Contacts of the helix formed by residues 60 - 79 (chain C) in PDB entry 5UWS
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 ASN 60 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C ASP* 3.7 24.0 + - + +
20C VAL* 3.5 21.6 - - - +
21C SER* 3.4 23.8 + - - +
58C SER* 3.2 4.0 + - - +
59C THR* 1.3 78.8 + - - +
61C PRO* 1.3 67.4 - - - +
62C GLN* 3.0 31.3 + - - +
63C SER* 3.1 25.8 + - - +
64C LYS* 3.3 14.0 + - - +
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Residues in contact with PRO 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C THR 3.5 10.1 - - - +
60C ASN* 1.3 89.1 - - - +
62C GLN* 1.3 73.2 + - - +
64C LYS* 3.3 12.0 + - + +
65C PHE* 2.9 28.4 + - - +
111C GLN* 3.5 35.4 - - - +
114C LEU* 4.0 19.1 - - + +
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Residues in contact with GLN 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 4.0 19.0 - - + +
82A GLN* 3.5 27.3 + - - +
20C VAL* 3.3 20.8 - - + +
21C SER* 5.8 0.8 + - - +
24C TYR* 3.7 31.7 - - + +
25C GLN* 4.2 15.6 + - - -
60C ASN* 3.0 18.1 + - - +
61C PRO* 1.3 90.6 - - - +
63C SER* 1.3 58.1 + - - +
65C PHE* 3.2 9.1 + - - +
66C ILE* 2.9 32.1 + - - +
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Residues in contact with SER 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 4.2 7.6 - - - +
17C ASP* 3.3 15.8 + - - -
20C VAL* 3.2 29.9 - - - +
54C ILE* 3.6 14.2 - - - +
58C SER* 3.6 14.1 - - - -
60C ASN* 3.1 18.9 + - - +
62C GLN* 1.3 78.9 - - - +
64C LYS* 1.3 56.6 + - - +
66C ILE* 3.3 6.4 + - - +
67C ALA* 2.9 27.0 + - - +
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Residues in contact with LYS 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ILE* 4.1 12.1 - - - +
55C LEU* 3.6 39.4 + - + +
56C GLN 5.4 1.6 + - - -
58C SER* 3.2 29.9 + - - -
59C THR* 5.0 2.2 - - - +
60C ASN 3.6 15.5 - - - +
61C PRO* 3.3 4.6 + - - +
63C SER* 1.3 72.7 - - - +
65C PHE* 1.3 65.0 + - - +
67C ALA* 3.1 4.3 + - - +
68C LEU* 2.9 27.0 + - - +
97C MET* 4.5 5.5 - - + +
101C MET* 6.1 1.8 - - - +
114C LEU* 3.5 37.5 - - + +
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Residues in contact with PHE 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ASP* 3.6 16.8 - - - -
78A GLY* 3.9 22.2 - - - -
81A ILE* 3.6 29.4 - - + -
111A VAL* 4.0 23.6 - - + -
61C PRO 2.9 14.6 + - - +
62C GLN 3.4 7.9 - - - +
64C LYS* 1.3 74.2 - - - +
66C ILE* 1.3 65.8 + - + +
68C LEU* 3.1 5.7 + - - +
69C SER* 3.0 32.0 + - - -
113C ASN* 4.4 18.4 - - + -
114C LEU* 3.7 10.8 - - + +
117C LYS* 3.6 49.3 - - + -
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Residues in contact with ILE 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 4.7 14.1 - - + -
78A GLY* 5.7 3.4 - - - -
16C LEU* 6.3 1.6 - - + -
20C VAL* 4.2 23.3 - - + -
24C TYR* 4.1 26.2 - - + +
38C LEU* 4.2 20.6 - - + +
41C PHE* 5.2 7.9 - - + -
42C GLN* 4.8 15.9 - - + +
54C ILE* 6.4 0.7 - - + -
62C GLN 2.9 17.4 + - - +
63C SER* 3.6 8.1 - - - +
65C PHE* 1.3 77.8 - - + +
67C ALA* 1.3 63.1 + - - +
69C SER* 3.1 9.7 + - - -
70C ILE* 3.0 39.2 + - + +
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Residues in contact with ALA 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ALA* 4.1 14.3 - - + +
54C ILE* 4.1 24.7 - - + -
55C LEU* 3.8 20.2 - - + -
63C SER 2.9 14.9 + - - +
64C LYS 3.1 9.4 + - - +
66C ILE* 1.3 77.8 - - - +
68C LEU* 1.3 57.3 + - - +
70C ILE* 3.3 13.5 + - - +
71C LEU* 2.9 26.9 + - - +
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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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55C LEU* 4.0 24.2 - - + -
64C LYS 2.9 17.9 + - - +
65C PHE 3.6 5.4 - - - +
67C ALA* 1.3 72.3 - - - +
69C SER* 1.3 54.5 + - - +
71C LEU* 3.2 11.4 + - + +
72C ASP* 2.6 36.0 + - - +
94C VAL* 5.1 5.2 - - + -
97C MET* 4.5 6.1 - - + -
114C LEU* 4.0 13.2 - - + -
117C LYS* 3.6 18.2 - - + -
118C SER* 3.1 42.4 - - - +
121C THR* 3.7 30.6 + - + +
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Residues in contact with SER 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU 4.9 3.9 + - - -
77A ASP* 4.0 6.5 + - - -
78A GLY* 5.2 0.7 + - - -
42C GLN* 4.2 16.8 - - - -
65C PHE* 3.0 20.1 + - - -
66C ILE* 3.1 12.0 + - - -
68C LEU* 1.3 73.1 - - - +
70C ILE* 1.3 65.4 + - - +
72C ASP* 3.1 6.9 + - - +
73C LYS* 3.0 33.6 + - - +
117C LYS* 3.3 27.7 + - - +
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Residues in contact with ILE 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C PHE* 3.7 31.0 - - + -
