Contacts of the helix formed by residues 13 - 37 (chain A) in PDB entry 5F0L
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 SER 13 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLY* 1.3 76.7 - - - +
14A LYS* 1.3 62.5 + - - +
15A LEU* 3.4 9.2 - - - +
16A LEU* 3.8 24.1 + - - +
17A ASP* 3.4 15.8 + - - +
62A SER* 5.2 3.1 + - - -
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Residues in contact with LYS 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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12A GLY* 3.1 23.7 - - - +
13A SER* 1.3 76.0 - - - +
15A LEU* 1.3 57.7 + - + +
17A ASP* 2.7 33.5 + - - +
18A GLU* 2.8 35.8 + - + +
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Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 5.0 7.4 - - - +
14A LYS* 1.3 77.0 - - + +
16A LEU* 1.3 56.1 + - - +
18A GLU* 3.6 16.8 + - - +
19A ALA* 2.9 31.7 + - - +
55A THR* 5.8 1.1 - - - +
57A MET* 3.9 46.0 - - + +
58A LEU* 3.9 15.0 - - + +
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Residues in contact with LEU 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 3.8 20.3 + - - +
14A LYS 2.9 1.6 + - - -
15A LEU* 1.3 78.0 - - - +
17A ASP* 1.3 61.1 + - - +
19A ALA* 3.2 5.2 + - - +
20A ILE* 2.9 60.6 + - + +
58A LEU* 3.7 16.8 - - + +
62A SER* 3.6 46.0 - - - +
65A GLU* 4.3 11.4 - - + +
66A LEU* 4.2 13.9 - - + +
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Residues in contact with ASP 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER 3.4 17.5 - - - +
14A LYS* 2.7 13.8 + - - +
16A LEU* 1.3 74.4 - - - +
18A GLU* 1.3 54.0 + - - +
20A ILE* 3.2 14.2 + - - +
21A GLN* 2.7 38.1 + - - +
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Residues in contact with GLU 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 LYS* 2.8 46.6 + - + +
15A LEU* 3.7 17.0 - - - +
17A ASP* 1.3 71.3 - - + +
19A ALA* 1.3 56.3 + - - +
21A GLN* 3.4 7.7 - - - +
22A ALA* 3.1 27.0 + - - +
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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 LEU 2.9 19.0 + - - +
16A LEU* 3.4 6.3 - - - +
18A GLU* 1.3 74.7 - - - +
20A ILE* 1.3 60.1 + - - +
22A ALA* 3.1 4.3 + - - +
23A VAL* 2.8 33.2 + - - +
52A GLU* 3.3 29.2 - - - +
55A THR* 6.4 0.2 - - + -
58A LEU* 5.4 2.0 - - + -
66A LEU* 4.2 22.0 - - + -
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Residues in contact with ILE 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 2.9 51.0 + - + +
17A ASP* 3.8 13.7 - - - +
19A ALA* 1.3 71.3 - - - +
21A GLN* 1.3 65.0 + - - +
23A VAL* 3.3 9.0 + - + +
24A LYS* 3.0 25.5 + - + +
65A GLU* 4.9 11.4 - - + -
66A LEU* 4.4 14.8 - - + -
69A ALA* 4.7 16.2 - - + -
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Residues in contact with GLN 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASP 2.7 21.8 + - - +
18A GLU* 3.4 10.1 - - - +
20A ILE* 1.3 71.1 - - - +
22A ALA* 1.3 58.0 + - - +
24A LYS* 3.0 14.3 + - - +
25A VAL* 3.0 41.0 + - + +
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Residues in contact with ALA 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 GLU 3.1 11.1 + - - +
19A ALA 3.5 7.2 - - - +
21A GLN* 1.3 79.0 - - - +
23A VAL* 1.3 57.3 + - - +
25A VAL* 3.4 9.6 + - - +
26A GLN* 3.0 37.0 + - + +
49A MET* 6.0 0.2 - - - -
52A GLU* 3.5 23.6 - - + +
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Residues in contact with VAL 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA 2.8 19.5 + - - +
20A ILE* 3.5 10.3 - - + +
22A ALA* 1.3 76.8 - - - +
24A LYS* 1.3 53.0 + - - +
26A GLN* 3.5 1.8 + - - +
27A SER* 2.7 36.8 + - - +
49A MET* 3.9 23.1 - - - +
52A GLU* 4.1 10.3 - - + -
66A LEU* 3.7 16.2 - - + -
69A ALA* 4.6 11.9 - - + -
70A ILE* 3.7 35.9 - - + -
73A GLU* 4.4 11.9 - - + -
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Residues in contact with LYS 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 ILE* 3.0 16.7 + - + +
21A GLN* 3.6 15.0 - - - +
23A VAL* 1.3 76.0 - - - +
25A VAL* 1.3 64.5 + - - +
27A SER* 3.3 8.0 + - - +
28A PHE* 3.2 30.1 + - - +
73A GLU* 6.1 1.6 - - - +
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Residues in contact with VAL 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLN* 3.0 33.8 + - + +
22A ALA* 3.5 10.3 - - - +
24A LYS* 1.3 76.4 - - - +
26A GLN* 1.3 72.5 + - + +
28A PHE* 3.2 8.5 + - - +
29A GLN* 3.2 41.9 + - - +
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Residues in contact with GLN 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA* 3.0 22.8 + - + +
23A VAL 4.2 0.2 - - - +
25A VAL* 1.3 82.1 - - + +
