Contacts of the helix formed by residues 10 - 30 (chain A) in PDB entry 2FE2
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 THR 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A GLU 2.6 20.7 + - - +
9A ALA* 1.3 77.7 - - + +
11A PRO* 1.3 63.3 - - - +
12A ALA 3.2 0.2 + - - -
13A PRO* 3.3 11.4 - - + +
14A VAL* 3.1 25.1 + - - +
56A ARG* 4.5 4.6 + - - +
60A SER* 2.6 18.5 + - - -
66A LYS* 3.8 33.2 - - + -
87A LYS* 3.3 24.9 + - - +
209A ALA* 4.3 6.4 + - + -
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Residues in contact with PRO 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A GLU 2.8 26.9 - - - +
8A THR* 2.8 23.6 - - + +
10A THR* 1.3 82.1 - - - +
12A ALA* 1.3 52.7 + - - +
14A VAL* 3.0 6.5 + - + +
15A GLU* 2.6 35.3 + - - +
57A ASN* 3.5 22.3 + - - +
60A SER* 2.8 33.4 - - - +
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Residues in contact with ALA 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A THR 3.4 5.1 + - - +
9A ALA* 2.6 25.8 + - - +
11A PRO* 1.3 73.2 - - - +
13A PRO* 1.3 65.5 - - + +
15A GLU* 3.7 7.4 - - - +
16A LYS* 2.7 30.8 + - - +
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Residues in contact with PRO 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A SER 5.5 10.1 - - - +
9A ALA* 2.8 24.4 - - + +
10A THR* 3.3 10.3 - - + +
12A ALA* 1.3 87.3 - - + +
14A VAL* 1.3 62.1 + - + +
16A LYS* 3.2 12.2 + - + +
17A SER* 2.9 23.9 + - - -
56A ARG* 6.3 0.2 - - - +
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Residues in contact with VAL 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A THR 3.1 17.0 + - - +
11A PRO* 3.0 10.2 + - + +
13A PRO* 1.3 74.4 - - + +
15A GLU* 1.3 60.1 + - - +
17A SER* 3.2 2.7 + - - -
18A PRO* 2.8 33.9 - - + +
53A SER* 2.9 35.2 - - - +
56A ARG* 3.1 40.2 - - + +
57A ASN* 3.1 25.6 - - + +
60A SER* 5.2 1.3 - - - -
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Residues in contact with GLU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PRO 2.6 20.3 + - - +
12A ALA* 3.9 5.9 - - - +
14A VAL* 1.3 74.9 - - - +
16A LYS* 1.3 64.6 + - - +
17A SER 3.3 0.2 + - - -
18A PRO* 3.3 5.0 - - + +
19A ALA* 2.9 29.2 + - + +
57A ASN* 4.1 13.4 - - - +
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Residues in contact with LYS 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A SER 6.3 0.7 - - - +
12A ALA 2.7 18.3 + - - +
13A PRO* 3.4 12.3 - - + +
15A GLU* 1.3 78.6 - - - +
17A SER* 1.3 62.1 + - - +
19A ALA* 3.2 4.6 + - - +
20A LYS* 2.9 36.2 + - + +
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Residues in contact with SER 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A PRO 2.9 15.2 + - - -
14A VAL* 3.2 2.4 + - - -
16A LYS* 1.3 77.1 - - - +
18A PRO* 1.3 72.5 - - - +
20A LYS* 3.1 18.6 + - - +
21A LYS* 2.7 40.1 + - - +
53A SER* 4.3 4.1 + - - -
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Residues in contact with PRO 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 2.8 27.1 - - + +
15A GLU* 4.1 4.7 - - + +
17A SER* 1.3 90.5 - - - +
19A ALA* 1.3 60.8 + - - +
21A LYS* 3.8 12.0 - - - +
22A LYS* 2.9 25.3 + - - +
50A VAL* 4.3 2.7 - - + +
53A SER* 3.0 38.1 - - - +
54A LYS* 3.5 29.1 + - + +
57A ASN* 5.8 0.7 - - + -
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Residues in contact with ALA 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLU* 2.9 29.9 + - + +
16A LYS* 3.8 5.8 - - - +
18A PRO* 1.3 71.5 - - - +
20A LYS* 1.3 57.7 + - - +
22A LYS* 3.8 3.9 - - - +
23A ALA* 2.9 29.9 + - - +
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Residues in contact with LYS 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LYS* 2.9 24.7 + - + +
