Contacts of the helix formed by residues 78 - 86 (chain M) in PDB entry 4E45
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 78 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74M ARG* 3.2 33.8 + - - +
76M THR* 4.6 2.2 - - + +
77M ILE* 1.3 73.4 - - - +
79M THR* 1.3 60.8 + - - +
80M GLU* 3.2 18.8 + - - +
81M ASP* 2.8 48.1 + - - +
82M VAL* 3.3 14.7 + - - +
31N SER* 4.2 8.1 - - - +
34N ALA* 3.8 8.9 - - - +
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Residues in contact with THR 79 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78M ASN* 1.3 74.0 - - - +
80M GLU* 1.3 62.4 + - - +
82M VAL* 3.3 4.8 + - - +
83M LYS* 2.9 39.9 + - - +
100M SER* 4.1 14.8 + - - +
31N SER* 4.7 0.7 - - - +
33N ASP* 3.7 17.0 - - + +
34N ALA 3.5 25.6 - - - +
37N LEU* 3.7 25.7 - - + +
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Residues in contact with GLU 80 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71K HIS* 3.8 31.2 + - + +
73K LYS* 4.7 13.5 + - - -
72M ALA* 5.5 0.5 - - - +
74M ARG* 4.2 6.6 + - - -
78M ASN* 3.2 19.0 - - - +
79M THR* 1.3 80.9 + - - +
81M ASP* 1.3 62.4 + - - +
83M LYS* 3.5 21.7 + - + +
84M LEU* 3.1 22.3 + - - +
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Residues in contact with ASP 81 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71K HIS* 2.8 34.2 + - - -
65M LEU* 3.7 24.5 - - + +
68M PHE* 3.6 8.1 - - + -
69M ALA* 3.5 15.9 + - - +
74M ARG* 2.8 31.0 + - - -
77M ILE* 3.3 9.8 - - + -
78M ASN* 2.8 25.1 + - - +
80M GLU* 1.3 78.3 - - - +
82M VAL* 1.3 60.7 + - - +
84M LEU* 3.3 5.5 + - - +
85M LEU* 3.1 17.3 + - - +
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Residues in contact with VAL 82 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65M LEU* 3.8 19.5 - - + -
77M ILE* 4.7 1.3 - - + -
78M ASN 3.5 13.0 - - - +
79M THR* 3.3 7.7 + - - +
81M ASP* 1.3 75.1 - - - +
83M LYS* 1.3 63.0 + - - +
85M LEU* 3.1 19.1 - - - +
86M ALA* 3.2 9.2 + - - +
96M ILE* 4.4 8.5 - - + -
34N ALA* 4.0 24.9 - - + +
37N LEU* 3.8 29.2 - - + +
38N MET* 3.8 25.4 - - + -
41N LEU* 4.4 9.5 - - + +
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Residues in contact with LYS 83 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79M THR* 2.9 26.4 + - - +
80M GLU* 3.7 19.6 - - + +
82M VAL* 1.3 73.3 - - - +
84M LEU* 1.3 60.2 + - - +
86M ALA* 2.9 18.5 + - - +
87M ARG* 3.2 9.7 + - - +
93M LEU* 3.6 17.9 - - + +
96M ILE* 4.4 14.6 - - + -
97M THR* 3.9 34.6 - - + +
100M SER* 4.0 20.5 + - - -
37N LEU* 5.4 0.7 - - + -
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Residues in contact with LEU 84 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67K MET* 4.1 34.1 - - + +
68K PHE* 3.9 19.7 - - + -
71K HIS* 3.7 33.0 - - + +
68M PHE* 3.8 30.1 - - + -
71M HIS* 6.4 0.2 - - + -
80M GLU 3.1 11.9 + - - +
81M ASP* 3.3 9.4 + - - +
83M LYS* 1.3 77.3 - - - +
85M LEU* 1.3 56.7 + - - +
87M ARG* 2.8 56.1 + - - +
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Residues in contact with LEU 85 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61M PHE* 3.6 49.9 - - + +
64M ASP* 3.5 38.6 - - + +
65M LEU* 3.9 19.5 - - + -
68M PHE* 3.9 9.8 - - + -
81M ASP 3.1 9.9 + - - +
82M VAL 3.1 12.5 + - - +
84M LEU* 1.3 78.1 - - - +
86M ALA* 1.3 57.1 + - - +
87M ARG* 3.4 8.8 + - - +
88M ARG* 4.8 5.9 + - - +
92M LEU* 5.4 1.4 - - - +
38N MET* 3.9 6.7 - - - -
41N LEU* 3.8 18.8 - - + -
81N PHE* 4.8 11.1 - - - +
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Residues in contact with ALA 86 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82M VAL 3.2 9.7 + - - +
83M LYS 2.9 10.4 + - - +
85M LEU* 1.3 73.7 - - + +
87M ARG* 1.3 57.8 + - - +
88M ARG* 3.0 12.1 + - - -
89M SER* 3.4 18.9 + - - +
92M LEU* 3.9 31.9 - - + +
93M LEU* 3.6 19.3 + - + +
96M ILE* 4.2 15.3 - - + -
41N LEU* 5.4 4.0 - - + -
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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