Contacts of the helix formed by residues 80 - 95 (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 GLU 80 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69C HIS* 6.6 0.2 - - + -
78C ASP 3.0 27.4 + - - +
79C SER* 1.3 73.3 - - - +
81C PHE* 1.3 71.8 + - + +
82C CYS 3.2 0.4 - - - -
83C LYS* 3.3 42.4 + - - +
84C ALA* 4.1 3.8 + - - +
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Residues in contact with PHE 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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63C PHE* 4.7 10.9 - + - -
67C THR* 4.3 26.7 - - + -
78C ASP 4.7 2.0 + - - +
80C GLU* 1.3 82.7 - - + +
82C CYS* 1.3 56.3 + - - +
84C ALA* 2.8 13.8 + - - +
85C LEU* 2.7 47.4 + - + +
115C LEU* 5.9 6.3 - - + -
118C GLN 5.5 7.9 - - - +
119C ARG* 5.8 7.2 - - + +
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Residues in contact with CYS 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ASP 4.6 2.0 - - - -
79C SER* 3.8 29.2 - - - -
80C GLU 3.2 1.4 - - - -
81C PHE* 1.3 80.3 - - - +
83C LYS* 1.3 63.0 + - - +
85C LEU* 4.1 5.2 - - - -
86C ARG* 2.7 40.9 + - - +
119C ARG* 4.0 14.8 - - - -
120C ASN 4.6 2.2 - - - -
121C CYS* 2.0 54.1 - - + -
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Residues in contact with LYS 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C SER* 2.7 29.9 + - - +
80C GLU* 3.3 38.7 + - - +
82C CYS* 1.3 80.1 - - - +
84C ALA* 1.3 61.9 + - + +
86C ARG* 3.6 7.0 + - - +
87C ALA* 3.3 18.6 + - - +
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Residues in contact with ALA 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C PHE* 3.3 25.2 - - + -
66C LEU* 4.3 28.9 - - + +
67C THR* 4.7 8.5 - - + +
80C GLU 4.1 3.3 + - - +
81C PHE* 2.8 15.4 + - - +
83C LYS* 1.3 74.6 - - + +
85C LEU* 1.3 58.2 + - - +
87C ALA* 3.3 8.7 + - - +
88C TYR 2.9 24.1 + - - -
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Residues in contact with LEU 85 (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* 3.7 25.7 - - + -
81C PHE* 2.7 33.1 + - + +
82C CYS* 4.0 5.6 - - - +
83C LYS 3.4 0.2 - - - -
84C ALA* 1.3 68.9 - - - +
86C ARG* 1.3 61.5 + - - +
88C TYR* 3.4 2.7 + - + +
89C ALA* 2.8 31.0 + - - +
112C ILE* 3.8 26.5 - - + +
115C LEU* 3.7 51.8 - - + +
116C MET* 3.7 14.3 - - + +
118C GLN 5.7 0.7 - - - +
119C ARG 6.1 0.2 - - - +
121C CYS* 4.1 16.8 - - - -
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Residues in contact with ARG 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C SER* 4.6 9.3 - - - -
82C CYS* 2.7 42.8 + - - +
83C LYS* 3.9 6.2 - - - +
85C LEU* 1.3 76.4 - - - +
87C ALA* 1.3 58.0 + - - +
89C ALA* 3.6 2.6 + - - +
90C GLY* 3.1 23.0 + - - -
116C MET* 3.9 21.3 - - + -
121C CYS* 4.2 2.9 - - - +
122C SER* 3.4 46.4 - - - +
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Residues in contact with ALA 87 (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* 5.1 11.0 - - + -
83C LYS 3.3 13.5 + - - +
84C ALA* 3.4 13.7 - - - +
85C LEU 3.1 0.6 - - - -
86C ARG* 1.3 75.6 - - - +
88C TYR* 1.3 60.1 + - - +
90C GLY* 3.2 2.1 + - - -
91C CYS* 2.9 28.6 + - - +
94C ARG* 4.6 3.5 + - - -
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Residues in contact with TYR 88 (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* 4.5 1.3 - - + -
59C CYS* 3.4 43.1 - - + -
60C THR* 3.1 33.1 + - + +
