Contacts of the helix formed by residues 14 - 30 (chain F) in PDB entry 2EFW
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 LYS 14 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8F SER* 5.8 2.4 + - - -
12F LEU 3.9 2.2 + - - -
13F VAL* 1.3 75.3 - - - +
15F GLN* 1.3 50.8 + - - +
16F ARG* 3.9 18.6 - - + +
17F ALA* 2.7 50.3 + - + +
18F PHE 2.8 13.2 + - - -
63F GLU* 6.1 0.9 - - - -
11G PHE* 4.1 0.7 - - - -
12I A 3.7 51.0 + - - +
13I T 4.6 1.1 - - - -
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Residues in contact with GLN 15 (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 LYS* 1.3 69.7 - - - +
16F ARG* 1.3 61.5 + - - +
18F PHE* 3.1 1.3 + - - +
19F LEU* 2.8 36.1 + - + +
50F PHE* 3.2 28.9 - - + -
52F PRO* 4.2 9.7 - - - +
56F GLU* 5.2 4.5 - - + +
9G THR* 3.3 10.3 + - - -
11G PHE* 3.3 45.5 - - + +
13I T 2.9 38.0 + - - +
14I G 3.3 32.4 + - - -
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Residues in contact with ARG 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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14F LYS* 3.9 18.6 - - + -
15F GLN* 1.3 76.2 - - - +
17F ALA* 1.3 56.3 + - - +
19F LEU* 2.7 26.9 + - - +
20F LYS* 2.8 15.8 + - + +
56F GLU* 1.7 48.4 + - - +
59F ARG* 3.6 26.0 + - - +
60F SER* 3.9 21.7 + - - +
63F GLU* 2.8 58.0 + - - +
12I A 5.4 4.1 - - + +
13I T 3.7 27.7 + - - +
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Residues in contact with ALA 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 VAL* 4.3 7.9 - - + -
14F LYS* 2.7 33.8 + - + +
16F ARG* 1.3 76.5 - - + +
18F PHE* 1.3 57.1 + - - +
19F LEU 3.3 0.2 - - - -
20F LYS* 3.9 6.6 - - - +
21F LEU* 3.5 15.8 + - - +
99F TYR* 3.6 20.9 - - - +
103F LEU* 3.5 26.8 - - + +
106F GLU* 4.6 4.3 - - - +
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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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13F VAL* 3.9 21.1 - - + -
14F LYS 2.8 9.3 + - - +
15F GLN 3.5 4.3 - - - +
17F ALA* 1.3 77.1 - - - +
19F LEU* 1.3 70.0 + - + +
21F LEU* 3.4 17.4 - - + +
22F TYR* 3.6 24.3 - + - -
45F PHE* 3.7 30.3 - + - -
50F PHE* 4.0 15.7 - + - -
103F LEU* 5.1 1.6 - - - -
107F LEU* 4.3 8.5 - - + -
11G PHE* 2.9 47.6 - + + -
12G LEU* 6.0 0.2 - - + -
113G LEU* 4.7 16.6 - - + -
114G ILE* 4.8 2.2 - - + -
117G ALA* 4.0 20.9 - - + -
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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 GLN* 2.8 29.6 + - + +
16F ARG 2.7 4.7 + - - +
18F PHE* 1.3 81.7 - - + +
20F LYS* 1.3 71.1 + - - +
21F LEU 3.2 0.2 - - - -
22F TYR* 3.0 14.2 + - + +
23F MET* 3.3 16.8 + - + +
41F LEU* 3.8 28.7 - - + -
50F PHE* 4.6 11.4 - - + -
52F PRO* 4.3 18.4 - - + -
56F GLU* 3.9 24.2 - - + +
57F VAL* 3.9 29.6 - - + +
60F SER* 3.7 8.5 - - - +
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Residues in contact with LYS 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 ARG* 2.8 20.0 + - - +
17F ALA* 4.1 6.1 - - - +
19F LEU* 1.3 74.1 - - - +
21F LEU* 1.3 53.9 + - - +
23F MET* 2.4 45.4 + - - +
24F ILE* 3.4 4.8 + - - -
60F SER* 4.0 13.4 + - - +
63F GLU* 3.1 41.9 + - + +
64F LEU* 3.5 28.3 - - + -
67F ASP* 3.2 20.3 + - - +
99F TYR* 2.7 47.4 - - + +
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Residues in contact with LEU 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 ALA 3.5 12.3 + - - +
18F PHE* 3.4 15.5 - - + +
20F LYS* 1.3 75.9 - - - +
22F TYR* 1.3 65.6 + - + +
23F MET 3.1 0.5 + - - -
24F ILE* 3.3 12.5 + - - +
25F THR* 3.3 14.9 + - - +
99F TYR* 4.6 8.7 - - + -
100F LYS* 4.9 11.8 - - + -
103F LEU* 3.8 26.5 - - + -
107F LEU* 3.6 27.4 - - + -
117G ALA* 3.8 7.9 - - + -
121G ASN* 3.0 50.8 + - + +
122G PHE* 4.2 11.0 - - + -
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Residues in contact with TYR 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* 3.6 37.7 - + - +
19F LEU* 3.0 11.1 + - + +
