Contacts of the helix formed by residues 57 - 74 (chain C) in PDB entry 3LL8
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 57 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ARG* 3.7 23.3 - - + +
29C LEU 2.9 20.4 + - - +
30C THR* 3.4 30.3 - - - +
31C ALA 4.8 0.9 + - - -
56C LEU* 1.3 74.4 - - - +
58C GLU* 1.3 67.1 + - - +
59C SER* 3.3 15.4 + - - +
60C VAL* 3.0 23.3 + - + +
61C ALA* 3.0 10.9 + - - +
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Residues in contact with GLU 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ARG* 3.9 15.9 + - - +
56C LEU 3.5 2.0 + - - -
57C GLU* 1.3 73.0 - - - +
59C SER* 1.3 57.4 + - - +
60C VAL 3.2 0.2 + - - -
61C ALA* 3.3 6.9 + - - +
62C LEU* 3.0 32.5 + - + +
170C TYR* 3.4 8.6 - - + +
171C SER* 2.6 47.3 + - - -
173C ARG* 3.5 25.1 + - - +
174C VAL* 3.6 16.8 - - + -
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Residues in contact with SER 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ALA* 6.0 0.2 - - - +
57C GLU* 3.9 17.3 + - - +
58C GLU* 1.3 76.4 - - - +
60C VAL* 1.3 63.5 + - - +
62C LEU* 3.6 12.9 + - - +
63C ARG* 3.1 25.1 + - - +
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Residues in contact with VAL 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LEU 3.6 11.0 - - - +
30C THR* 3.6 6.7 - - - +
31C ALA* 3.3 35.4 - - + +
34C VAL* 3.9 38.6 - - + -
35C PHE* 4.2 8.3 - - + -
56C LEU* 4.3 7.9 - - + -
57C GLU* 3.0 20.7 + - + +
59C SER* 1.3 81.7 - - - +
61C ALA* 1.3 64.8 + - - +
62C LEU 3.2 0.2 - - - -
63C ARG* 3.1 6.8 + - - +
64C ILE* 3.0 23.6 + - - +
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Residues in contact with ALA 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LEU* 4.2 6.3 - - + +
57C GLU 3.0 11.0 + - - +
58C GLU 3.4 8.5 - - - +
60C VAL* 1.3 74.4 - - - +
62C LEU* 1.3 63.1 + - - +
64C ILE* 3.2 3.8 + - - +
65C ILE* 3.0 31.1 + - + +
131C LEU* 4.1 22.7 - - + -
170C TYR* 4.1 25.6 - - + -
174C VAL* 4.3 11.0 - - + -
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Residues in contact with LEU 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLU* 3.0 32.2 + - + +
59C SER* 3.6 10.8 - - - +
61C ALA* 1.3 76.5 - - - +
63C ARG* 1.3 52.1 + - - +
65C ILE* 3.8 3.5 - - + -
66C THR* 2.7 47.0 + - + +
173C ARG* 3.7 42.8 - - + +
174C VAL* 3.9 21.5 - - + +
177C ALA* 3.7 28.3 - - + -
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Residues in contact with ARG 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ALA* 4.1 19.7 + - - +
35C PHE* 3.5 56.1 - - + +
36C ASP 5.2 0.8 + - - -
39C GLY* 4.3 14.1 + - - -
59C SER 3.1 15.3 + - - +
60C VAL* 3.1 10.3 + - - +
62C LEU* 1.3 76.3 - - - +
64C ILE* 1.3 63.4 + - - +
66C THR* 3.7 5.6 - - - +
67C GLU* 3.0 58.4 + - + +
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Residues in contact with ILE 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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34C VAL* 4.2 15.9 - - + -
35C PHE* 3.7 17.7 - - + -
41C PRO* 5.9 0.2 - - + -
46C LEU* 4.3 15.9 - - + -
56C LEU* 3.6 30.3 - - + -
60C VAL 3.0 14.6 + - - +
61C ALA 3.2 6.3 + - - +
63C ARG* 1.3 77.5 - - - +
65C ILE* 1.3 57.9 + - - +
68C GLY* 3.0 25.5 + - - -
131C LEU* 3.6 25.6 - - + +
134C TRP* 3.6 25.1 - - + -
135C ALA* 3.8 10.8 - - + +
138C ILE* 3.6 11.4 - - + +
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Residues in contact with ILE 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ALA 3.0 25.4 + - - +
62C LEU* 4.0 5.6 - - - +
64C ILE* 1.3 77.4 - - + +
66C THR* 1.3 58.5 + - - +
69C ALA* 3.0 26.7 + - - +
127C ILE* 4.7 1.1 - - + -
130C VAL* 4.8 7.6 - - + -
131C LEU* 4.0 19.5 - - + -
134C TRP* 3.6 11.3 + - + +
174C VAL* 3.8 24.7 - - + +
177C ALA* 3.4 39.7 - - + +
