Contacts of the helix formed by residues 57 - 69 (chain C) in PDB entry 1X1O
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 GLY 57 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56C ALA* 1.3 73.5 - - - +
58C LEU* 1.3 64.7 + - - +
59C TRP* 3.3 5.4 - - - -
60C VAL* 2.9 31.2 + - - +
61C ALA 2.9 10.9 + - - -
80C GLU* 2.5 16.7 + - - -
111C LEU* 3.4 13.8 - - - +
114C LEU* 4.1 10.3 - - - -
151C TYR* 4.5 2.1 - - - -
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Residues in contact with LEU 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ILE* 6.3 0.2 - - + -
55C LEU* 3.3 22.0 - - + -
57C GLY* 1.3 76.5 - - - +
59C TRP* 1.3 58.8 - - + +
61C ALA* 3.2 5.5 + - - +
62C GLU* 3.0 27.4 + - - +
74C PHE* 3.8 27.9 - - + -
76C PRO* 3.9 17.0 - - + -
78C VAL 3.0 28.9 - - - +
80C GLU* 3.1 21.2 + - + +
90C VAL* 3.3 28.0 - - + -
91C ALA* 4.3 3.4 - - + -
111C LEU* 3.6 14.8 - - + +
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Residues in contact with TRP 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C TRP* 4.1 39.9 - + + -
14C LEU* 3.5 32.3 - - + -
57C GLY 4.4 0.2 - - - -
58C LEU* 1.3 80.3 - - - +
60C VAL* 1.3 76.8 + - + +
62C GLU* 3.5 14.6 + - - +
63C ARG* 3.1 40.1 + - + +
80C GLU* 4.4 11.7 - - + -
148C LEU* 4.8 6.5 - - + -
151C TYR* 3.2 50.0 + + - -
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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
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14C LEU* 4.8 2.7 - - + -
18C LEU* 4.2 13.9 - - + +
57C GLY* 2.9 19.1 + - - +
59C TRP* 1.3 111.1 - - + +
61C ALA* 1.3 64.4 + - - +
63C ARG* 3.1 7.5 + - - +
64C VAL* 3.1 24.5 + - - +
110C LEU* 3.5 35.7 - - + -
114C LEU* 4.2 7.4 - - + -
148C LEU* 4.1 21.5 - - + -
151C TYR* 5.4 0.4 - - + -
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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
----------------------------------------------------------
47C ILE* 6.5 1.1 - - + -
57C GLY 2.9 11.8 + - - +
58C LEU* 3.6 9.6 - - - +
60C VAL* 1.3 78.0 - - - +
62C GLU* 1.3 61.8 + - - +
64C VAL* 3.0 19.3 + - - +
65C PHE* 3.1 22.6 + - + -
74C PHE* 4.1 13.0 - - + -
107C ALA* 4.2 26.9 - - + +
110C LEU* 5.8 0.4 - - - +
111C LEU* 4.6 13.5 - - + +
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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
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58C LEU 3.0 14.8 + - - +
59C TRP* 3.7 13.8 - - - +
60C VAL 3.2 0.2 - - - -
61C ALA* 1.3 77.5 - - - +
63C ARG* 1.3 77.1 + - - +
65C PHE* 3.6 2.4 + - - +
66C ALA* 3.2 25.2 + - + +
74C PHE* 3.3 59.3 + - + +
76C PRO* 5.0 4.5 - - - +
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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
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10C TRP 6.2 1.6 - - - +
14C LEU* 5.8 1.6 - - + -
18C LEU* 3.8 18.2 - - + -
59C TRP* 3.1 27.1 + - + +
60C VAL* 3.1 9.2 + - - +
62C GLU* 1.3 105.4 + - - +
64C VAL* 1.3 66.6 + - - +
66C ALA* 3.0 30.2 - - - +
67C LEU* 3.0 35.1 + - + +
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Residues in contact with VAL 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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18C LEU* 4.2 13.5 - - + -
22C LEU* 4.2 5.9 - - + +
60C VAL 3.1 16.3 + - - +
61C ALA* 3.0 9.5 + - - +
63C ARG* 1.3 77.4 - - - +
65C PHE* 1.3 57.8 + - - +
67C LEU* 3.3 8.1 + - - +
68C ALA* 2.9 26.3 + - - +
103C GLY* 3.7 29.8 - - - +
106C LEU* 3.9 23.6 - - + -
107C ALA* 3.9 9.4 - - + +
110C LEU* 4.0 24.7 - - + -
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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
----------------------------------------------------------
47C ILE* 4.8 7.0 - - + -
61C ALA* 3.1 21.5 + - + +
62C GLU* 4.0 4.5 - - - +
64C VAL* 1.3 74.4 - - - +
66C ALA* 1.3 60.6 + - - +
68C ALA* 3.2 4.1 + - - +
69C ASP 2.9 32.2 + - - +
72C THR* 3.1 19.1 + - + +
74C PHE* 3.6 32.5 - + + -
93C VAL* 4.5 16.2 - - + -
99C GLY 4.5 1.8 - - - -
100C ILE* 3.6 38.4 - - + -
103C GLY* 3.9 8.7 - - - -
104C GLU* 3.9 9.6 - - - -
107C ALA* 3.6 24.9 - - + -
281C LEU* 3.6 25.8 - - + -
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Residues in contact with ALA 66 (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 GLU 3.2 11.7 + - - +
63C ARG* 3.0 38.1 - - - +
65C PHE* 1.3 77.7 - - - +
67C LEU* 1.3 61.4 + - + +
69C ASP 3.9 2.0 - - - -
70C PRO* 3.0 38.0 - - + +
72C THR* 3.6 9.1 + - - +
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Residues in contact with LEU 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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15C GLU* 4.1 15.9 - - + +
18C LEU* 3.5 36.8 - - + -
19C ARG* 3.5 59.2 + - + +
22C LEU* 4.1 13.5 - - + +
63C ARG* 3.0 25.4 + - + +
64C VAL* 3.7 4.9 - - - +
66C ALA* 1.3 79.0 - - + +
68C ALA* 1.3 65.0 + - - +
70C PRO* 4.9 2.9 - - - +
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Residues in contact with ALA 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LEU* 3.8 16.5 - - + +
26C LEU* 5.6 2.7 - - + -
64C VAL 2.9 16.2 + - - +
65C PHE* 3.2 7.4 + - - +
67C LEU* 1.3 80.9 - - - +
69C ASP* 1.3 60.4 + - - +
70C PRO* 4.5 1.4 - - - +
99C GLY* 3.6 25.0 - - - +
102C ALA* 4.6 7.4 - - + +
103C GLY 4.2 12.1 - - - +
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Residues in contact with ASP 69 (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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65C PHE 2.9 6.0 + - - +
66C ALA 3.2 2.2 - - - -
68C ALA* 1.3 80.6 - - - +
70C PRO* 1.3 65.4 - - - +
71C ARG* 2.9 63.7 + - - +
72C THR* 2.9 43.1 + - + +
96C PRO* 3.6 17.7 - - - +
98C ARG* 6.0 0.2 - - - +
99C GLY* 3.9 14.8 + - - -
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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