Contacts of the helix formed by residues 14 - 29 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11F PHE* 4.3 0.9 - - + -
11G PHE* 6.6 0.4 - - - -
12G LEU 3.6 7.8 + - - +
13G VAL* 1.3 80.1 - - - +
15G GLN* 1.3 72.6 + - - +
16G ARG* 3.4 4.7 - - + +
17G ALA* 2.7 28.6 + - + +
18G PHE 2.9 3.0 + - - -
106G GLU* 5.2 1.6 + - - -
12I A 4.4 6.7 + - - -
13I T 4.1 27.1 + - - -
12J T 5.9 6.7 - - - +
13J G 6.3 4.1 - - - -
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Residues in contact with GLN 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F THR* 3.8 7.5 + - - -
11F PHE* 3.5 48.1 - - + +
14G LYS* 1.3 69.1 - - - +
16G ARG* 1.3 70.1 + - - +
18G PHE* 2.4 22.7 + - - +
19G LEU* 2.9 9.1 + - + -
50G PHE* 3.3 32.9 - - + -
56G GLU* 2.3 35.9 + - - +
13J G 4.4 18.6 + - - +
14J G 4.1 14.5 + - - -
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Residues in contact with ARG 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G LYS* 3.4 4.2 - - + +
15G GLN* 1.3 83.3 - - - +
17G ALA* 1.3 66.6 + - - +
19G LEU* 2.8 2.0 + - - +
20G LYS* 2.6 33.2 + - + +
56G GLU* 4.8 1.4 + - - -
59G ARG* 4.0 35.7 + - - +
60G SER* 3.7 23.9 + - - +
63G GLU* 2.0 64.0 + - - +
12J T 4.2 31.2 + - - +
13J G 3.3 38.2 + - - +
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Residues in contact with ALA 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G VAL* 3.7 8.7 - - + -
14G LYS* 2.7 24.8 + - + +
16G ARG* 1.3 75.0 - - - +
18G PHE* 1.3 60.5 + - - +
20G LYS* 5.2 0.2 - - - +
21G LEU* 2.9 23.9 + - - +
99G TYR* 2.7 26.1 + - + +
103G LEU* 3.7 21.1 - - + +
106G GLU* 4.9 4.7 - - - +
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Residues in contact with PHE 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F PHE* 3.8 29.6 - + + -
12F LEU* 5.5 0.7 - - + -
113F LEU* 4.1 30.5 - - + -
114F ILE* 4.9 4.5 - - + -
117F ALA* 3.6 27.8 - - + -
13G VAL* 4.2 17.9 - - + +
14G LYS 2.9 5.8 + - - +
15G GLN 2.4 25.3 + - - +
17G ALA* 1.3 72.2 - - - +
19G LEU* 1.3 66.7 + - + +
21G LEU* 3.0 23.4 - - + +
22G TYR* 3.5 15.7 + + - -
45G PHE* 3.5 36.8 - + - -
50G PHE* 4.0 17.5 - + - -
103G LEU* 4.6 1.8 - - - -
107G LEU* 5.2 4.5 - - + -
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Residues in contact with LEU 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G GLN* 2.9 12.5 + - + +
16G ARG* 2.8 10.7 + - - -
18G PHE* 1.3 73.5 - - + +
20G LYS* 1.3 67.8 + - - +
21G LEU 2.7 3.1 + - - -
22G TYR* 3.1 17.0 + - - +
23G MET* 3.4 14.8 + - - +
41G LEU* 4.8 12.6 - - + +
45G PHE* 4.9 6.1 - - + -
50G PHE* 3.8 35.9 - - + -
52G PRO* 4.0 13.2 - - + -
56G GLU* 3.9 35.2 - - + +
57G VAL* 4.1 7.6 - - + +
60G SER* 2.7 31.4 - - - +
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Residues in contact with LYS 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G ARG* 2.6 19.5 + - + +
17G ALA* 5.2 0.8 - - - +
19G LEU* 1.3 71.5 - - - +
21G LEU* 1.3 60.3 + - - +
23G MET* 3.7 6.1 - - - +
24G ILE* 3.0 27.0 + - + +
60G SER* 3.2 31.3 - - - +
63G GLU* 3.0 29.6 + - + +
64G LEU* 3.6 24.9 - - + +
67G ASP* 3.4 23.6 + - - -
99G TYR* 2.6 50.1 + - + +
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Residues in contact with LEU 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F ALA* 4.5 3.1 - - + +
121F ASN* 3.3 33.0 + - + +
122F PHE* 3.8 20.4 - - + -
17G ALA 2.9 12.0 + - - +
18G PHE* 3.0 13.2 - - + +
19G LEU 2.7 4.8 + - - -
20G LYS* 1.3 69.5 - - - +
22G TYR* 1.3 79.2 + - + +
24G ILE* 2.7 22.3 + - + +
25G THR* 3.1 3.3 + - - -
99G TYR* 4.3 5.8 - - + -
100G LYS* 3.8 43.1 - - + +
103G LEU* 3.9 14.4 - - + -
107G LEU* 4.3 13.9 - - + -