63C PHE* 3.4 49.8 - + + -
84C ALA 2.9 7.0 + - - +
85C LEU* 3.5 4.7 - - + +
87C ALA* 1.3 73.6 - - - +
89C ALA* 1.3 58.5 + - - +
91C CYS* 3.0 8.2 + - - +
92C THR* 3.0 39.3 + - + +
108C ALA* 4.0 16.4 - - + +
111C GLY 6.2 0.4 - - - -
112C ILE* 3.3 30.1 - - + -
115C LEU* 6.4 1.3 - - + -
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Residues in contact with ALA 89 (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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85C LEU 2.8 18.2 + - - +
86C ARG* 3.7 6.1 - - - +
87C ALA 3.2 0.2 - - - -
88C TYR* 1.3 78.0 - - - +
90C GLY* 1.3 58.6 + - - +
92C THR* 2.8 22.2 + - - -
93C GLN* 3.2 22.6 - - - +
112C ILE* 3.6 22.1 - - + +
116C MET* 3.9 11.2 - - + -
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Residues in contact with GLY 90 (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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86C ARG 3.1 15.8 + - - -
87C ALA* 3.2 3.3 + - - -
89C ALA* 1.3 72.6 - - - +
91C CYS* 1.3 65.4 + - - +
93C GLN* 3.3 14.8 + - - +
94C ARG* 3.0 38.7 + - - -
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Residues in contact with CYS 91 (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* 4.9 4.0 - - - -
59C CYS* 2.1 53.5 - - + -
62C ASP* 5.3 5.2 - - - -
87C ALA 2.9 12.2 + - - +
88C TYR* 3.2 11.7 - - - +
90C GLY* 1.3 76.5 - - - +
92C THR* 1.3 61.3 + - - +
94C ARG* 3.1 36.3 + - - +
95C THR* 3.1 11.3 + - - +
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Residues in contact with THR 92 (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* 3.4 27.4 - - + -
59C CYS* 4.1 1.6 - - + -
88C TYR* 3.0 19.7 + - + +
89C ALA* 2.8 18.4 + - - -
91C CYS* 1.3 73.3 - - - +
93C GLN* 1.3 70.7 + - - +
95C THR* 3.2 14.5 + - - +
96C SER* 2.8 27.0 + - - -
105C TYR* 3.5 15.8 - - - -
108C ALA* 4.9 4.3 - - + -
109C VAL* 5.1 8.0 - - + +
112C ILE* 3.8 18.8 - - + +
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Residues in contact with GLN 93 (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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89C ALA* 3.2 20.6 + - - +
90C GLY* 3.3 13.9 + - - +
92C THR* 1.3 84.6 + - - +
94C ARG* 1.3 59.1 + - + +
96C SER* 2.7 27.5 - - - -
97C LYS* 5.7 0.2 - - - -
105C TYR* 5.0 3.4 - - - +
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Residues in contact with ARG 94 (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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87C ALA 4.6 2.8 + - - -
90C GLY* 3.0 17.2 + - - +
91C CYS* 3.5 44.5 - - - +
92C THR 3.1 0.6 - - - -
93C GLN* 1.3 77.0 - - + +
95C THR* 1.3 59.0 + - - +
96C SER* 3.1 4.8 + - - -
97C LYS 5.1 0.9 + - - -
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Residues in contact with THR 95 (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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53C GLN 4.5 0.3 + - - -
54C CYS* 3.7 2.4 - - - -
55C ARG* 3.0 48.0 + - - +
56C ILE* 4.1 4.3 - - + +
59C CYS* 4.2 3.4 - - - -
91C CYS 3.1 11.7 + - - +
92C THR* 3.3 17.9 - - - +
94C ARG* 1.3 75.5 - - - +
96C SER* 1.3 66.3 + - - +
97C LYS 3.4 1.6 - - - -
98C ALA* 3.2 17.3 + - - +
99C CYS* 3.2 22.4 - - - -
105C TYR* 4.8 0.9 - - + -
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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