Contacts of the helix formed by residues 18 - 33 (chain B) in PDB entry 1EGD
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B GLU* 4.4 5.7 - - - +
16B PHE 4.5 0.2 - - - +
17B THR* 1.3 72.6 - - - +
19B GLN* 1.3 59.3 + - - +
21B LYS* 2.9 42.2 + - - +
22B GLU* 2.9 42.6 + - - +
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Residues in contact with GLN 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B THR* 3.0 9.4 + - - +
18B GLU* 1.3 78.6 - - - +
20B GLN* 1.3 62.9 + - + +
22B GLU* 3.1 22.5 + - - +
23B PHE* 3.1 41.9 + - + -
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Residues in contact with GLN 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B PHE* 3.2 24.1 - - + -
17B THR* 2.9 33.2 + - - +
19B GLN* 1.3 77.8 - - + +
21B LYS* 1.3 61.7 + - - +
23B PHE* 3.2 9.1 + - + +
24B GLN* 3.0 21.0 + - - +
78B PHE* 3.3 31.2 - - - +
79B ASP* 3.1 29.0 + - - +
82B LEU* 3.3 23.9 - - + +
11C GLY* 4.5 6.9 - - - -
12C PHE 5.1 0.4 + - - +
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Residues in contact with LYS 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLU* 3.9 16.6 + - - +
16B PHE* 3.9 31.9 - - + +
17B THR 2.9 11.5 + - - +
18B GLU* 2.9 45.0 + - - +
19B GLN 3.2 0.2 - - - -
20B GLN* 1.3 78.3 - - - +
22B GLU* 1.3 67.5 + - - +
24B GLN* 3.7 15.2 + - - +
25B ALA* 3.2 21.5 + - - +
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Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLU* 2.9 36.5 - - + +
19B GLN* 3.1 16.3 + - - +
21B LYS* 1.3 83.7 - - - +
23B PHE* 1.3 66.6 - - + +
25B ALA* 3.1 7.8 + - - +
26B THR* 2.9 28.5 + - - +
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Residues in contact with PHE 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLN* 3.1 44.9 + - + -
20B GLN* 3.2 15.0 + - + +
22B GLU* 1.3 78.4 - - + +
24B GLN* 1.3 57.3 + - - +
26B THR* 3.3 7.4 + - - -
27B ALA* 2.9 30.9 + - - +
60B GLY 5.9 1.1 - - - -
61B LEU* 4.3 6.5 - - + +
73B LEU* 4.7 13.0 - - + -
75B LEU* 3.8 41.5 - - + -
79B ASP* 4.5 15.5 - - + -
82B LEU* 4.6 4.7 - - + -
83B ILE* 4.4 24.2 - - + -
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Residues in contact with GLN 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B PHE* 4.2 19.4 - - - -
20B GLN 3.0 13.2 + - - +
21B LYS* 3.8 15.0 + - - +
23B PHE* 1.3 77.1 - - - +
25B ALA* 1.3 61.9 + - - +
27B ALA* 4.5 1.3 - - - -
28B ARG* 2.8 52.9 + - - +
82B LEU* 3.3 31.2 - - + +
86B GLU* 3.4 32.6 - - - +
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Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LYS 3.2 11.6 + - - +
22B GLU* 3.1 13.8 + - - +
24B GLN* 1.3 79.3 - - - +
26B THR* 1.3 58.7 + - - +
28B ARG* 3.1 6.8 + - - +
29B LYS* 2.9 31.6 + - - +
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Residues in contact with THR 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B GLU* 2.9 13.7 + - - +
23B PHE* 3.6 11.0 - - - -
25B ALA* 1.3 77.0 - - - +
27B ALA* 1.3 60.3 + - - +
29B LYS* 3.7 6.6 + - - +
30B PHE* 3.3 22.7 + - - +
59B LEU* 4.3 30.8 - - + +
61B LEU* 4.0 17.2 - - + +
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Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B PHE 2.9 17.5 + - - +
24B GLN* 3.9 1.8 - - - +
26B THR* 1.3 77.4 - - - +
28B ARG* 1.3 58.4 + - - +
30B PHE* 3.6 2.4 + - - +
31B ALA* 3.1 27.5 + - - +
61B LEU* 3.8 12.8 - - + -
83B ILE* 4.0 19.1 - - + -
86B GLU* 3.6 23.4 - - + +
87B LEU* 4.0 16.9 - - + +
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Residues in contact with ARG 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLN* 2.8 38.2 + - - +
25B ALA* 3.6 7.0 - - - +
27B ALA* 1.3 76.2 - - - +
29B LYS* 1.3 66.5 + - - +
31B ALA 3.2 0.9 + - - -
32B ARG* 3.0 70.3 + - + +
86B GLU* 3.2 32.9 + - - +
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Residues in contact with LYS 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ALA 2.9 17.4 + - - +
26B THR* 4.0 6.5 - - - +
28B ARG* 1.3 76.3 - - - +
30B PHE* 1.3 58.7 + - - +
32B ARG* 4.0 2.0 - - - -
33B GLU* 2.9 71.4 + - - +
34B GLU* 5.8 0.7 - - - +
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Residues in contact with PHE 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B THR 3.3 15.2 + - - +
27B ALA 3.7 2.9 - - - +
28B ARG 3.2 0.6 - - - -
29B LYS* 1.3 79.7 - - - +
31B ALA* 1.3 57.4 + - - +
34B GLU* 2.8 73.0 + - + +
35B ILE* 3.1 36.8 + - + -
52B LEU* 3.4 32.5 - - + -
55B ARG* 3.7 13.5 - - + -
56B ALA* 4.0 17.7 - - + -
59B LEU* 3.6 22.0 - - + -
61B LEU* 4.1 15.0 - - + -
87B LEU* 4.2 9.9 - - + -
98B ILE* 5.2 2.7 - - + -
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Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ALA 3.1 14.7 + - - +
28B ARG 3.2 4.5 + - - +
30B PHE* 1.3 76.8 - - - +
32B ARG* 1.3 65.0 + - - +
35B ILE* 3.1 21.3 + - + +
36B ILE* 2.8 33.9 + - - +
86B GLU 3.0 30.1 - - - +
87B LEU* 4.4 0.7 - - - -
90B GLY 4.2 11.2 - - - +
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Residues in contact with ARG 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ARG* 3.0 52.5 + - + +
29B LYS* 4.1 2.7 - - - +
31B ALA* 1.3 80.1 - - - +
33B GLU* 1.3 64.7 + - + +
36B ILE* 3.8 19.1 - - + +
37B PRO* 3.4 17.3 - - - +
86B GLU* 3.3 31.1 + - - -
89B TYR* 3.4 53.1 + - + -
268B GLN* 5.9 0.8 - - - +
272B ASP* 5.0 1.8 + - - -
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Residues in contact with GLU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LYS* 2.9 58.7 + - + +
32B ARG* 1.3 81.4 - - + +
34B GLU* 1.3 70.9 + - + +
37B PRO* 3.6 16.2 - - - +
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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
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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