17A SER* 3.6 25.2 - - - +
19A ALA* 1.3 75.9 - - - +
21A LYS* 1.3 66.6 + - - +
23A ALA* 3.2 8.0 + - + +
24A THR* 2.9 32.3 + - - +
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Residues in contact with LYS 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A SER* 2.7 22.9 + - - +
18A PRO* 3.8 19.6 - - - +
20A LYS* 1.3 75.8 - - - +
22A LYS* 1.3 61.9 + - - +
24A THR* 3.0 18.5 + - - -
25A LYS* 3.1 10.9 + - - +
46A ILE* 3.1 40.4 - - + +
49A ALA* 3.0 37.3 + - + -
50A VAL* 3.2 29.9 - - + +
53A SER* 3.9 3.0 + - - -
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Residues in contact with LYS 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PRO 2.9 16.8 + - - +
19A ALA* 4.0 4.5 - - - +
21A LYS* 1.3 76.5 - - - +
23A ALA* 1.3 63.0 + - - +
25A LYS* 2.9 41.4 + - + +
26A LYS* 2.9 13.8 + - + +
46A ILE* 5.3 0.7 - - - -
50A VAL* 4.4 8.7 - - + +
54A LYS* 5.7 6.3 - - - +
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Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ALA 2.9 19.4 + - - +
20A LYS* 3.4 10.3 - - + +
21A LYS 3.2 0.2 - - - -
22A LYS* 1.3 75.0 - - - +
24A THR* 1.3 52.5 + - - +
26A LYS* 3.1 9.1 + - - +
27A ALA* 2.8 34.2 + - - +
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Residues in contact with THR 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LYS* 2.9 23.6 + - - +
21A LYS* 3.0 11.5 + - - -
23A ALA* 1.3 73.4 - - - +
25A LYS* 1.3 56.3 + - - +
27A ALA* 3.2 6.3 + - + +
28A ALA* 2.7 39.5 + - + +
42A VAL* 5.7 6.5 - - + -
46A ILE* 5.2 10.3 - - + -
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Residues in contact with LYS 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LYS 3.1 5.8 + - - +
22A LYS* 2.9 37.4 + - + +
24A THR* 1.3 76.3 - - - +
26A LYS* 1.3 53.9 + - - +
28A ALA* 3.2 5.2 + - - +
29A GLY* 2.7 34.3 + - - -
43A SER* 4.4 13.4 - - - -
46A ILE* 2.9 35.2 - - + +
47A THR* 4.4 17.4 - - + +
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Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LYS* 2.9 13.1 + - + +
23A ALA* 3.1 10.7 + - - +
25A LYS* 1.3 78.1 - - - +
27A ALA* 1.3 63.2 + - - +
29A GLY* 3.1 3.1 + - - -
30A ALA* 3.0 21.6 + - + +
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Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ALA 2.8 19.9 + - - +
24A THR* 3.7 8.1 - - + +
26A LYS* 1.3 74.0 - - - +
28A ALA* 1.3 52.5 + - - +
30A ALA* 2.7 38.4 + - - +
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A THR* 2.7 28.0 + - + +
25A LYS* 3.7 5.2 - - - +
27A ALA* 1.3 69.5 - - - +
29A GLY* 1.3 61.0 + - - +
30A ALA 2.5 17.1 - - - +
31A GLY* 4.4 0.7 - - - -
32A ALA 5.2 1.6 + - - +
36A LYS* 3.7 34.7 - - + +
39A GLY* 5.7 6.1 - - - +
42A VAL* 5.9 7.9 - - + -
43A SER* 6.1 4.5 - - - +
46A ILE* 6.3 0.2 - - + -
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Residues in contact with GLY 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LYS 2.7 20.3 + - - -
26A LYS* 3.1 3.3 + - - -
28A ALA* 1.3 73.8 - - - +
30A ALA* 1.3 60.7 + - - +
31A GLY* 3.4 4.3 + - - -
32A ALA 4.8 3.8 + - - +
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Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LYS* 3.0 11.2 + - + +
27A ALA* 2.7 22.2 + - - +
28A ALA* 2.5 20.3 - - - +
29A GLY* 1.3 75.0 - - - +
31A GLY* 1.3 57.7 + - - +
36A LYS* 5.2 1.7 - - - +
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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
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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