Contacts of the helix formed by residues 18 - 33 (chain C) in PDB entry 1EGE
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 18 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B LEU* 5.3 10.0 - - + +
16C PHE 3.5 2.0 + - - +
17C THR* 1.3 74.3 - - + +
19C GLN* 1.3 59.7 + - - +
21C LYS* 3.1 53.8 + - - +
22C GLU* 3.5 11.4 + - - +
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Residues in contact with GLN 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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17C THR* 2.8 15.7 + - + +
18C GLU* 1.3 77.4 - - - +
20C GLN* 1.3 66.3 + - + +
22C GLU* 3.1 43.7 + - - +
23C PHE* 3.3 33.1 + - + -
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Residues in contact with GLN 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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11B GLY* 4.3 4.5 - - - -
16C PHE* 3.2 27.4 - - + -
17C THR* 2.7 49.0 + - - +
19C GLN* 1.3 69.4 - - + +
21C LYS* 1.3 56.0 + - - +
22C GLU 2.9 5.1 + - - -
23C PHE* 3.1 11.5 + - + -
24C GLN* 2.9 31.4 + - - +
78C PHE* 3.0 35.0 + - - -
79C ASP* 2.9 28.8 + - - +
82C LEU* 3.7 12.2 - - + +
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Residues in contact with LYS 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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15C GLU* 3.2 31.0 + - - -
16C PHE* 3.5 28.3 + - + +
17C THR 3.2 7.1 + - - +
18C GLU* 3.1 41.7 + - - +
19C GLN 3.3 0.2 - - - -
20C GLN* 1.3 75.9 - - - +
22C GLU* 1.3 57.0 + - - +
24C GLN* 3.9 12.3 - - - +
25C ALA* 3.2 27.9 + - - +
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Residues in contact with GLU 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 GLU 3.5 7.4 + - - +
19C GLN* 3.1 35.1 + - - +
20C GLN 2.9 0.2 - - - -
21C LYS* 1.3 77.1 - - - +
23C PHE* 1.3 77.1 + - + +
24C GLN 3.0 1.1 + - - -
25C ALA* 3.1 5.1 + - - +
26C THR* 2.8 35.5 + - - +
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Residues in contact with PHE 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 GLN* 3.3 39.7 + - + -
20C GLN* 3.1 13.6 + - + +
22C GLU* 1.3 89.1 - - - +
24C GLN* 1.3 57.9 + - - +
26C THR* 3.7 8.0 - - + +
27C ALA* 2.9 31.6 + - - +
60C GLY 5.4 3.6 - - - -
61C LEU* 5.5 1.3 - - + +
73C LEU* 4.9 13.2 - - + -
75C LEU* 3.7 40.2 - - + -
79C ASP* 4.9 11.2 - - + -
82C LEU* 4.2 5.4 - - + -
83C ILE* 3.6 30.3 - - + +
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Residues in contact with GLN 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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16C PHE* 3.8 33.0 - - - -
20C GLN 2.9 15.3 + - - +
21C LYS* 3.9 11.4 - - - +
23C PHE* 1.3 75.7 - - - +
25C ALA* 1.3 53.6 + - - +
27C ALA* 2.9 8.5 + - - +
28C ARG* 2.7 60.3 + - - +
82C LEU* 3.7 22.0 - - + +
86C GLU* 3.1 30.4 + - + +
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Residues in contact with ALA 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 LYS 3.2 16.9 + - - +
22C GLU* 3.1 5.0 + - - +
24C GLN* 1.3 79.5 - - - +
26C THR* 1.3 55.5 + - - +
28C ARG* 4.0 12.0 - - - +
29C LYS* 3.1 28.4 + - - +
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Residues in contact with THR 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 GLU* 2.8 26.6 + - - +
23C PHE* 3.7 7.9 - - + +
25C ALA* 1.3 74.5 - - - +
27C ALA* 1.3 61.8 + - - +
29C LYS* 3.3 20.5 + - - +
30C PHE* 2.9 27.9 + - - +
59C LEU* 4.6 17.7 - - + +
61C LEU* 4.2 18.4 - - + -
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Residues in contact with ALA 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 PHE 2.9 17.6 + - - +
24C GLN 2.9 3.5 + - - +
26C THR* 1.3 74.4 - - - +
28C ARG* 1.3 60.0 + - - +
30C PHE* 3.3 1.9 + - - +
31C ALA* 2.8 35.2 + - - +
61C LEU* 4.2 11.9 - - + -
83C ILE* 4.0 14.6 - - + +
86C GLU* 3.6 21.8 - - + -
87C LEU* 3.7 17.4 - - + +
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Residues in contact with ARG 28 (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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24C GLN* 2.7 49.3 + - - +
25C ALA* 4.1 11.0 - - - +
27C ALA* 1.3 73.1 - - - +
29C LYS* 1.3 63.1 + - - +
31C ALA* 5.0 0.4 - - - -
32C ARG* 3.0 80.1 + - - +
86C GLU* 3.1 41.0 + - - +
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Residues in contact with LYS 29 (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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25C ALA 3.1 20.2 + - - +
26C THR* 3.4 23.3 + - - +
27C ALA 3.2 0.2 - - - -
28C ARG* 1.3 76.5 - - - +
30C PHE* 1.3 57.3 + - - +
32C ARG* 5.3 0.2 - - - -
33C GLU* 2.9 61.3 + - + +
34C GLU* 5.4 5.6 + - - +
55C ARG* 4.4 8.9 - - - +
59C LEU* 4.1 27.9 - - - +
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Residues in contact with PHE 30 (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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26C THR 2.9 15.3 + - - +
27C ALA* 3.7 3.4 - - - +
29C LYS* 1.3 84.1 - - - +
31C ALA* 1.3 62.6 + - - +
32C ARG 3.0 0.3 + - - -
34C GLU* 2.7 77.9 + - + +
35C ILE* 3.5 28.9 - - + -
52C LEU* 3.7 26.7 - - + -
55C ARG* 3.5 13.5 - - + -
56C ALA* 4.1 12.3 - - + -
59C LEU* 3.5 29.8 - - + -
61C LEU* 4.6 4.0 - - + -
87C LEU* 3.7 27.4 - - + -
94C VAL* 5.9 0.9 - - + -
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Residues in contact with ALA 31 (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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27C ALA 2.8 19.0 + - - +
28C ARG* 4.6 0.4 - - - +
30C PHE* 1.3 75.5 - - + +
32C ARG* 1.3 60.0 + - + +
35C ILE* 3.1 32.2 - - + +
36C ILE* 3.1 29.3 + - - +
86C GLU 3.1 27.4 - - - +
87C LEU* 3.9 7.2 - - + +
90C GLY* 3.9 3.9 - - - +
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Residues in contact with ARG 32 (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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28C ARG* 3.0 64.7 + - - +
29C LYS 4.4 0.2 - - - +
31C ALA* 1.3 81.3 - - + +
33C GLU* 1.3 65.3 + - + +
34C GLU 3.4 0.2 - - - -
36C ILE* 3.5 27.4 - - + +
37C PRO* 3.8 4.7 - - - +
86C GLU* 3.9 10.1 + - - +
89C TYR* 3.5 59.4 + - + +
268C GLN* 5.7 3.0 - - - +
272C ASP* 4.6 4.9 + - - -
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Residues in contact with GLU 33 (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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29C LYS* 2.9 44.1 + - + +
32C ARG* 1.3 82.0 - - + +
34C GLU* 1.3 68.2 + - + +
37C PRO* 4.1 11.5 - - - +
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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