178C CYS* 3.7 26.5 - - - +
181C ALA* 3.8 12.1 - - + -
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Residues in contact with THR 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LEU* 2.7 29.2 + - + +
63C ARG* 3.4 7.8 + - - -
65C ILE* 1.3 75.3 - - + +
67C GLU* 1.3 66.7 + - - +
69C ALA* 3.4 6.7 + - - +
70C SER* 3.0 27.4 + - - -
73C ARG* 5.4 0.5 + - - -
177C ALA* 4.6 17.0 - - + +
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Residues in contact with GLU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C PHE* 3.9 15.7 - - - -
39C GLY 4.6 3.8 - - - +
63C ARG* 3.0 57.6 + - + +
66C THR* 1.3 74.6 + - - +
68C GLY* 1.3 66.3 + - - +
70C SER* 3.5 8.2 + - - -
71C ILE* 3.4 24.4 + - + +
138C ILE* 3.6 22.8 - - + +
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Residues in contact with GLY 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ILE 3.0 13.0 + - - -
67C GLU* 1.3 75.6 - - - +
69C ALA* 1.3 61.6 + - - +
71C ILE* 3.1 9.8 + - - +
72C LEU* 3.0 26.5 + - - +
134C TRP* 3.7 24.0 - - - -
137C LYS* 4.8 5.2 - - - +
138C ILE* 3.9 14.3 - - - +
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Residues in contact with ALA 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ILE 3.0 18.4 + - - +
66C THR* 3.6 8.3 - - - +
67C GLU 3.3 0.2 - - - -
68C GLY* 1.3 76.7 - - - +
70C SER* 1.3 53.9 + - - +
72C LEU* 3.2 12.8 + - - +
73C ARG* 2.8 53.1 + - - +
134C TRP* 4.1 1.0 - - - +
180C ASP* 5.1 1.3 - - + -
181C ALA* 3.8 25.8 - - + +
184C CYS* 3.9 4.3 - - - -
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Residues in contact with SER 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C THR 3.0 17.0 + - - -
67C GLU* 3.6 9.3 - - - -
68C GLY 3.3 0.2 - - - -
69C ALA* 1.3 76.8 - - - +
71C ILE* 1.3 61.1 + - - +
73C ARG* 3.5 24.7 + - - +
74C GLN* 3.2 28.6 + - - +
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Residues in contact with ILE 71 (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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67C GLU* 3.4 16.1 + - + +
68C GLY* 3.1 8.4 + - - +
70C SER* 1.3 75.5 - - - +
72C LEU* 1.3 65.1 + - - +
74C GLN* 3.3 24.3 + - - +
75C GLU* 3.5 13.7 - - + +
137C LYS* 3.8 31.0 - - + +
138C ILE* 3.7 40.2 - - + +
141C PRO* 4.1 19.7 - - + +
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Residues in contact with LEU 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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68C GLY 3.0 17.9 + - - +
69C ALA* 3.6 7.2 - - - +
71C ILE* 1.3 75.1 - - - +
73C ARG* 1.3 58.8 + - - +
75C GLU* 2.9 35.1 + - - +
134C TRP* 3.8 24.7 - - + +
137C LYS* 4.0 23.1 - - + -
146C LEU* 4.7 9.2 - - + +
181C ALA 4.0 9.2 - - - +
184C CYS* 3.5 16.6 - - + +
185C LEU* 3.6 31.9 - - + -
186C PRO* 4.2 10.3 - - + -
217C ARG* 2.8 22.0 + - - -
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Residues in contact with ARG 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C THR 5.5 0.2 + - - -
69C ALA* 2.8 29.8 + - - +
70C SER* 3.5 34.6 + - - +
71C ILE 3.2 0.2 - - - -
72C LEU* 1.3 79.1 - - - +
74C GLN* 1.3 59.7 + - + +
75C GLU 3.5 2.3 + - - +
180C ASP* 5.3 5.5 + - - +
184C CYS* 3.7 30.0 - - - -
218C PHE* 3.6 30.5 - - + -
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Residues in contact with GLN 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C SER* 3.2 19.6 - - - +
71C ILE* 3.6 16.2 - - - +
72C LEU 3.1 1.0 - - - -
73C ARG* 1.3 77.2 - - + +
75C GLU* 1.3 63.2 + - + +
76C LYS* 5.4 1.7 - - - +
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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
------------------------------------------------------------
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