Contacts of the helix formed by residues 78 - 85 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74K ARG* 3.1 38.0 + - - +
76K THR* 4.6 2.2 - - + +
77K ILE* 1.3 74.5 - - - +
79K THR* 1.3 66.6 + - - +
80K GLU* 3.2 14.0 + - - +
81K ASP* 3.0 32.0 + - - +
82K VAL* 3.2 13.5 + - - +
31L SER* 4.0 10.1 - - - +
33L ASP* 6.3 0.2 - - + -
34L ALA* 3.9 8.7 - - - -
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Residues in contact with THR 79 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78K ASN* 1.3 75.9 - - - +
80K GLU* 1.3 57.8 + - - +
82K VAL* 3.3 6.1 + - - +
83K LYS* 2.9 37.8 + - - +
100K SER* 4.0 15.8 + - - +
31L SER* 4.6 0.2 + - - -
33L ASP* 3.5 45.3 - - + +
34L ALA* 3.6 1.9 - - - +
37L LEU* 3.7 23.3 - - + +
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Residues in contact with GLU 80 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74K ARG* 4.8 0.7 - - - +
78K ASN* 3.1 18.9 + - - +
79K THR* 1.3 77.3 + - - +
81K ASP* 1.3 65.4 + - - +
83K LYS* 3.4 16.1 + - - +
84K LEU* 3.3 25.8 + - - +
71M HIS* 3.8 18.5 + - + +
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Residues in contact with ASP 81 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65K LEU* 3.4 25.8 - - + +
68K PHE* 3.7 10.7 - - + -
69K ALA* 2.8 37.2 + - - +
74K ARG* 3.0 15.1 + - - -
77K ILE* 3.2 5.2 - - + +
78K ASN* 3.0 19.6 + - - +
80K GLU* 1.3 73.7 - - - +
82K VAL* 1.3 64.8 + - - +
84K LEU* 3.2 18.2 + - - +
85K LEU* 3.6 3.5 + - - +
71M HIS* 2.7 33.5 + - - -
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Residues in contact with VAL 82 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65K LEU* 3.6 19.7 - - + -
77K ILE* 4.6 0.2 - - + -
78K ASN 3.2 12.2 + - - +
79K THR* 3.3 7.2 + - - +
81K ASP* 1.3 75.8 - - - +
83K LYS* 1.3 63.0 + - - +
85K LEU* 3.0 21.4 + - - +
86K ALA* 3.9 2.9 + - - +
96K ILE* 4.6 5.0 - - + +
34L ALA* 4.0 20.0 - - + +
37L LEU* 3.5 35.2 - - + +
38L MET* 3.9 33.2 - - + -
41L LEU* 4.5 8.2 - - + +
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Residues in contact with LYS 83 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79K THR* 2.9 26.0 + - - +
80K GLU* 3.8 15.2 - - - +
81K ASP 3.2 0.6 - - - -
82K VAL* 1.3 78.7 - - - +
84K LEU* 1.3 61.8 + - + +
86K ALA* 3.0 13.0 + - - +
87K ARG* 3.7 1.2 + - - -
93K LEU* 3.5 25.9 - - + +
96K ILE* 4.3 14.4 - - + -
97K THR* 3.7 40.7 + - + +
100K SER* 4.4 12.8 - - - +
37L LEU* 4.2 12.1 - - + -
70M ARG* 5.9 3.2 - - - +
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Residues in contact with LEU 84 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68K PHE* 3.7 30.5 - - + -
80K GLU 3.3 12.0 + - - +
81K ASP 3.2 9.9 + - - +
83K LYS* 1.3 77.5 - - + +
85K LEU* 1.3 52.0 + - - +
87K ARG* 2.7 47.3 + - - +
67M MET* 4.0 38.1 - - + +
68M PHE* 4.2 15.3 - - + -
70M ARG* 5.7 3.4 - - - +
71M HIS* 3.7 36.3 - - + +
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Residues in contact with LEU 85 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61K PHE* 3.6 31.9 - - + +
64K ASP* 4.0 29.6 - - + +
65K LEU* 3.9 20.4 - - + -
68K PHE* 4.2 9.2 - - + -
81K ASP 3.6 0.6 + - - +
82K VAL 3.0 13.2 + - - +
84K LEU* 1.3 76.4 - - - +
86K ALA* 1.3 55.3 + - - +
87K ARG* 3.3 8.4 + - - +
88K ARG* 5.1 1.2 + - - +
92K LEU* 4.7 2.3 - - - +
38L MET* 3.6 21.1 - - + -
41L LEU* 3.5 29.8 - - + -
80L ASP 4.9 1.0 - - - +
81L PHE* 4.4 26.2 - - - +
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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