Contacts of the helix formed by residues 60 - 82 (chain C) in PDB entry 3LOC
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 60 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LEU* 4.5 5.6 - - - +
54C LEU* 5.7 0.2 - - - +
55C LEU* 4.5 5.4 - - - -
58C PHE 3.2 5.8 + - - +
59C PRO* 1.3 83.0 - - - +
61C LYS* 1.3 63.2 + - - +
62C GLU* 3.3 11.4 + - - +
63C ALA* 3.0 24.5 + - - +
64C LEU* 3.1 22.3 + - - +
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Residues in contact with LYS 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C PHE* 4.0 16.4 - - + -
35C PHE* 3.0 47.5 + - + +
36C HIS* 3.3 14.5 + - - +
38C THR* 3.1 27.5 + - + +
39C ARG* 4.8 0.4 - - - -
40C LEU* 4.0 39.2 - - + +
60C SER* 1.3 70.3 - - - +
62C GLU* 1.3 68.0 + - - +
64C LEU* 3.2 3.4 + - - +
65C TYR* 3.0 24.3 + - - +
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Residues in contact with GLU 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C PHE* 3.7 19.7 - - + -
60C SER* 3.3 10.3 + - - +
61C LYS* 1.3 79.1 - - - +
63C ALA* 1.3 63.3 + - - +
65C TYR* 3.2 1.4 + - - +
66C ILE* 2.9 47.8 + - + +
124C LEU* 3.8 23.1 - - + +
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Residues in contact with ALA 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C PHE* 4.4 4.3 - - + -
59C PRO* 3.8 26.7 - - + -
60C SER* 3.0 21.8 + - - +
62C GLU* 1.3 77.3 - - - +
64C LEU* 1.3 57.4 + - - +
66C ILE* 3.9 6.6 - - - +
67C ALA* 2.9 29.5 + - - +
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Residues in contact with LEU 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE* 4.1 17.9 - - + -
23C LEU* 3.8 20.9 - - + -
26C ALA* 3.7 32.8 - - + -
30C PHE* 4.1 3.8 - - + -
40C LEU* 4.2 3.8 - - + -
43C ILE* 4.0 19.7 - - + -
54C LEU* 4.1 18.2 - - + -
58C PHE* 3.9 26.9 - - + +
60C SER 3.1 12.4 + - - +
61C LYS* 3.6 8.5 - - - +
62C GLU 3.2 0.2 - - - -
63C ALA* 1.3 73.8 - - - +
65C TYR* 1.3 60.9 + - - +
67C ALA* 3.0 3.8 + - - +
68C VAL* 2.9 31.9 + - - +
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Residues in contact with TYR 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C PHE* 3.6 38.5 - + + -
35C PHE* 3.7 32.6 + + + +
61C LYS 3.0 17.2 + - - +
62C GLU 3.5 3.8 - - - +
64C LEU* 1.3 77.5 - - - +
66C ILE* 1.3 65.8 + - + +
68C VAL* 3.2 3.9 + - - +
69C LEU* 3.1 43.4 + - + +
113C LEU* 4.2 22.6 - - + +
116C MSE 5.1 1.0 - - - +
117C GLU* 2.6 46.2 + - - +
124C LEU* 4.0 24.7 - - + -
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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
----------------------------------------------------------
62C GLU* 2.9 52.8 + - + +
63C ALA* 4.0 5.4 - - - +
65C TYR* 1.3 80.4 - - + +
67C ALA* 1.3 59.1 + - - +
69C LEU* 3.7 5.8 - - - +
70C ARG* 2.7 35.0 + - + +
124C LEU* 3.8 33.0 - - + +
125C LEU* 4.5 11.7 - - + -
128C GLU* 4.6 21.5 - - + +
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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
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23C LEU* 4.0 7.4 - - + +
58C PHE* 3.6 27.1 - - + -
63C ALA 2.9 18.8 + - - +
64C LEU 3.0 7.8 + - - +
66C ILE* 1.3 78.5 - - - +
68C VAL* 1.3 60.6 + - - +
