
98E ASP* 5.5 4.6 + - - -
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Residues in contact with HIS 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E ASN 3.1 16.7 + - - +
87E LEU 3.8 3.1 - - - +
89E LYS* 1.3 79.4 - - + +
91E VAL* 1.3 68.7 + - + +
92E PHE 3.4 0.2 + - - -
93E GLY* 3.6 6.6 + - - -
91G VAL* 3.4 35.2 + - + +
92G PHE* 3.6 24.7 - + + -
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Residues in contact with VAL 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87E LEU* 2.9 22.9 + - + +
88E GLU 4.1 2.2 - - - +
90E HIS* 1.3 78.5 - - + +
92E PHE* 1.3 76.1 + - + +
93E GLY 3.9 0.2 + - - -
87F LEU* 4.1 15.3 - - + -
90F HIS* 3.3 36.6 + - + +
91F VAL* 3.9 21.8 - - + -
91G VAL* 4.4 18.6 - - + -
85J SER* 4.2 7.3 + - - -
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Residues in contact with PHE 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C ARG* 2.8 26.0 + - - -
88E GLU* 2.9 41.8 + - + +
91E VAL* 1.3 94.7 - - + +
93E GLY* 1.3 61.2 + - - +
94E SER* 3.6 11.0 - - - +
87F LEU* 4.8 0.7 - - + -
90F HIS* 4.6 5.8 - - - -
-1J MET* 4.7 1.6 - - + -
78J PHE* 3.1 52.5 - + - -
81J LEU* 3.7 46.9 - - + +
82J LYS* 3.9 21.1 - - + -
85J SER* 3.6 13.5 - - - -
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Residues in contact with GLY 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C ARG* 3.5 17.3 + - - -
89E LYS 2.9 10.1 + - - -
90E HIS 3.6 5.8 + - - -
91E VAL 3.5 2.6 - - - -
92E PHE* 1.3 78.7 - - - +
94E SER* 1.3 60.8 + - - +
85J SER* 5.4 0.2 - - - -
88J GLU* 4.5 3.0 - - - +
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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