Contacts of the helix formed by residues 14 - 32 (chain A) in PDB entry 2FIU
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 ASP 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A VAL* 3.7 2.6 - - - +
13A ARG* 1.3 79.0 - - + +
15A SER* 1.3 57.4 + - - +
16A GLU* 3.1 24.3 + - - +
17A ARG* 3.2 31.0 + - - +
18A TYR* 2.9 26.7 + - - +
84A VAL* 3.4 23.6 + - + +
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Residues in contact with SER 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 3.7 16.8 - - - +
13A ARG 4.0 2.0 + - - -
14A ASP* 1.3 72.4 + - - +
16A GLU* 1.3 59.8 + - - +
18A TYR* 3.3 2.9 + - - +
19A LYS* 3.0 37.9 + - - +
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Residues in contact with GLU 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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14A ASP* 3.1 11.2 + - - +
15A SER* 1.3 83.6 + - - +
17A ARG* 1.3 66.7 + - + +
19A LYS* 3.4 22.0 + - + +
20A ASP* 3.6 10.8 + - - +
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Residues in contact with ARG 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASP* 3.2 24.4 + - - +
16A GLU* 1.3 82.3 - - + +
18A TYR* 1.3 65.0 + - - +
20A ASP* 3.0 26.6 + - - +
21A TYR 3.2 9.4 + - - -
80A ILE* 3.4 25.2 - - + +
83A GLU* 2.9 42.0 + - - +
84A VAL* 3.6 31.6 - - + +
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Residues in contact with TYR 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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10A VAL* 3.7 37.6 - - + +
12A VAL* 3.6 26.2 - - + -
14A ASP 2.9 17.2 + - - +
15A SER* 3.3 7.4 + - - +
17A ARG* 1.3 77.4 - - - +
19A LYS* 1.3 56.7 + - + +
21A TYR* 3.2 32.6 + + - +
22A VAL* 3.0 41.5 + - + +
53A ARG* 3.3 35.2 + - - -
55A VAL* 5.2 2.1 - - - +
81A ARG* 4.0 15.3 - - + -
84A VAL* 4.1 10.7 - - + +
85A ALA* 4.2 8.5 - - + -
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Residues in contact with LYS 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 SER* 3.0 21.9 + - - +
16A GLU* 3.5 14.1 - - + +
17A ARG 3.2 0.2 - - - -
18A TYR* 1.3 78.3 - - + +
20A ASP* 1.3 58.0 + - - +
22A VAL* 3.3 9.6 + - + +
23A SER* 3.0 30.2 + - - -
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Residues in contact with ASP 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLU* 3.6 11.4 + - - +
17A ARG* 3.0 23.7 + - - +
19A LYS* 1.3 75.2 - - - +
21A TYR* 1.3 60.4 + - - +
23A SER* 3.3 6.8 + - - -
24A THR* 2.9 39.2 + - + +
80A ILE* 4.2 15.7 - - + -
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Residues in contact with TYR 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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6A TRP* 4.9 1.4 + - - -
17A ARG 3.2 7.3 + - - +
18A TYR* 3.2 50.7 + + - +
20A ASP* 1.3 76.9 - - - +
22A VAL* 1.3 64.1 + - + +
24A THR* 3.3 5.5 + - - -
25A ALA* 2.7 45.6 + - + +
29A PHE* 4.6 7.6 - + - -
53A ARG* 6.0 0.2 - - - -
74A TYR* 2.6 42.4 + + - -
77A ALA* 3.2 28.9 - - + +
78A ALA* 4.1 2.2 - - - -
80A ILE* 4.2 11.0 - - + +
81A ARG* 3.3 33.2 + - + -
89A MSE 5.0 1.2 - - - +
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Residues in contact with VAL 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 TYR* 3.0 43.5 + - + +
19A LYS* 3.3 11.6 + - + +
21A TYR* 1.3 82.2 - - + +
23A SER* 1.3 64.1 + - - +
25A ALA* 3.4 4.8 + - - +
26A LYS* 3.1 24.7 + - + +
39A ARG* 3.5 30.8 + - - +
53A ARG* 4.0 13.9 - - - +
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Residues in contact with SER 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 LYS 3.0 17.0 + - - -
20A ASP* 3.3 10.9 + - - -
22A VAL* 1.3 79.9 - - - +
24A THR* 1.3 64.8 + - - +