70C ARG* 3.3 6.2 + - - +
71C GLN* 3.1 24.9 + - - +
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Residues in contact with VAL 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 4.1 20.4 - - + +
26C ALA* 3.8 26.7 - - + -
27C LEU* 4.2 17.3 - - + +
30C PHE* 4.2 8.1 - - + -
64C LEU 2.9 19.8 + - - +
65C TYR 3.2 4.9 + - - +
67C ALA* 1.3 73.3 - - - +
69C LEU* 1.3 66.2 + - + +
71C GLN* 3.3 16.1 + - + +
72C ILE* 3.4 13.1 + - + +
110C ALA* 5.7 2.3 - - + +
113C LEU* 3.4 32.1 - - + -
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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
----------------------------------------------------------
65C TYR* 3.1 50.6 + - + +
66C ILE* 3.8 3.4 - - - +
68C VAL* 1.3 81.1 - - + +
70C ARG* 1.3 62.7 + - - +
72C ILE* 3.3 11.8 - - + +
73C LEU* 3.1 26.4 + - - +
113C LEU* 4.0 16.4 - - + -
114C PHE* 3.6 43.2 - - + +
117C GLU* 4.0 10.3 - - + -
125C LEU* 3.9 32.3 - - + -
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Residues in contact with ARG 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ILE* 2.7 26.9 + - + +
67C ALA* 3.7 7.6 - - - +
69C LEU* 1.3 74.9 - - - +
71C GLN* 1.3 61.9 + - - +
73C LEU* 3.5 26.9 + - - +
74C ASP* 3.0 55.7 + - - +
77C LEU* 4.1 20.2 - - - +
125C LEU* 5.4 1.9 - - + +
128C GLU* 2.6 50.3 + - - +
132C ASP* 4.7 14.5 - - - +
133C LEU* 5.4 3.8 - - - +
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Residues in contact with GLN 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LYS* 6.3 0.8 - - - +
23C LEU* 3.7 36.5 - - + +
67C ALA 3.1 14.7 + - - +
68C VAL* 3.4 12.7 - - - +
69C LEU 3.2 0.2 - - - -
70C ARG* 1.3 75.9 - - - +
72C ILE* 1.3 63.4 + - - +
74C ASP* 3.3 7.6 + - - +
75C ILE* 3.2 36.2 + - + +
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Residues in contact with ILE 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C VAL* 3.4 9.5 + - + +
69C LEU* 3.3 25.8 - - + +
71C GLN* 1.3 76.4 - - - +
73C LEU* 1.3 66.7 + - - +
75C ILE* 3.4 9.2 + - + +
76C TRP* 3.0 49.2 + - + +
103C VAL* 4.6 3.6 - - + -
107C TYR* 3.9 17.5 - - + +
110C ALA* 2.6 59.7 - - + +
111C SER* 3.4 7.0 - - - +
114C PHE* 4.6 10.1 - - + -
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Residues in contact with LEU 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 3.1 17.6 + - - +
70C ARG* 3.6 39.9 - - - +
72C ILE* 1.3 78.4 - - - +
74C ASP* 1.3 56.7 + - - +
76C TRP* 3.3 6.1 + - + +
77C LEU* 2.9 47.0 + - + +
114C PHE* 3.8 28.7 - - + -
125C LEU* 4.4 15.5 - - + -
128C GLU* 4.9 3.4 - - + +
129C LEU* 5.3 3.8 - - + -
133C LEU* 4.7 10.1 - - + -
212C URA 3.6 31.2 - - + -
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Residues in contact with ASP 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ARG* 3.0 52.7 + - - +
71C GLN* 3.6 6.4 - - - +
72C ILE 3.2 0.2 - - - -
73C LEU* 1.3 74.7 - - - +
75C ILE* 1.3 62.0 + - + +
77C LEU* 4.2 4.3 - - - +
78C ALA* 3.0 28.9 + - - +
81C LYS* 5.6 6.8 - - - +
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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 GLN* 3.2 28.9 + - + +
72C ILE* 3.9 8.5 - - + +
73C LEU 3.4 0.2 - - - -
74C ASP* 1.3 76.5 - - + +
