Contacts of the helix formed by residues 9 - 32 (chain F) in PDB entry 3E8C
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 9 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8F LYS* 1.3 68.0 + - - -
10F SEP 1.3 60.7 + - - +
11F GLU 3.4 1.8 - - - -
12F GLN* 3.4 41.2 + - - +
13F GLU* 3.8 10.4 - - - +
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Residues in contact with SEP 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F LYS* 3.3 29.2 + - - +
8F LYS* 3.4 0.6 - - - -
9F GLY* 1.3 76.2 + - - +
11F GLU* 1.3 63.8 + - - -
13F GLU* 3.5 9.7 + - - +
14F SER* 3.4 21.1 + - - -
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Residues in contact with GLU 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F LYS* 2.7 36.3 + - + +
8F LYS* 3.7 26.1 + - + -
9F GLY 3.4 0.2 - - - -
10F SEP 1.3 71.9 + - - -
12F GLN* 1.3 71.5 + - - +
14F SER* 2.9 22.4 + - - +
15F VAL* 2.9 44.4 + - + +
292F LYS* 5.3 5.5 + - - -
303F ILE* 4.0 27.8 - - + +
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Residues in contact with GLN 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F LYS* 3.1 36.7 - - - +
9F GLY* 3.4 26.8 + - - +
11F GLU* 1.3 90.9 + - - +
13F GLU* 1.3 66.0 + - + +
14F SER 3.4 0.5 + - - -
15F VAL* 4.4 3.7 - - - +
16F LYS* 3.5 25.8 + - - +
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Residues in contact with GLU 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F GLY 3.8 11.4 - - - +
10F SEP 3.5 12.6 + - - +
11F GLU 3.2 0.4 - - - -
12F GLN* 1.3 81.9 - - + +
14F SER* 1.3 63.5 + - - +
16F LYS* 4.5 2.9 - - - +
17F GLU* 2.9 50.5 + - - +
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Residues in contact with SER 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F SEP 3.4 10.2 + - - -
11F GLU* 2.9 17.5 + - - -
13F GLU* 1.3 84.4 - - - +
15F VAL* 1.3 61.0 + - - +
16F LYS 3.2 2.2 - - - -
17F GLU* 3.2 11.1 + - - +
18F PHE* 2.9 27.7 + - - +
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Residues in contact with VAL 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F GLU* 2.9 46.4 + - + +
12F GLN* 3.7 5.1 + - - +
14F SER* 1.3 80.9 - - - +
16F LYS* 1.3 60.9 + - - +
18F PHE* 3.6 11.2 + - + +
19F LEU* 3.4 30.5 + - + +
155F GLU* 4.6 16.8 - - - +
292F LYS* 4.9 8.3 - - - +
303F ILE* 5.4 8.1 - - + -
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Residues in contact with LYS 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F GLN 3.5 15.6 + - - +
13F GLU* 4.5 4.5 - - - +
14F SER 3.2 0.2 - - - -
15F VAL* 1.3 78.8 - - - +
17F GLU* 1.3 61.8 + - + +
19F LEU* 3.4 12.2 + - + +
20F ALA* 3.2 21.1 + - - +
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Residues in contact with GLU 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F GLU* 2.9 41.8 - - - +
14F SER* 3.2 12.5 + - - +
16F LYS* 1.3 76.3 - - + +
18F PHE* 1.3 63.7 + - - +
20F ALA* 3.4 8.0 + - - +
21F LYS* 3.2 26.3 + - - +
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Residues in contact with PHE 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F SER 2.9 13.5 + - - +
15F VAL* 3.6 14.6 - - + +
17F GLU* 1.3 76.0 - - - +
19F LEU* 1.3 77.7 + - + +
21F LYS* 3.3 8.1 + - + +
22F ALA* 3.0 36.8 + - + +
99F ASN 5.8 1.6 - - - -
100F PHE* 4.3 21.8 - + - -
156F TYR* 4.8 3.4 - + - -
306F TYR* 3.2 40.6 - + - -
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Residues in contact with LEU 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F VAL* 3.4 20.6 + - + +
16F LYS* 3.4 12.2 + - + +
17F GLU 3.3 0.4 - - - -
18F PHE* 1.3 93.6 - - + +
20F ALA* 1.3 60.3 + - - +
22F ALA* 3.6 5.5 - - + +
23F LYS* 3.1 27.7 + - - +
155F GLU* 4.3 28.9 - - + +
156F TYR* 4.3 12.3 - - + -
159F SER* 3.6 36.8 + - - +
160F LEU* 5.1 0.2 - - - +
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Residues in contact with ALA 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F LYS 3.2 12.8 + - - +
17F GLU* 3.6 12.6 - - - +
19F LEU* 1.3 75.1 - - - +
21F LYS* 1.3 64.3 + - - +
23F LYS* 3.4 6.9 + - - +
24F GLU* 3.2 26.0 + - - +
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Residues in contact with LYS 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F GLU 3.2 11.5 + - - +
18F PHE* 3.6 10.8 - - + +
20F ALA* 1.3 76.2 - - + +
22F ALA* 1.3 64.5 + - - +
24F GLU* 3.4 13.6 + - + +
25F ASP* 3.1 24.4 + - - +
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Residues in contact with ALA 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F PHE* 3.0 25.8 + - + +