42C GLN* 3.4 39.5 - - + +
44C ASN 5.1 1.6 - - - +
47C ALA* 3.7 13.9 - - + +
48C TRP* 3.5 33.8 - - + +
51C ALA* 5.5 1.1 - - + -
54C ILE* 5.6 1.1 - - + -
66C ILE* 3.0 21.3 + - + +
67C ALA* 3.6 11.0 - - - +
69C SER* 1.3 74.8 - - - +
71C LEU* 1.3 62.5 + - - +
73C LYS* 3.4 11.3 + - + +
74C LEU* 3.3 19.8 + - - +
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Residues in contact with LEU 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C TRP* 4.5 24.2 - - + +
51C ALA* 4.6 6.3 - - + -
55C LEU* 4.8 4.5 - - + -
67C ALA 2.9 14.3 + - - +
68C LEU* 3.4 23.3 - - + +
70C ILE* 1.3 76.9 - - - +
72C ASP* 1.3 57.6 + - - +
74C LEU* 3.1 9.0 + - + +
75C ILE* 2.9 39.1 + - + +
90C ILE* 3.9 35.4 - - + -
93C PHE* 4.2 15.3 - - + -
94C VAL* 4.0 27.6 - - + -
121C THR* 4.3 4.3 - - + -
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Residues in contact with ASP 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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76A ARG* 5.9 1.2 + - - -
68C LEU 2.6 20.4 + - - +
69C SER* 3.1 9.8 + - - +
71C LEU* 1.3 71.1 - - - +
73C LYS* 1.3 70.1 + - + +
74C LEU 3.1 0.2 + - - -
75C ILE* 3.2 10.5 + - - +
76C THR* 2.9 32.7 + - - -
117C LYS* 5.0 10.1 + - - +
120C LEU* 5.0 8.5 - - - +
121C THR* 4.9 10.3 + - + +
124C GLN* 3.4 27.3 + - + +
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Residues in contact with LYS 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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74A GLY 4.1 4.9 + - - -
75A LEU 5.4 0.2 - - - -
76A ARG* 3.6 42.8 - - - +
42C GLN* 3.6 44.4 + - + +
43C ASP* 4.2 8.7 - - - +
69C SER* 3.0 19.9 + - - +
70C ILE* 3.6 12.6 - - + +
71C LEU 3.4 0.2 - - - -
72C ASP* 1.3 78.3 + - - +
74C LEU* 1.3 61.6 + - - +
76C THR* 4.7 2.9 - - - -
77C ARG* 3.2 39.3 + - - +
78C LYS* 5.5 0.2 - - - +
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Residues in contact with LEU 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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48C TRP* 4.0 33.9 - - + +
70C ILE 3.3 9.2 + - - +
71C LEU* 3.1 12.4 + - + +
73C LYS* 1.3 77.0 - - - +
75C ILE* 1.3 75.0 + - + +
78C LYS* 2.9 49.6 + - + +
79C TRP* 3.2 12.4 + - + -
82C LEU* 3.8 38.1 - - + -
90C ILE* 3.9 18.4 - - + -
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Residues in contact with ILE 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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71C LEU* 2.9 30.6 + - + +
72C ASP* 3.9 5.4 - - - +
74C LEU* 1.3 78.8 - - + +
76C THR* 1.3 62.6 + - - +
79C TRP* 3.2 43.0 - - + +
90C ILE* 4.6 1.8 - - + -
121C THR* 3.7 28.0 - - + +
124C GLN* 3.9 34.8 - - + +
125C ILE* 3.6 26.5 - - + +
128C GLN* 3.1 26.9 + - + -
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Residues in contact with THR 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 ASP* 2.9 29.6 + - - -
73C LYS* 4.0 4.5 - - - -
75C ILE* 1.3 80.2 - - - +
77C ARG* 1.3 72.5 + - + +
124C GLN* 3.9 18.6 + - - +
128C GLN* 4.0 11.7 + - - +
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Residues in contact with ARG 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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70A GLU* 5.4 6.7 + - - -
76A ARG* 5.7 7.5 - - - +
73C LYS* 3.2 26.2 + - - +
76C THR* 1.3 96.5 - - + +
78C LYS* 1.3 74.9 + - + +
79C TRP 3.8 1.3 - - - -
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Residues in contact with LYS 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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45C PRO* 4.4 23.0 + - - +
74C LEU* 2.9 28.2 + - + +
77C ARG* 1.3 91.6 - - + +
79C TRP* 1.3 68.1 + - - +
80C LYS 3.3 2.2 - - - -
81C LEU* 3.1 37.8 + - + +
82C LEU* 3.7 11.4 + - + +
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Residues in contact with TRP 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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74C LEU* 3.2 10.8 + - + -
75C ILE* 3.2 55.1 + - + +
77C ARG 3.8 1.0 - - - -
78C LYS* 1.3 78.6 - - - +
80C LYS* 1.3 69.3 + - + +
81C LEU 3.2 0.3 + - - -
82C LEU* 3.2 15.1 + - + +
87C ARG* 3.2 65.4 + - + +
90C ILE* 3.9 28.7 - - + -
91C ARG* 4.6 1.8 - - + -
125C ILE* 4.4 16.8 - - + -
128C GLN* 3.5 33.8 - - + +
129C GLU* 2.7 39.1 + - + -
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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