Contacts of the helix formed by residues 13 - 27 (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 13 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ARG* 5.3 8.5 - - - +
10C TRP 3.2 3.8 + - - -
11C GLN 3.3 5.1 + - - -
12C GLY* 1.3 78.6 - - - +
14C LEU* 1.3 63.7 + - - +
15C GLU 3.2 3.1 + - - -
16C GLU* 3.4 27.5 + - - +
17C ALA* 3.3 18.2 + - - +
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Residues in contact with LEU 14 (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* 3.5 24.3 + - + +
12C GLY 3.4 3.2 + - - -
13C GLY* 1.3 75.4 - - - +
15C GLU* 1.3 61.0 + - - +
17C ALA* 3.1 12.5 + - + +
18C LEU* 2.8 59.9 + - + +
21C TRP* 4.6 0.7 - - + -
59C TRP* 3.5 40.2 - - + -
60C VAL* 4.8 5.4 - - + -
63C ARG* 5.8 2.0 - - + -
148C LEU* 3.9 36.8 - - + -
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Residues in contact with GLU 15 (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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19A ARG* 4.3 24.5 + - - +
10C TRP 4.8 4.1 + - - +
13C GLY* 3.2 0.4 - - - -
14C LEU* 1.3 79.9 - - - +
16C GLU* 1.3 70.8 + - - +
18C LEU* 3.3 10.6 + - - +
19C ARG* 3.0 58.7 + - - +
67C LEU* 4.1 13.8 - - + +
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Residues in contact with GLU 16 (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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19A ARG* 3.6 31.8 + - - +
23A ARG* 4.1 16.7 + - - +
13C GLY* 3.6 23.2 - - - +
14C LEU 3.3 0.2 - - - -
15C GLU* 1.3 91.9 - - + +
17C ALA* 1.3 62.4 + - - +
19C ARG* 3.5 10.6 + - - +
20C ALA* 3.1 23.9 + - - +
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Residues in contact with ALA 17 (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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13C GLY 3.3 10.2 + - - +
14C LEU* 3.1 14.6 + - + +
16C GLU* 1.3 76.9 - - - +
18C LEU* 1.3 60.3 + - - +
20C ALA* 3.1 7.2 + - - +
21C TRP* 2.8 62.6 + - + -
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Residues in contact with LEU 18 (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* 2.8 46.9 + - + +
15C GLU* 3.6 2.7 - - - +
17C ALA* 1.3 74.9 - - - +
19C ARG* 1.3 57.8 + - - +
21C TRP* 3.2 28.0 + - + +
22C LEU* 2.8 31.2 + - - +
60C VAL* 4.2 9.0 - - + +
63C ARG* 3.8 30.7 - - + -
64C VAL* 4.2 9.9 - - + +
67C LEU* 3.5 22.0 - - + -
106C LEU* 3.8 4.6 - - + +
110C LEU* 3.9 19.3 - - + -
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Residues in contact with ARG 19 (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* 3.0 42.4 + - - +
16C GLU* 3.8 9.2 - - - +
18C LEU* 1.3 75.8 - - - +
20C ALA* 1.3 64.0 + - - +
22C LEU* 3.3 8.6 + - - +
23C ARG* 3.0 54.5 + - - +
67C LEU* 3.5 45.3 + - + +
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Residues in contact with ALA 20 (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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16C GLU 3.1 15.0 + - - +
17C ALA* 3.4 10.5 - - - +
19C ARG* 1.3 77.5 - - - +
21C TRP* 1.3 62.4 + - + +
23C ARG* 3.3 11.7 + - - +
24C GLU* 3.0 26.2 + - - +
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Residues in contact with TRP 21 (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* 4.6 0.9 - - + -
17C ALA* 2.8 36.1 + - + +
18C LEU* 3.8 29.6 - - + +
20C ALA* 1.3 79.7 - - + +
22C LEU* 1.3 65.9 + - - +
24C GLU* 3.4 33.0 + - + +
25C ASP* 3.5 9.0 + - - +
106C LEU* 3.8 23.0 - - + +
110C LEU* 4.2 15.5 - - + -
144C GLY* 3.8 16.4 - - - -
145C LEU* 3.2 32.8 - - + -
148C LEU* 3.8 24.7 - - + -
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Residues in contact with LEU 22 (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 2.8 17.5 + - - +
19C ARG* 3.5 8.1 - - - +
21C TRP* 1.3 77.1 - - - +
23C ARG* 1.3 60.8 + - + +
25C ASP* 3.2 6.5 + - + +
26C LEU* 2.8 48.1 + - + +
64C VAL* 4.2 8.7 - - + +
67C LEU* 4.1 13.0 - - + +
68C ALA* 3.8 33.0 - - + +
102C ALA 4.1 19.3 - - - +
103C GLY* 4.2 12.8 - - - -
106C LEU* 3.5 21.7 - - + +
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Residues in contact with ARG 23 (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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19C ARG* 3.0 49.8 + - - +
20C ALA* 3.6 9.4 - - - +
22C LEU* 1.3 73.6 - - + +
24C GLU* 1.3 64.8 + - - +
25C ASP 3.0 2.0 - - - -
26C LEU* 4.3 3.4 - - - +
27C GLY* 3.0 28.4 + - - +
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Residues in contact with GLU 24 (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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20C ALA 3.0 14.0 + - - +
21C TRP* 3.4 27.0 - - + +
22C LEU 3.2 0.4 - - - -
23C ARG* 1.3 76.9 - - - +
25C ASP* 1.3 59.8 + - - +
27C GLY 5.1 0.3 + - - -
106C LEU* 6.1 0.2 - - - +
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Residues in contact with ASP 25 (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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21C TRP 3.5 7.8 + - - +
22C LEU* 3.2 9.5 + - + +
23C ARG 3.0 0.2 - - - -
24C GLU* 1.3 81.7 - - + +
26C LEU* 1.3 67.0 + - + +
27C GLY 3.7 0.2 - - - -
102C ALA 4.4 11.4 - - - +
105C ARG* 3.8 28.1 - - - +
106C LEU* 4.7 9.5 + - + +
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Residues in contact with LEU 26 (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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22C LEU* 2.8 49.7 + - + +
23C ARG* 4.7 2.2 - - - -
25C ASP* 1.3 81.5 - - + +
27C GLY* 1.3 68.7 + - - +
28C GLN 3.2 0.3 + - - -
29C GLY* 2.8 27.2 + - - +
30C ASP* 4.2 21.1 - - + +
68C ALA* 5.6 2.7 - - + -
102C ALA* 3.7 41.3 - - + +
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Residues in contact with GLY 27 (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 ARG* 3.0 20.8 + - - +
24C GLU 4.9 0.2 - - - -
25C ASP 3.7 0.8 - - - -
26C LEU* 1.3 79.9 - - - +
28C GLN* 1.3 63.0 + - - -
29C GLY* 3.1 1.9 + - - -
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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
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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