Contacts of the helix formed by residues 73 - 83 (chain C) in PDB entry 1F9N
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 LEU 73 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72C PRO* 1.3 73.5 - - - +
74C SER* 1.4 59.9 + - - +
75C LYS 3.2 0.7 - - - -
76C LEU* 3.0 35.5 + - + +
77C LYS* 3.1 10.3 + - - +
113C LEU* 3.3 33.4 - - + -
115C TRP* 4.1 15.0 - - + +
144C ARG* 6.2 3.1 - - + -
148C LEU* 4.0 27.3 - - + +
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Residues in contact with SER 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C PRO* 3.4 23.2 - - - +
73C LEU* 1.4 73.7 - - - +
75C LYS* 1.3 66.0 + - - +
76C LEU 3.0 1.8 - - - -
77C LYS* 2.9 21.8 + - - +
78C ARG* 3.0 16.3 + - - +
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Residues in contact with LYS 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C GLN* 5.4 8.6 - - - +
71C ASN* 3.7 36.2 - - + +
72C PRO* 3.4 17.0 + - + +
73C LEU 3.2 0.2 - - - -
74C SER* 1.3 82.7 + - - +
76C LEU* 1.3 59.0 + - - +
78C ARG* 4.2 4.5 + - + +
79C ALA* 3.7 12.8 + - - +
109C LEU* 3.1 42.5 - - + +
82D ASP* 4.8 11.5 + - - -
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Residues in contact with LEU 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C PRO 4.3 0.6 + - - +
73C LEU* 3.0 28.6 + - + +
74C SER 3.0 0.4 - - - -
75C LYS* 1.3 80.5 - - - +
77C LYS* 1.3 56.9 + - - +
78C ARG 3.5 0.2 - - - -
79C ALA* 3.5 0.5 + - - +
80C LEU* 2.9 53.9 + - + +
106C ILE* 4.0 7.4 - - + -
109C LEU* 3.5 22.2 - - + +
110C MET* 4.0 21.3 - - + -
113C LEU* 3.5 35.0 - - + -
115C TRP* 4.7 0.2 - - + -
145C LEU* 4.5 7.4 - - + -
148C LEU* 4.0 12.3 - - + -
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Residues in contact with LYS 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C LEU 3.1 7.0 + - - +
74C SER* 2.9 20.3 + - - +
76C LEU* 1.3 77.9 - - - +
78C ARG* 1.3 63.6 + - - +
80C LEU* 3.2 5.3 + - - +
81C MET* 2.9 43.0 + - + +
148C LEU* 4.7 26.2 - - + +
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Residues in contact with ARG 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C SER 3.0 10.4 + - - +
75C LYS* 4.5 4.7 - - + +
77C LYS* 1.3 78.5 - - - +
79C ALA* 1.3 63.4 + - - +
81C MET* 3.4 14.0 + - + +
82C ASP* 2.8 36.3 + - - +
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Residues in contact with ALA 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C LYS 3.7 16.4 + - - +
76C LEU 3.5 4.0 + - - +
77C LYS 3.3 0.2 - - - -
78C ARG* 1.3 78.4 - - - +
80C LEU* 1.3 62.1 + - - +
82C ASP* 3.3 5.6 + - - +
83C ALA* 3.0 26.5 + - - +
105C ALA* 6.4 0.4 - - + -
106C ILE* 3.3 25.0 - - + +
109C LEU* 3.9 10.3 - - + -
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Residues in contact with LEU 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C LEU* 2.9 30.9 + - + +
77C LYS* 3.6 4.3 - - - +
79C ALA* 1.3 74.9 - - - +
81C MET* 1.3 62.3 + - + +
84C PHE* 2.7 53.6 + - + +
96C LEU* 4.6 11.7 - - + -
98C THR* 5.9 2.2 - - + -
106C ILE* 3.5 35.9 - - + -
110C MET* 5.9 0.2 - - - -
145C LEU* 4.1 43.5 - - + +
148C LEU* 4.3 9.4 - - + -
149C LEU* 4.3 9.2 - - + -
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Residues in contact with MET 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C LYS* 2.9 43.4 + - + +
78C ARG* 3.8 12.1 - - + +
80C LEU* 1.3 72.9 - - - +
82C ASP* 1.3 63.7 + - - +
148C LEU 3.9 19.7 - - - +
149C LEU* 4.4 15.9 - - - -
11D ARG* 3.3 28.5 + - - +
48D LEU* 4.9 6.6 - - - +
49D HIS* 6.0 10.7 - - + -
64D LEU* 3.7 3.8 - - - +
65D PRO* 5.1 0.3 - - - +
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Residues in contact with ASP 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C ARG* 2.8 26.7 + - - +
79C ALA* 3.9 4.3 - - - +
80C LEU 3.1 0.6 - - - -
81C MET* 1.3 84.0 - - - +
83C ALA* 1.3 57.8 + - - +
49D HIS* 5.1 7.4 - - - +
64D LEU* 3.1 19.4 - - - +
65D PRO* 3.1 34.7 - - + +
66D ALA* 3.0 27.5 + - + +
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Residues in contact with ALA 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C ALA 3.0 14.2 + - - +
82C ASP* 1.3 76.0 - - - +
84C PHE* 1.3 69.5 + - - +
85C VAL* 3.2 3.7 - - - +
98C THR* 3.2 9.3 - - - -
99C MET* 2.9 30.4 + - - +
102C ASN* 3.8 24.9 - - + +
106C ILE* 5.0 5.4 - - + -
64D LEU* 4.4 1.3 - - - -
66D ALA* 3.4 20.9 - - + -
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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