Contacts of the helix formed by residues 62 - 74 (chain C) in PDB entry 4B94
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 PRO 62 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0C GLY* 1.4 83.1 - - - +
63C GLU* 1.3 61.8 + - - +
65C TRP* 4.4 0.2 - - + -
66C LEU* 2.8 36.4 + - - +
98C LEU* 3.7 15.9 - - + -
103C TYR* 3.5 46.4 - - + -
106C ASN* 3.7 15.0 - - - +
108C SER* 3.9 2.2 - - - -
109C PHE* 3.6 31.0 - - + +
112C ILE* 3.5 5.9 - - + +
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Residues in contact with GLU 63 (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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0C GLY* 4.4 3.1 - - - -
62C PRO* 1.3 82.3 - - - +
64C ASP* 1.4 59.5 + - - +
66C LEU* 3.5 2.5 + - - +
67C SER* 3.1 29.3 + - - -
106C ASN* 2.8 31.1 + - - +
108C SER* 3.6 20.1 + - - +
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Residues in contact with ASP 64 (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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-1C PRO* 3.8 17.4 - - + +
0C GLY* 3.4 9.2 + - - +
62C PRO 3.4 0.4 - - - -
63C GLU* 1.4 75.4 - - - +
65C TRP* 1.3 63.4 + - - +
67C SER* 3.5 8.2 + - - -
68C LEU* 3.2 21.8 + - - +
1196C PGE 3.6 38.5 + - - +
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Residues in contact with TRP 65 (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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-1C PRO* 3.5 26.5 + - + +
0C GLY 3.1 24.4 + - - +
62C PRO 3.8 3.8 - - - +
64C ASP* 1.3 75.9 - - - +
66C LEU* 1.4 58.3 + - - +
68C LEU* 3.2 15.0 + - + +
69C LEU* 2.9 36.5 + - + +
90C ARG* 3.9 34.1 - - + -
93C GLN* 4.1 5.6 - - + -
94C ALA* 3.5 36.3 - - + -
97C ALA* 3.9 28.0 - - + +
98C LEU* 3.9 13.7 - - + -
112C ILE* 3.9 13.0 - - + -
1196C PGE 3.7 39.5 - - - -
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Residues in contact with LEU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C PRO 2.8 22.5 + - - +
63C GLU* 3.9 4.3 - - - +
65C TRP* 1.4 70.8 - - - +
67C SER* 1.3 54.4 + - - +
69C LEU* 4.3 3.1 - - + -
70C LEU* 2.8 63.1 + - + +
91C TYR* 4.7 9.0 - - - +
108C SER* 3.9 23.8 - - - +
111C ARG* 3.8 50.3 - - + +
112C ILE* 3.9 24.8 - - + +
115C ARG* 6.2 0.7 - - + -
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Residues in contact with SER 67 (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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63C GLU 3.1 17.6 + - - -
64C ASP* 3.5 9.2 - - - -
65C TRP 3.3 0.2 - - - -
66C LEU* 1.3 76.8 - - - +
68C LEU* 1.4 60.0 + - - +
70C LEU* 3.7 6.0 + - - +
71C LYS* 3.2 23.9 + - - +
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Residues in contact with LEU 68 (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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64C ASP 3.2 9.3 + - - +
65C TRP* 3.2 16.2 + - + +
67C SER* 1.4 78.1 - - - +
69C LEU* 1.3 63.7 + - + +
71C LYS* 3.4 10.0 + - - +
72C LEU* 3.0 30.4 + - + +
90C ARG* 3.8 45.5 - - + +
1196C PGE 3.6 33.4 - - - +
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Residues in contact with LEU 69 (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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65C TRP* 2.9 26.8 + - + +
66C LEU* 3.8 4.7 - - + +
68C LEU* 1.3 78.9 - - + +
70C LEU* 1.3 60.0 + - - +
72C LEU* 3.3 7.9 + - + +
73C GLU* 3.0 26.7 + - - +
87C LEU* 4.1 4.5 - - - +
90C ARG* 3.7 47.1 - - + +
91C TYR* 3.7 46.1 + - + +
94C ALA* 3.8 24.7 - - + -
112C ILE* 4.1 11.4 - - + -
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Residues in contact with LEU 70 (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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66C LEU* 2.8 46.2 + - + +
67C SER* 4.2 4.9 - - - +
69C LEU* 1.3 72.1 - - - +
71C LYS* 1.4 56.1 + - - +
73C GLU* 3.4 15.7 + - + +
74C LYS* 3.0 27.8 + - - +
91C TYR* 4.4 10.3 - - - +
111C ARG* 3.7 29.4 - - - +
115C ARG* 6.0 2.9 - - - -
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Residues in contact with LYS 71 (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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67C SER 3.2 18.6 + - - +
68C LEU* 3.5 9.2 - - - +
69C LEU 3.3 0.2 - - - -
70C LEU* 1.4 74.8 - - - +
72C LEU* 1.3 57.7 + - - +
74C LYS* 3.4 11.0 + - + +
75C ASN* 3.0 50.0 + - - +
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Residues in contact with LEU 72 (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 LEU* 3.0 15.9 + - + +
69C LEU* 3.3 9.4 + - + +
71C LYS* 1.3 73.8 - - - +
73C GLU* 1.4 58.5 + - - +
75C ASN* 3.2 11.8 + - + +
76C SER* 2.7 39.9 + - - +
86C LYS* 4.8 17.0 - - + +
87C LEU* 3.8 22.2 - - + -
90C ARG* 3.7 40.6 - - + +
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Residues in contact with GLU 73 (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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69C LEU 3.0 11.1 + - - +
70C LEU* 3.5 20.8 - - + +
72C LEU* 1.4 74.7 - - - +
74C LYS* 1.4 61.8 + - - +
76C SER* 3.1 16.0 + - - -
77C VAL* 3.9 10.6 - - - +
79C LEU* 5.8 1.0 - - + +
87C LEU* 3.7 28.2 - - + +
91C TYR* 3.3 27.4 + - - -
115C ARG* 2.7 44.2 + - - +
119C LEU* 5.1 0.7 - - - -
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Residues in contact with LYS 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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70C LEU 3.0 12.8 + - - +
71C LYS* 3.6 14.6 - - + +
72C LEU 3.3 0.2 - - - -
73C GLU* 1.4 75.6 - - - +
75C ASN* 1.3 64.4 + - - +
76C SER 3.3 2.8 + - - -
77C VAL* 3.9 18.8 + - - +
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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