Contacts of the helix formed by residues 27 - 41 (chain G) in PDB entry 1EA4
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 27 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21G ALA* 4.2 0.4 - - - -
26G LEU* 1.3 77.8 - - - +
28G LYS* 1.3 59.4 + - - +
29G SER* 3.1 8.8 + - - -
30G ALA* 2.7 25.7 + - - +
31G MET* 2.7 28.6 + - - +
25J GLY* 3.1 22.4 + - - -
26J LEU* 5.1 0.2 - - - +
204W C 5.6 0.4 - - - -
205W C 4.0 14.3 + - - -
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Residues in contact with LYS 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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5F LEU* 4.4 23.3 - - + -
7F ILE* 5.0 3.4 - - + -
14G LEU* 4.7 7.2 - - + -
17G LEU* 4.3 16.8 - - + -
18G GLU* 2.7 42.6 - - - +
21G ALA* 4.3 9.6 - - + +
26G LEU 4.0 0.2 + - - -
27G SER* 1.3 73.0 - - - +
29G SER* 1.3 59.2 + - - +
31G MET* 3.2 6.6 + - - +
32G ILE* 2.8 38.7 + - + +
205W C 3.9 6.4 + - - +
206W G 2.5 38.3 + - - +
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Residues in contact with SER 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F ILE* 2.8 34.9 - - - +
8F THR* 3.0 26.5 + - - -
9F LEU* 3.9 1.7 - - - +
27G SER* 3.1 3.2 + - - -
28G LYS* 1.3 79.9 - - - +
30G ALA* 1.3 52.3 + - - +
32G ILE* 3.4 4.7 + - - +
33G SER* 2.6 37.2 + - - -
205W C 3.0 24.3 + - - -
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Residues in contact with ALA 30 (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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26G LEU* 3.9 8.7 - - + -
27G SER* 2.7 24.6 + - - +
29G SER* 1.3 69.9 - - - +
31G MET* 1.3 58.4 - - - +
33G SER* 2.8 10.5 + - - -
34G VAL* 2.7 39.8 + - + +
24J MET 4.5 4.9 - - - +
25J GLY* 3.5 27.4 - - - +
26J LEU* 5.3 1.1 - - + -
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Residues in contact with MET 31 (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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36F LEU* 5.0 1.1 - - + -
39F TYR* 4.3 7.6 - - - -
17G LEU* 3.1 29.6 - - + -
20G MET* 3.3 48.5 - - + +
21G ALA* 3.4 11.0 - - + +
24G MET* 3.1 38.1 - - + +
26G LEU* 4.2 12.9 - - + +
27G SER 2.7 21.3 + - - +
28G LYS* 3.3 7.0 - - - +
30G ALA* 1.3 73.4 - - - +
32G ILE* 1.3 55.8 + - - +
34G VAL* 3.3 4.1 + - - +
35G ALA* 2.9 27.0 + - - +
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Residues in contact with ILE 32 (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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5F LEU* 5.1 0.9 - - + -
7F ILE* 3.7 40.8 - - + -
9F LEU* 4.9 1.1 - - + -
32F ILE* 3.7 26.0 - - + -
36F LEU* 4.1 14.1 - - + -
7G ILE* 4.3 7.9 - - + -
9G LEU* 5.0 0.2 - - + -
17G LEU* 3.6 28.9 - - + -
28G LYS 2.8 20.7 + - - +
29G SER* 3.6 4.5 - - - +
31G MET* 1.3 72.9 - - - +
33G SER* 1.3 62.2 + - - +
35G ALA* 3.2 1.4 + - - +
36G LEU* 2.8 51.0 + - + +
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Residues in contact with SER 33 (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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8F THR 4.4 1.2 + - - -
9F LEU* 3.1 20.1 - - - +
10F SER 5.5 0.5 + - - -
13F VAL* 4.2 18.3 - - - +
29G SER 2.6 20.5 + - - -
30G ALA* 2.8 14.4 + - - -
32G ILE* 1.3 73.1 - - - +
34G VAL* 1.3 59.8 + - - +
36G LEU* 3.3 9.9 + - - +
37G GLU* 2.8 36.3 + - - +