20F LYS 2.8 2.0 + - - -
21F LEU* 1.3 80.6 - - + +
23F MET* 1.3 54.3 + - + +
25F THR* 4.5 2.0 - - + -
26F MET* 2.6 55.2 + - + +
41F LEU* 3.6 31.0 - - + -
44F GLU* 4.3 8.5 - - - -
45F PHE* 3.0 21.8 - + - -
116G LYS* 3.0 16.1 - - - +
117G ALA* 4.4 1.6 - - - -
120G ASP* 2.6 33.7 + - + -
121G ASN* 2.7 39.4 + - - +
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Residues in contact with MET 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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19F LEU* 3.3 23.8 - - + +
20F LYS* 2.4 29.7 + - - +
22F TYR* 1.3 70.0 - - + +
24F ILE* 1.3 57.0 + - - +
26F MET* 4.3 2.0 - - - -
27F THR* 2.7 34.8 + - - -
37F LEU* 2.5 45.5 - - + -
41F LEU* 3.6 31.2 - - + -
57F VAL* 4.2 19.1 - - + -
60F SER* 4.6 5.2 - - - -
61F LEU* 3.7 32.5 - - + -
64F LEU* 3.9 12.1 - - + -
70F LEU* 5.0 1.1 - - + -
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Residues in contact with ILE 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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20F LYS 3.4 4.3 + - - +
21F LEU* 3.3 6.8 + - - +
23F MET* 1.3 73.7 - - - +
25F THR* 1.3 70.4 - - - +
27F THR* 4.7 0.7 - - - -
28F GLU* 3.2 18.5 + - - +
64F LEU* 4.1 20.9 - - + -
69F ILE* 4.0 15.7 - - + -
70F LEU* 5.2 2.9 - - + -
90F PHE* 3.2 25.8 - - + -
93F TYR* 4.9 2.0 - - + -
96F ALA* 3.3 45.1 - - + +
99F TYR* 3.8 25.8 - - + -
100F LYS* 3.4 24.0 - - + -
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Residues in contact with THR 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 LEU* 3.3 16.4 + - - +
22F TYR* 4.2 2.5 - - + +
24F ILE* 1.3 75.1 - - - +
26F MET* 1.3 57.6 + - + +
28F GLU* 2.5 54.1 + - + +
29F GLN* 3.6 2.1 + - - +
100F LYS* 3.1 17.2 + - - +
120G ASP 3.7 23.3 - - - +
121G ASN* 3.4 25.1 + - - +
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Residues in contact with MET 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 TYR* 2.6 39.7 + - + +
23F MET* 4.1 3.8 - - - +
24F ILE 3.4 0.2 - - - -
25F THR* 1.3 79.6 - - + +
27F THR* 1.3 68.2 + - - +
29F GLN* 3.0 14.7 + - + +
30F GLU* 3.2 16.3 + - - +
32F LEU* 5.1 8.3 - - + -
37F LEU* 4.4 29.6 - - + +
40F VAL* 4.1 24.0 - - + -
41F LEU* 3.8 32.5 - - + -
44F GLU* 4.2 9.9 - - - +
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Residues in contact with THR 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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23F MET* 2.7 29.3 + - - +
24F ILE 3.8 4.5 - - - -
26F MET* 1.3 72.8 - - - +
28F GLU* 1.3 65.0 + - - +
29F GLN 3.0 1.2 + - - -
30F GLU 3.3 18.3 + - - -
31F ARG* 4.0 9.6 + - + +
32F LEU 5.6 0.4 - - - +
37F LEU* 5.7 4.6 - - - +
61F LEU* 5.6 1.2 - - - +
70F LEU* 3.8 14.7 - - + +
88F TYR* 3.8 28.6 - - - +
89F GLN* 4.1 8.5 - - + -
90F PHE* 3.3 30.7 - - + +
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Residues in contact with GLU 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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24F ILE* 3.2 9.5 + - - +
25F THR* 2.5 44.5 + - + +
27F THR* 1.3 71.9 - - - +
29F GLN* 1.3 56.8 + - + +
90F PHE* 3.6 18.6 - - + -
93F TYR* 3.9 18.6 + - + +
100F LYS* 2.4 40.2 + - - -
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Residues in contact with GLN 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 THR 3.6 1.7 + - - +
26F MET* 3.0 7.9 + - + +
28F GLU* 1.3 79.0 - - + +
30F GLU* 1.3 74.4 + - - +
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Residues in contact with GLU 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 MET 3.2 15.8 + - - +
27F THR* 3.3 7.6 + - - -
28F GLU 4.0 0.2 + - - -
29F GLN* 1.3 86.1 - - + +
31F ARG* 1.3 56.3 + - - +
32F LEU* 2.6 63.5 + - + +
36F LYS* 5.8 0.9 + - - -
37F LEU* 4.9 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
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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