Contacts of the helix formed by residues 55 - 69 (chain C) in PDB entry 4UI2
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 ARG 55 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52C ALA 3.4 27.5 - - - +
53C GLN* 3.1 20.0 + - - +
54C CYS* 1.3 71.8 - - - +
56C ILE* 1.3 62.0 + - - +
57C GLN* 3.4 3.6 - - + +
58C LYS* 3.8 27.2 + - + +
59C CYS* 3.5 16.8 + - - -
95C THR* 3.0 20.1 + - - +
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Residues in contact with ILE 56 (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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54C CYS* 3.4 27.3 - - - +
55C ARG* 1.3 73.4 - - - +
57C GLN* 1.3 76.1 + - + +
58C LYS 3.1 2.7 - - - -
59C CYS* 2.9 19.2 + - + +
60C THR* 3.0 24.9 + - - +
88C TYR* 4.5 0.9 - - + -
92C THR* 3.4 36.1 - - + -
95C THR* 4.1 2.9 - - + +
99C CYS* 4.5 1.6 - - - -
102C ASN* 4.2 10.3 - - - +
104C VAL* 4.1 22.0 - - + -
105C TYR* 4.1 20.2 - - + +
108C ALA* 4.1 17.9 - - + -
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Residues in contact with GLN 57 (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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54C CYS 5.5 4.0 - - - +
55C ARG* 3.4 3.5 - - + -
56C ILE* 1.3 82.2 - - + +
58C LYS* 1.3 61.2 + - - +
60C THR* 3.4 8.5 + - - -
61C THR* 3.1 32.6 + - + +
102C ASN* 6.1 0.4 - - - +
104C VAL* 3.9 33.3 - - - +
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Residues in contact with LYS 58 (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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55C ARG* 3.8 29.4 + - + +
56C ILE 3.1 0.4 - - - -
57C GLN* 1.3 77.4 - - - +
59C CYS* 1.3 66.6 + - - +
61C THR* 2.8 20.7 + - - +
62C ASP* 3.1 46.0 + - - +
91C CYS* 5.7 0.2 - - - -
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Residues in contact with CYS 59 (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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55C ARG 3.5 17.3 - - - -
56C ILE* 2.9 12.2 + - + +
58C LYS* 1.3 77.3 - - - +
60C THR* 1.3 57.4 + - - +
62C ASP* 3.6 4.0 + - - +
63C PHE* 3.0 30.1 + - - +
88C TYR* 3.4 23.8 - - + +
91C CYS* 2.1 62.4 - - + -
92C THR* 3.7 5.6 - - + -
95C THR* 4.2 3.8 - - - -
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Residues in contact with THR 60 (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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56C ILE* 3.0 20.7 + - - +
57C GLN* 3.7 11.8 + - - -
59C CYS* 1.3 75.3 - - - +
61C THR* 1.3 61.9 + - - +
63C PHE* 3.1 4.9 + - + +
64C VAL* 2.8 44.1 + - + +
88C TYR* 3.1 30.2 + - + +
104C VAL* 5.3 4.9 - - - +
108C ALA* 5.5 0.2 - - - +
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Residues in contact with THR 61 (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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57C GLN* 3.1 17.2 + - + +
58C LYS* 2.8 24.4 + - - +
60C THR* 1.3 76.7 - - - +
62C ASP* 1.3 61.4 + - - -
64C VAL* 3.0 10.1 + - - +
65C SER* 2.9 33.2 + - - -
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Residues in contact with ASP 62 (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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58C LYS* 3.1 49.7 + - - +
59C CYS* 3.8 5.8 - - - +
61C THR* 1.3 85.8 + - - +
63C PHE* 1.3 64.7 + - - +
65C SER* 3.3 5.8 + - - -
66C LEU* 3.1 35.2 + - + +
91C CYS* 5.3 4.2 - - - -
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Residues in contact with PHE 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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59C CYS 3.0 19.0 + - - +
60C THR* 3.3 6.5 - - + +
62C ASP* 1.3 75.8 - - - +
64C VAL* 1.3 69.4 + - + +
66C LEU* 3.3 9.4 + - - +
67C THR* 3.0 49.5 + - + +
81C PHE* 4.7 9.2 - + - -
84C ALA* 3.3 41.7 - - + -
85C LEU* 3.7 30.5 - - + -
88C TYR* 3.4 33.2 - + + -
115C LEU* 4.8 9.9 - - + -
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Residues in contact with VAL 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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60C THR* 2.8 35.8 + - + +
61C THR* 3.0 10.5 + - - +
63C PHE* 1.3 79.6 - - + +
65C SER* 1.3 57.8 + - - +
67C THR* 2.5 24.2 + - - +
68C SER* 2.9 26.2 + - - +
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Residues in contact with SER 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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61C THR* 2.9 15.4 + - - -
62C ASP* 3.7 9.4 - - - -
64C VAL* 1.3 77.0 - - - +
66C LEU* 1.3 66.8 + - - +
68C SER* 3.3 8.3 + - - -
69C HIS* 3.1 19.9 + - - -
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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
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62C ASP* 3.1 24.9 + - + +
63C PHE* 3.7 6.3 - - - +
65C SER* 1.3 77.9 - - - +
67C THR* 1.3 64.0 + - - +
69C HIS* 3.3 19.7 + - - +
84C ALA* 4.3 25.6 - - + +
87C ALA* 5.1 10.1 - - + -
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Residues in contact with THR 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 PHE* 3.0 49.1 + - + +
64C VAL* 2.5 30.5 + - - +
66C LEU* 1.3 76.0 - - - +
68C SER* 1.3 50.0 + - - -
69C HIS* 2.3 31.5 + - - -
81C PHE* 4.3 23.3 - - + -
84C ALA* 4.7 7.2 - - + -
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Residues in contact with SER 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 VAL* 2.9 23.6 + - - +
65C SER* 3.3 11.0 + - - -
67C THR* 1.3 70.8 + - - +
69C HIS* 1.3 87.4 + - - +
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Residues in contact with HIS 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 SER 3.1 12.8 + - - -
66C LEU* 3.3 13.3 + - - +
67C THR 2.3 30.6 + - - -
68C SER* 1.3 88.1 + - - +
80C GLU* 6.6 0.2 - - + -
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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