26A LYS* 3.6 9.6 + - - +
27A PRO* 3.5 17.0 - - - +
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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 ASP* 2.9 28.0 + - + +
21A TYR* 3.5 3.3 + - - -
23A SER* 1.3 77.9 - - - +
25A ALA* 1.3 62.2 + - - +
26A LYS 3.3 0.4 - - - -
27A PRO* 3.6 10.7 - - - +
28A ALA* 5.0 1.6 + - - +
73A GLU* 4.3 10.9 - - - +
77A ALA* 3.3 29.6 - - - +
80A ILE* 3.9 10.9 - - + +
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Residues in contact with ALA 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 TYR* 2.7 29.9 + - + +
22A VAL* 3.7 4.7 - - - +
24A THR* 1.3 72.7 - - - +
26A LYS* 1.3 64.9 + - - +
27A PRO 3.5 0.4 - - - -
28A ALA* 3.0 19.0 + - - +
29A PHE* 3.2 35.2 + - + -
74A TYR* 3.9 20.6 - - + +
77A ALA* 3.6 8.9 - - + +
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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
----------------------------------------------------------
22A VAL* 3.1 17.8 + - + +
23A SER* 3.7 8.7 - - - +
24A THR 3.3 0.2 - - - -
25A ALA* 1.3 76.3 - - - +
27A PRO* 1.4 64.9 - - + +
29A PHE* 3.3 13.0 + - + +
30A GLU* 2.9 54.5 + - + +
39A ARG* 5.5 9.6 - - - +
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Residues in contact with PRO 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A SER 3.5 12.8 - - - +
24A THR* 3.6 9.2 - - - +
25A ALA 3.6 2.9 - - - -
26A LYS* 1.4 95.6 - - + +
28A ALA* 1.3 56.3 + - - +
30A GLU* 3.8 12.2 - - + +
31A ARG* 3.0 30.3 + - - +
73A GLU* 5.8 5.8 - - + -
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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 5.0 0.6 + - - +
25A ALA 3.0 12.3 + - - +
27A PRO* 1.3 75.3 - - - +
29A PHE* 1.3 66.4 + - - +
31A ARG* 3.1 21.4 + - - +
32A PHE* 3.2 20.6 + - + -
68A CYS* 3.8 8.8 - - - -
71A SER* 4.0 8.5 - - - +
73A GLU* 4.2 9.3 - - + +
74A TYR* 3.9 37.5 - - + +
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Residues in contact with PHE 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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6A TRP* 3.7 34.3 - + - -
21A TYR* 4.6 5.8 - + - -
25A ALA* 3.2 38.9 + - + -
26A LYS* 3.5 11.2 - - + +
28A ALA* 1.3 80.6 - - - +
30A GLU* 1.3 62.4 + - + +
32A PHE* 3.3 5.2 + - - +
34A ALA* 3.1 38.4 + - + +
36A PHE* 3.9 23.6 - + + -
39A ARG* 4.9 5.6 - - - -
57A ILE* 3.4 25.8 - - + -
59A PHE* 3.8 13.2 - + - -
68A CYS* 3.7 15.3 - - - -
74A TYR* 3.9 9.6 - + - -
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Residues in contact with GLU 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* 2.9 50.2 + - + +
27A PRO* 3.8 11.4 - - - +
28A ALA 3.2 0.2 - - - -
29A PHE* 1.3 76.8 - - + +
31A ARG* 1.3 64.1 + - - +
32A PHE 3.3 0.5 + - - -
33A GLY* 3.4 10.0 + - - -
34A ALA 5.1 1.8 - - - +
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Residues in contact with ARG 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 PRO 3.0 13.9 + - - +
28A ALA* 3.4 15.0 - - - +
30A GLU* 1.3 77.2 - - - +
32A PHE* 1.3 100.7 + - + +
33A GLY 3.7 0.3 + - - -
71A SER* 3.8 11.1 + - - -
72A PRO* 4.8 4.2 - - - +
73A GLU* 2.6 42.8 + - - +
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Residues in contact with PHE 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 ALA 3.2 23.3 + - - +
29A PHE 3.3 0.2 + - - -
30A GLU 3.2 0.4 - - - -
31A ARG* 1.3 127.9 - - + +
33A GLY* 1.3 59.7 + - - +
34A ALA 3.5 1.8 - - - -
59A PHE* 3.3 16.3 - - + -
60A PRO* 3.5 9.4 - - - +
64A HIS* 3.6 28.5 - + - +
67A ASP* 3.5 39.7 - - + -
68A CYS* 3.5 35.0 - - + -
71A SER* 4.1 4.5 - - - -
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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