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Residues in contact with TYR 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F LYS* 3.8 3.5 + - - +
117F ALA* 3.5 29.8 + - - -
120F ASP* 3.5 21.4 + - + -
121F ASN* 2.6 34.8 - - - +
18G PHE* 3.9 24.1 - + - +
19G LEU 3.1 6.7 + - - +
21G LEU* 1.3 82.4 - - + +
23G MET* 1.3 55.7 + - - +
24G ILE 2.3 16.6 + - - -
25G THR* 2.3 20.3 + - - -
26G MET* 2.7 17.5 + - + -
31G ARG* 5.9 0.2 - - - -
41G LEU* 3.9 17.7 - - + -
44G GLU* 3.9 31.2 - - + -
45G PHE* 3.7 36.8 - + - -
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Residues in contact with MET 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G LEU* 3.4 11.5 + - + +
20G LYS* 3.7 12.3 - - - +
22G TYR* 1.3 78.0 - - - +
24G ILE* 1.3 55.0 + - - +
26G MET* 3.8 9.0 - - - -
27G THR* 2.8 33.0 + - - -
32G LEU* 3.6 16.3 - - + +
37G LEU* 4.2 6.3 - - + -
41G LEU* 3.6 14.4 - - + -
57G VAL* 3.1 50.9 - - + +
60G SER* 4.4 7.2 - - - -
61G LEU* 3.3 48.2 - - + -
64G LEU* 4.2 9.4 - - + -
70G LEU* 4.8 1.6 - - + -
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Residues in contact with ILE 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G LYS 3.0 19.3 - - - +
21G LEU* 2.7 11.7 + - + +
22G TYR 2.3 10.3 + - - -
23G MET* 1.3 67.6 - - - +
25G THR* 1.3 65.5 + - - +
27G THR* 3.3 3.7 + - - -
28G GLU* 3.1 25.6 + - - +
64G LEU* 3.9 25.6 - - + -
69G ILE* 4.5 10.3 - - + -
70G LEU* 5.5 1.3 - - + -
90G PHE* 3.5 27.1 - - + -
96G ALA* 4.6 15.5 - - + +
99G TYR* 4.1 35.0 - - + -
100G LYS* 5.0 12.3 - - + +
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Residues in contact with THR 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F ASP 3.4 23.6 - - - +
121F ASN* 1.9 51.8 + - - +
21G LEU 3.1 2.9 + - - -
22G TYR* 2.3 16.9 + - - -
24G ILE* 1.3 68.3 - - - +
26G MET* 1.3 66.0 + - + +
28G GLU* 2.9 24.3 + - + +
29G GLN* 3.0 30.1 + - + +
31G ARG* 6.0 1.1 - - - +
100G LYS* 4.0 7.8 + - - +
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Residues in contact with MET 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G TYR* 2.7 23.5 + - + +
23G MET 3.6 7.2 - - - +
25G THR* 1.3 74.4 - - - +
27G THR* 1.3 63.7 + - - +
29G GLN* 3.0 7.3 + - - -
31G ARG* 3.0 56.5 + - - +
32G LEU* 3.5 44.2 - - + +
33G TYR* 5.4 2.5 - - + -
37G LEU* 4.9 3.8 - - + -
40G VAL* 4.2 26.9 - - + -
41G LEU* 4.1 33.4 - - + +
44G GLU* 4.3 11.0 - - - +
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Residues in contact with THR 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G MET 2.8 17.8 + - - -
24G ILE 3.5 5.2 - - - -
25G THR 3.2 0.2 - - - -
26G MET* 1.3 71.8 - - - +
28G GLU* 1.3 52.8 + - - +
30G GLU* 2.6 32.7 + - - +
32G LEU* 3.2 29.0 - - - +
70G LEU* 3.8 11.6 - - - +
88G TYR* 4.3 8.6 + - - +
89G GLN* 4.5 7.6 - - + -
90G PHE* 3.0 52.0 - - + +
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Residues in contact with GLU 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G ILE* 3.1 16.8 + - - +
25G THR* 2.9 14.6 + - + +
27G THR* 1.3 74.9 - - - +
29G GLN* 1.3 58.7 + - + +
30G GLU* 3.0 9.8 + - - +
90G PHE* 3.2 29.7 - - + -
93G TYR* 2.6 37.0 + - + +
97G LYS* 4.6 6.4 + - - +
100G LYS* 4.5 15.0 + - - +
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Residues in contact with GLN 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F ASP 4.3 7.1 + - - -
25G THR* 3.0 33.1 + - + +
26G MET 3.0 6.3 + - - +
28G GLU* 1.3 75.8 - - + +
30G GLU* 1.3 62.1 + - - +
31G ARG* 1.9 77.5 + - + +
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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
------------------------------------------------------------
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