27A SER* 1.3 57.2 + - - +
29A GLN* 3.5 10.7 + - - +
30A MET* 2.9 27.6 + - - +
45A HIS* 2.9 51.5 + - - +
48A ASN* 3.7 29.3 - - + +
49A MET* 4.1 14.8 - - + +
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Residues in contact with SER 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL 2.7 22.7 + - - -
24A LYS* 3.3 16.3 + - - +
26A GLN* 1.3 74.0 - - - +
28A PHE* 1.3 62.4 + - - +
30A MET* 3.6 10.8 - - - +
31A LYS* 3.2 34.0 + - - +
49A MET* 4.0 10.0 - - - -
73A GLU* 3.4 40.9 + - - -
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Residues in contact with PHE 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LYS* 3.2 26.2 + - + +
25A VAL* 3.2 7.4 + - - +
27A SER* 1.3 76.3 + - - +
29A GLN* 1.3 66.2 + - + +
30A MET 3.4 0.2 + - - -
31A LYS* 3.5 10.1 + - + +
32A ARG* 3.1 54.3 + - + +
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Residues in contact with GLN 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 VAL* 3.2 28.8 + - - +
26A GLN* 3.7 11.7 + - - +
28A PHE* 1.3 81.1 - - + +
30A MET* 1.3 63.7 + - - +
32A ARG* 3.6 17.4 - - - +
33A CYS* 3.2 29.2 + - - -
45A HIS* 3.2 38.1 + - + +
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Residues in contact with MET 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 GLN 2.9 18.8 + - - +
27A SER* 3.6 13.7 - - - +
28A PHE 3.2 0.4 - - - -
29A GLN* 1.3 76.3 - - - +
31A LYS* 1.3 71.9 + - + +
33A CYS* 3.1 7.8 + - - +
34A LEU* 3.0 42.6 + - + +
42A ALA* 3.6 24.0 - - + +
45A HIS* 4.2 7.6 - - + +
46A ALA* 3.8 24.0 - - + +
49A MET* 4.1 12.6 - - - -
73A GLU* 3.8 34.8 - - + +
76A TYR* 4.9 1.3 - - + -
77A LEU* 4.5 17.5 - - + +
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Residues in contact with LYS 31 (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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27A SER* 3.2 27.8 + - - +
28A PHE* 4.1 8.4 - - + +
30A MET* 1.3 87.9 - - + +
32A ARG* 1.3 59.9 + - - +
34A LEU* 3.1 15.5 + - + +
35A ASP* 2.9 41.5 + - - +
73A GLU* 2.9 19.3 + - - -
76A TYR* 3.3 45.1 - - + -
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Residues in contact with ARG 32 (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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28A PHE* 3.1 42.8 + - + +
29A GLN* 3.6 20.7 - - - +
31A LYS* 1.3 75.6 - - - +
33A CYS* 1.3 65.0 + - - +
35A ASP* 3.4 13.7 + - - +
36A LYS* 3.3 26.7 + - + +
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Residues in contact with CYS 33 (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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29A GLN* 3.2 19.5 + - - -
30A MET 3.1 8.9 + - - +
32A ARG* 1.3 82.1 - - - +
34A LEU* 1.3 60.7 + - - +
36A LYS* 3.2 5.6 + - - +
37A ASN 2.9 8.7 + - - -
38A LYS* 2.9 52.5 + - + +
41A ASP* 3.9 20.4 - - - -
42A ALA* 3.8 6.5 - - - +
45A HIS* 4.1 15.7 - - - -
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Residues in contact with LEU 34 (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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30A MET* 3.0 36.1 + - + +
31A LYS* 3.1 20.4 + - + +
33A CYS* 1.3 72.3 - - - +
35A ASP* 1.3 65.3 + - - +
37A ASN* 3.6 10.4 + - - +
38A LYS 5.1 0.2 - - - +
39A LEU* 4.2 6.1 - - + -
42A ALA* 3.7 19.5 - - + -
76A TYR* 4.6 3.4 - - + +
77A LEU* 4.2 29.8 - - + +
80A TYR* 3.3 64.5 - - + -
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Residues in contact with ASP 35 (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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31A LYS* 2.9 27.4 + - - +
32A ARG* 3.5 11.6 - - - +
33A CYS 3.2 0.2 - - - -
34A LEU* 1.3 79.9 - - - +
36A LYS* 1.3 61.1 + - + +
37A ASN* 3.3 10.3 + - - -
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Residues in contact with LYS 36 (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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32A ARG* 3.3 15.9 + - + +
33A CYS* 3.2 10.3 + - - +
35A ASP* 1.3 77.2 - - + +
37A ASN* 1.3 66.6 + - - +
38A LYS* 3.5 37.8 + - + +
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Residues in contact with ASN 37 (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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33A CYS 2.9 5.2 + - - -
34A LEU* 3.6 10.8 + - - +
35A ASP 3.3 9.9 + - - -
36A LYS* 1.3 79.8 - - - +
38A LYS* 1.3 60.8 + - - +
39A LEU* 3.3 9.3 + - - +
80A TYR* 3.3 21.7 + - - +
84A GLU* 3.1 20.3 + - - +
89A ARG* 3.7 12.2 + - - +
504A GOL 4.0 8.7 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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