19F LEU* 3.6 11.4 - - + +
20F ALA 3.3 0.2 - - - -
21F LYS* 1.3 77.6 - - - +
23F LYS* 1.3 56.3 + - - +
25F ASP* 3.6 6.0 + - - +
26F PHE* 3.0 28.6 + - - +
156F TYR* 3.9 30.8 + - + -
160F LEU* 4.7 7.0 - - + +
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Residues in contact with LYS 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E GLU* 3.1 27.5 + - - -
32E ASN* 4.8 8.9 + - - +
19F LEU 3.1 15.7 + - - +
20F ALA* 3.8 6.5 - - - +
21F LYS 3.3 0.4 - - - -
22F ALA* 1.3 75.4 - - - +
24F GLU* 1.3 59.5 + - - +
26F PHE* 4.2 3.8 - - - -
27F LEU* 2.9 52.2 + - + +
159F SER* 4.1 20.2 - - - +
160F LEU* 4.5 12.7 - - + +
161F ASP* 4.4 6.7 - - - -
190F ARG* 4.4 11.0 - - - +
192F LYS* 5.1 1.5 - - - +
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Residues in contact with GLU 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E LYS* 5.9 2.4 + - - -
20F ALA 3.2 14.3 + - - +
21F LYS* 3.6 18.2 - - + +
23F LYS* 1.3 79.0 - - - +
25F ASP* 1.3 61.9 + - - +
27F LEU* 3.9 7.4 - - - +
28F LYS* 3.1 45.6 + - - +
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Residues in contact with ASP 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F LYS 3.1 14.2 + - - +
22F ALA* 3.9 6.1 - - - +
24F GLU* 1.3 75.9 - - - +
26F PHE* 1.3 64.2 + - - +
28F LYS* 3.6 9.4 + - - +
29F LYS* 3.3 53.4 + - - +
97F ALA 4.9 0.4 - - - -
99F ASN* 5.1 7.8 - - - +
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Residues in contact with PHE 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F ALA 3.0 18.6 + - - +
23F LYS 3.3 3.1 + - - +
25F ASP* 1.3 77.4 - - - +
27F LEU* 1.3 66.4 + - + +
29F LYS* 3.3 3.1 + - - +
30F TRP* 2.8 66.7 + + - +
94F ILE 4.5 1.3 - - - -
97F ALA* 3.4 43.0 + - + +
98F VAL* 4.0 14.8 - - + -
156F TYR* 5.0 1.3 - - - +
160F LEU* 3.5 31.6 - - + -
162F LEU* 4.1 20.2 - - + -
190F ARG* 3.8 30.1 - - - -
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Residues in contact with LEU 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E LYS* 5.7 7.0 - - - +
31E GLU* 3.6 27.6 - - + -
23F LYS* 2.9 44.1 + - + +
24F GLU* 3.9 7.0 - - - +
26F PHE* 1.3 95.0 - - + +
28F LYS* 1.3 70.0 + - - +
30F TRP* 3.8 7.2 - - + +
31F GLU* 3.0 30.3 + - - +
190F ARG* 3.9 23.3 - - - +
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Residues in contact with LYS 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E LEU* 5.1 12.7 - - - +
24F GLU* 3.1 33.6 + - - +
25F ASP* 3.7 12.1 - - - +
26F PHE 3.3 0.2 - - - -
27F LEU* 1.3 85.5 + - - +
29F LYS* 1.3 59.9 + - + +
31F GLU* 3.6 6.5 - - - +
32F ASN* 3.1 31.6 + - - +
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Residues in contact with LYS 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F ASP* 3.3 40.1 + - - +
26F PHE 3.3 4.1 + - - +
28F LYS* 1.3 76.0 - - + +
30F TRP* 1.3 64.3 + - - +
32F ASN 3.3 22.3 - - - +
96F GLN* 2.9 35.9 + - - +
97F ALA* 3.6 31.7 + - - +
98F VAL 5.2 1.0 + - - +
99F ASN* 4.4 16.6 - - - +
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Residues in contact with TRP 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F PHE* 2.8 46.2 + + + +
27F LEU* 3.8 11.0 - - + +
28F LYS 3.4 0.2 - - - -
29F LYS* 1.3 75.6 - - - +
31F GLU* 1.3 62.5 + - - +
33F PRO* 4.0 6.6 - - - +
90F ASN* 5.4 6.1 - - - -
93F ARG* 3.3 91.1 + - + +
94F ILE* 3.6 28.3 - - + -
96F GLN* 4.1 2.9 - - - +
97F ALA* 3.9 1.3 - - + +
190F ARG* 3.6 47.9 - - + +
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Residues in contact with GLU 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E LYS* 3.0 28.3 + - - +
27E LEU* 3.7 27.8 - - + -
190E ARG* 2.8 33.5 + - - +
192E LYS* 3.0 49.9 + - - -
27F LEU 3.0 19.5 + - - +
28F LYS* 3.6 9.6 - - - +
30F TRP* 1.3 80.7 - - - +
32F ASN* 1.3 62.5 + - - +
33F PRO* 3.3 8.5 - - - +
93F ARG* 5.5 0.7 - - - +
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Residues in contact with ASN 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E LYS* 4.6 7.6 + - - +
192E LYS* 2.7 29.4 + - - +
28F LYS 3.1 12.6 + - - +
29F LYS* 3.3 11.8 - - - +
31F GLU* 1.3 87.3 + - - +
33F PRO* 1.3 65.9 - - - +
96F GLN* 4.5 0.7 - - - +
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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
------------------------------------------------------------
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