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Residues in contact with VAL 34 (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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39F TYR* 4.0 29.4 - - + +
24G MET* 6.0 1.1 - - + -
26G LEU* 4.0 21.5 - - + -
30G ALA* 2.7 20.9 + - + +
31G MET* 3.3 10.5 - - - +
33G SER* 1.3 71.9 - - - +
35G ALA* 1.3 57.8 + - - +
37G GLU* 3.0 8.2 + - - +
38G ASN* 2.6 36.0 + - + +
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Residues in contact with ALA 35 (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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35F ALA* 4.1 10.9 - - + +
36F LEU* 3.4 33.2 - - + -
39F TYR* 3.9 32.0 - - + +
31G MET 2.9 6.8 + - - +
32G ILE 3.4 5.6 - - - +
34G VAL* 1.3 79.2 - - - +
36G LEU* 1.3 53.4 + - - +
38G ASN* 3.3 2.3 + - - +
39G TYR* 2.6 36.9 + - - +
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Residues in contact with LEU 36 (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 LEU* 4.8 4.9 - - + -
13F VAL* 4.7 17.5 - - + -
17F LEU* 3.2 35.7 - - + -
20F MET* 3.9 24.8 - - + +
31F MET* 4.4 7.0 - - + -
32F ILE* 4.6 6.5 - - + -
35F ALA* 4.1 20.9 - - + -
32G ILE* 2.8 48.0 + - + +
33G SER* 3.5 8.3 - - - +
35G ALA* 1.3 69.3 - - - +
37G GLU* 1.3 69.3 + - + +
39G TYR* 3.0 4.0 + - - +
40G LYS* 2.8 22.7 + - - +
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Residues in contact with GLU 37 (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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12F SER* 4.8 3.5 + - - -
13F VAL* 4.5 16.2 - - + +
16F ASN* 4.1 18.7 + - - -
33G SER* 2.8 20.6 + - - +
34G VAL* 3.4 9.9 - - - +
36G LEU* 1.3 72.0 - - - +
38G ASN* 1.3 66.0 + - - +
40G LYS* 2.9 42.3 + - - +
41G LYS* 3.2 15.9 + - - +
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Residues in contact with ASN 38 (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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38F ASN* 4.1 11.3 + - - -
39F TYR* 3.1 36.3 - - + +
34G VAL* 2.6 22.1 + - + +
35G ALA 3.4 3.4 - - - +
37G GLU* 1.3 71.5 - - - +
39G TYR* 1.3 69.9 + - - +
41G LYS* 2.8 31.5 + - - +
42G GLY* 5.1 2.2 - - - -
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Residues in contact with TYR 39 (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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20F MET* 3.8 17.7 - - + -
24F MET* 3.5 27.8 - - - +
31F MET* 3.3 28.9 - - + -
34F VAL* 4.0 18.0 - - + +
35F ALA* 3.9 16.6 - - + -
38F ASN* 3.4 37.0 - - + +
35G ALA 2.6 17.8 + - - +
36G LEU* 3.2 8.7 - - - +
38G ASN* 1.3 77.4 - - - +
40G LYS* 1.3 67.3 + - - +
42G GLY* 2.9 23.3 + - - -
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Residues in contact with LYS 40 (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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16F ASN* 4.2 27.3 + - + +
20F MET* 4.5 15.7 - - + -
36G LEU 2.8 11.2 + - - +
37G GLU* 2.9 37.7 + - - +
39G TYR* 1.3 81.9 - - - +
41G LYS* 1.3 80.7 + - + +
42G GLY 2.9 8.1 + - - -
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Residues in contact with LYS 41 (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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37G GLU* 3.4 18.4 - - - +
38G ASN* 2.8 20.4 + - - +
40G LYS* 1.3 101.6 - - + +
42G GLY* 1.3 55.9 + - - +
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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