Contacts of the helix formed by residues 75 - 94 (chain C) in PDB entry 5Y3R
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 SER 75 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C ARG* 3.0 10.8 + - - +
74C ASN* 1.3 84.4 - - - +
76C ILE* 1.3 71.7 + - - +
78C PHE* 2.7 12.8 + - - -
79C ARG* 2.4 62.1 + - - -
121C ALA* 5.3 3.3 - - - +
124C LYS* 5.2 5.4 + - - -
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Residues in contact with ILE 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C GLY* 5.8 1.8 - - - -
73C LEU* 5.9 0.2 - - + -
74C ASN* 4.9 14.4 - - + +
75C SER* 1.3 103.5 + - - +
77C GLU* 1.3 79.3 + - + +
78C PHE* 3.4 37.2 - - + -
79C ARG* 3.2 13.2 + - - +
80C GLU* 4.1 4.0 + - - +
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Residues in contact with GLU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C GLY* 4.0 7.7 - - - -
27C ALA 2.4 20.8 + - - -
28C ALA* 2.3 54.2 + - + +
32C HIS* 2.6 26.2 + - + -
76C ILE* 1.3 85.4 - - + +
78C PHE* 1.3 69.4 + - + +
80C GLU* 2.8 24.4 + - - +
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Residues in contact with PHE 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ASP* 3.9 9.6 - - + -
24C ARG* 5.7 0.7 - - - -
26C GLY* 3.6 12.8 - - - -
27C ALA* 3.5 25.4 - - + -
70C ARG* 2.7 43.7 + - - +
73C LEU* 3.5 39.3 - - + -
75C SER 2.7 1.7 + - - +
76C ILE* 3.4 26.7 - - + -
77C GLU* 1.3 108.7 - - + +
79C ARG* 1.3 60.1 + - - +
80C GLU 3.1 0.4 - - - -
81C CYS* 3.2 24.7 - - + -
82C ARG* 2.9 19.4 + - - +
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Residues in contact with ARG 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ARG* 2.8 14.3 - - - +
74C ASN 4.2 2.4 + - - -
75C SER* 2.4 52.7 + - - +
76C ILE 3.6 8.3 - - - +
78C PHE* 1.3 69.1 - - - +
80C GLU* 1.3 58.4 + - + +
82C ARG* 3.1 10.4 - - - +
83C GLU* 2.9 24.6 + - - +
117C LYS 2.9 19.0 + - - -
120C ALA* 4.3 3.4 - - - +
121C ALA* 2.6 48.5 + - - +
124C LYS* 3.2 27.0 - - - +
126C PRO* 3.8 22.0 - - + -
127C ALA* 3.3 15.2 - - - +
130C LEU* 3.5 30.5 - - - +
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Residues in contact with GLU 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LEU* 5.9 2.8 - - - +
32C HIS* 3.0 16.9 + - + +
76C ILE 4.8 2.0 - - - +
77C GLU* 2.8 22.6 + - - +
79C ARG* 1.3 73.2 - - + +
81C CYS* 1.3 64.9 + - - +
83C GLU* 3.0 28.9 + - - +
84C GLU* 2.9 27.0 + - - +
126C PRO* 4.8 13.9 - - + +
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Residues in contact with CYS 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ALA* 4.9 0.2 - - - -
31C GLY* 4.4 5.2 - - - -
32C HIS* 2.8 46.5 + - - -
35C ILE* 3.5 20.9 - - + -
70C ARG* 5.3 1.8 - - - -
73C LEU* 5.5 2.7 - - + -
77C GLU 2.9 1.0 + - - -
78C PHE* 3.2 37.6 + - + +
80C GLU* 1.3 77.9 - - - +
82C ARG* 1.3 56.7 + - - +
84C GLU* 3.3 2.8 + - - +
85C ILE* 2.8 39.1 + - + +
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Residues in contact with ARG 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 5.5 1.8 - - + -
70C ARG* 2.7 60.6 + - + +
74C ASN 4.1 0.2 + - - -
78C PHE 2.9 9.1 + - - +
79C ARG* 3.1 16.4 - - - +
81C CYS* 1.3 74.3 - - - +
83C GLU* 1.3 60.6 + - - +
85C ILE* 4.1 9.2 - - + -
86C LEU* 2.7 57.0 + - + +
114C VAL* 3.1 24.0 - - - +
117C LYS* 3.0 58.4 - - - +
130C LEU* 3.4 27.9 - - + +
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Residues in contact with GLU 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ARG 2.9 12.3 + - - +
80C GLU* 3.0 32.4 - - - +
82C ARG* 1.3 80.9 - - - +
84C GLU* 1.3 81.1 + - - +
87C LYS* 2.9 55.8 + - - +
125C ILE* 4.7 6.2 - - - +
126C PRO* 4.6 9.5 - - + +
129C ASP* 2.9 32.3 - - + +
130C LEU* 5.3 0.6 - - + +
133C LYS* 5.6 0.9 - - - -
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Residues in contact with GLU 84 (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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32C HIS* 3.6 30.6 - - + +
35C ILE* 3.3 23.6 - - + -
36C ARG* 3.1 41.8 + - + +
80C GLU* 2.9 13.6 + - - +
81C CYS 3.5 2.9 - - - +
83C GLU* 1.3 100.8 - - - +
85C ILE* 1.3 67.9 + - - +
87C LYS* 3.7 7.5 + - - +
88C PHE* 3.0 23.8 + - + -
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Residues in contact with ILE 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ILE* 3.3 34.3 - - + -
62C ASP* 5.5 4.0 - - - +