76C TRP* 1.3 63.4 + - - +
77C LEU 3.3 0.3 + - - -
78C ALA* 3.7 4.8 + - - +
79C PRO* 3.6 15.1 - - - +
103C VAL* 3.7 34.4 - - + +
107C TYR* 4.1 36.8 - - + +
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Residues in contact with TRP 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ILE* 3.0 29.9 + - + +
73C LEU* 3.4 11.0 - - + +
75C ILE* 1.3 76.7 - - - +
77C LEU* 1.3 61.2 + - - +
79C PRO* 3.6 9.0 - - - +
96C TYR* 3.9 10.4 + - - -
100C LYS* 3.1 40.4 + - + +
103C VAL* 3.5 33.2 - - + +
104C SER* 5.6 1.6 + - - +
111C SER* 3.8 28.3 + - - -
114C PHE* 3.5 53.6 - + + -
170C GLN* 3.8 22.6 - - + +
212C URA 3.3 40.0 - + + +
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Residues in contact with LEU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ARG* 4.1 22.0 - - - +
73C LEU* 2.9 28.0 + - + +
74C ASP* 4.2 4.7 - - - +
76C TRP* 1.3 77.4 - - - +
78C ALA* 1.3 66.8 + - - +
79C PRO* 3.2 3.4 - - - -
80C LEU* 2.9 22.4 + - + +
81C LYS* 2.7 35.1 + - + +
96C TYR* 5.2 0.9 - - - +
133C LEU* 4.0 25.8 - - + -
136C LEU* 3.6 26.0 - - + -
166C TRP* 4.6 1.8 - - + -
212C URA 4.2 20.9 - - + -
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Residues in contact with ALA 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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74C ASP 3.0 17.1 + - - +
75C ILE* 4.0 6.5 - - - +
77C LEU* 1.3 75.3 - - - +
79C PRO* 1.3 71.7 - - + +
81C LYS* 3.0 10.7 + - - +
82C ALA* 3.0 22.2 + - - +
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Residues in contact with PRO 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ILE 3.6 8.1 - - - +
76C TRP 3.6 11.0 - - - +
77C LEU 3.4 4.0 - - - -
78C ALA* 1.3 94.3 - - + +
80C LEU* 1.3 61.8 + - - +
82C ALA* 3.1 18.8 + - + +
83C PHE* 3.3 19.1 - - + -
96C TYR* 3.5 28.3 - - + -
99C LEU* 3.9 36.1 - - + -
100C LYS* 5.7 1.6 - - + +
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Residues in contact with LEU 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LEU* 2.9 25.4 + - + +
79C PRO* 1.3 76.6 - - - +
81C LYS* 1.3 63.6 + - - +
83C PHE* 3.3 40.8 + - + +
96C TYR* 3.7 35.5 - - + +
136C LEU* 4.4 3.8 - - + -
137C ILE* 3.4 33.4 - - + -
140C LYS* 3.6 29.0 - - + -
144C ILE* 5.3 2.0 - - + -
162C ILE* 4.6 15.0 - - + -
166C TRP* 4.5 4.0 - - + -
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Residues in contact with LYS 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ASP* 5.6 6.5 - - - +
77C LEU* 2.7 31.2 + - + +
78C ALA* 3.5 11.2 - - - +
80C LEU* 1.3 70.9 - - - +
82C ALA* 1.3 57.6 + - - +
83C PHE 3.0 6.1 + - - -
84C ARG* 3.1 18.9 + - - -
136C LEU* 3.9 28.7 - - + -
140C LYS* 3.1 18.7 + - - +
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Residues in contact with ALA 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ALA 3.0 11.5 + - - +
79C PRO* 3.1 13.4 + - + +
81C LYS* 1.3 74.4 - - - +
83C PHE* 1.3 64.3 + - - +
84C ARG* 3.3 15.2 + - - +
87C PHE* 3.2 25.2 - - + -
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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
------------------------------------------------------------
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