66C LEU* 3.3 52.7 - - + -
70C ARG* 5.1 1.3 - - + -
73C LEU* 6.5 0.2 - - + -
81C CYS* 2.8 32.9 + - + +
82C ARG* 4.1 4.5 - - + -
84C GLU* 1.3 68.6 - - - +
86C LEU* 1.3 56.0 + - + +
88C PHE* 2.2 39.4 + - + -
89C LEU* 2.7 30.0 + - + -
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Residues in contact with LEU 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 5.9 1.6 - - + -
82C ARG* 2.7 58.4 + - + +
85C ILE* 1.3 73.9 - - + +
87C LYS* 1.3 55.8 + - - +
89C LEU* 3.2 26.0 - - + +
90C CYS* 2.9 35.0 + - - +
111C CYS* 4.9 2.2 - - - -
114C VAL* 4.2 14.6 - - + -
129C ASP 4.7 0.2 - - - +
130C LEU* 3.8 28.9 - - - +
133C LYS* 3.8 12.8 - - + -
134C LEU* 3.5 25.4 - - + -
137C THR* 4.1 3.5 + - - +
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Residues in contact with LYS 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C GLU* 2.9 58.7 + - - +
84C GLU* 3.7 7.5 + - - +
85C ILE 2.7 2.8 + - - -
86C LEU* 1.3 71.5 - - - +
88C PHE* 1.3 68.9 + - + +
89C LEU 2.9 1.2 + - - -
90C CYS* 3.1 11.9 - - - -
91C ILE* 3.0 30.7 + - + +
129C ASP* 4.3 9.7 + - - -
133C LYS* 3.4 39.5 - - + +
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Residues in contact with PHE 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ILE* 3.2 32.8 - - + -
36C ARG* 3.3 11.4 - - + -
39C GLY* 3.6 11.7 - - - -
40C GLN* 3.2 53.4 - - + -
84C GLU* 3.0 18.9 + - - +
85C ILE* 2.2 25.0 + - + +
87C LYS* 1.3 72.9 - - + +
89C LEU* 1.3 55.1 + - + -
91C ILE* 3.1 22.3 - - + +
92C PHE* 2.8 50.3 + + + -
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Residues in contact with LEU 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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62C ASP* 5.5 5.6 - - - +
63C PHE* 5.2 17.5 - - + -
66C LEU* 4.6 8.7 - - + -
85C ILE* 2.7 37.0 + - + -
86C LEU* 3.2 38.6 - - + +
87C LYS 2.9 1.2 + - - -
88C PHE* 1.3 71.0 - - + +
90C CYS* 1.3 58.6 + - - +
91C ILE 3.0 0.9 - - - -
92C PHE* 2.4 34.4 + - + +
93C LEU* 2.9 15.7 + - + +
107C ILE* 6.1 3.6 - - + -
111C CYS* 5.2 9.4 - - - -
137C THR* 4.7 8.3 - - + +
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Residues in contact with CYS 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 LEU 2.9 23.7 + - - -
87C LYS* 3.1 21.3 - - - -
89C LEU* 1.3 77.0 - - - +
91C ILE* 1.3 60.2 + - - +
93C LEU* 3.2 30.4 - - - +
94C GLU* 4.3 5.5 + - - +
133C LYS* 3.8 7.6 - - - -
136C GLN* 2.7 40.7 - - + +
137C THR* 3.1 35.3 + - - +
140C SER* 4.5 1.6 + - - -
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Residues in contact with ILE 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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87C LYS* 3.0 23.8 + - + +
88C PHE* 3.1 43.5 - - + +
89C LEU 3.0 1.0 - - - -
90C CYS* 1.3 84.5 - - - +
92C PHE* 1.3 69.9 + - + +
93C LEU 3.2 0.9 + - - -
94C GLU* 3.6 23.8 + - - +
95C LYS* 4.0 4.0 + - - +
136C GLN* 4.3 8.7 - - - +
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Residues in contact with PHE 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C GLY* 3.4 30.5 - - - -
40C GLN* 5.4 0.4 - - - -
42C CYS* 3.6 11.4 - - + -
43C VAL* 3.2 24.2 - - + -
59C PHE* 3.3 33.3 - + + -
63C PHE* 5.8 8.6 - + + -
88C PHE* 2.8 39.9 + + + +
89C LEU* 2.4 27.9 + - + +
91C ILE* 1.3 79.2 - - + +
93C LEU* 1.3 63.9 + - - +
95C LYS* 3.1 33.0 - - + +
96C MET* 3.8 2.6 + - - +
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Residues in contact with LEU 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C LEU* 2.9 11.6 + - + +
90C CYS* 3.2 17.5 - - - +
91C ILE 3.2 0.4 - - - -
92C PHE* 1.3 77.0 - - - +
94C GLU* 1.3 57.5 + - - +
96C MET 2.7 36.8 + - - +
97C GLY* 4.5 0.3 - - - -
100C ILE* 6.3 1.1 - - + -
107C ILE* 5.4 13.9 - - + -
136C GLN 3.0 21.1 - - - +
137C THR* 3.1 30.3 - - + +
140C SER* 3.0 30.1 - - - +
141C SER* 3.1 24.0 - - - +
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Residues in contact with GLU 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C CYS 4.7 5.6 - - - +
91C ILE* 3.6 15.8 + - - +
92C PHE 3.4 0.2 - - - -
93C LEU* 1.3 74.5 - - - +
95C LYS* 1.3 64.3 + - - +
96C MET 4.3 1.1 - - - -
97C GLY* 4.1 7.3 + - - +
140C SER* 4.6 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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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