Contacts of the helix formed by residues 20 - 29 (chain W) in PDB entry 4E2I
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 GLU 20 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18W ASP* 5.4 1.2 + - - -
19W CYS* 1.3 77.6 - - - +
21W GLU* 1.3 67.9 + - - +
22W ALA* 3.8 20.2 + - - +
23W LEU* 3.0 36.1 + - + +
24W ILE* 3.0 11.0 + - - +
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Residues in contact with GLU 21 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20W GLU* 1.3 74.6 + - - +
22W ALA* 1.3 59.9 + - - +
24W ILE* 4.2 8.2 - - + +
25W GLU* 3.1 42.5 + - + +
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Residues in contact with ALA 22 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20W GLU* 3.1 20.0 + - + +
21W GLU* 1.3 79.7 - - - +
23W LEU* 1.3 63.3 + - + +
25W GLU* 3.8 10.2 + - - +
26W LYS* 3.4 19.8 + - - +
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Residues in contact with LEU 23 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18W ASP 4.3 1.3 - - - +
19W CYS* 3.5 27.8 - - + -
20W GLU* 3.0 37.1 + - + +
22W ALA* 1.3 79.2 - - + +
24W ILE* 1.3 64.1 + - - +
26W LYS* 3.1 22.9 + - + +
27W LEU* 3.1 14.8 - - + +
57W LEU 4.0 17.5 - - - +
58W THR* 3.6 23.3 - - - +
59W SER* 3.4 26.9 - - - +
62W LEU* 5.4 3.1 - - + +
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Residues in contact with ILE 24 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5W ALA* 3.5 35.7 - - + +
8W LEU* 4.6 4.6 - - + +
9W ALA* 3.9 24.2 - - + +
12W LEU* 3.8 16.6 - - + -
19W CYS* 3.2 30.1 - - + +
20W GLU 3.0 15.2 + - - +
21W GLU* 4.2 8.1 - - + +
23W LEU* 1.3 75.9 - - - +
25W GLU* 1.3 59.5 + - - +
26W LYS 3.1 0.4 - - - -
27W LEU* 3.3 16.1 + - - +
28W VAL* 3.2 13.2 + - - +
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Residues in contact with GLU 25 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5W ALA* 4.4 13.7 - - + -
21W GLU* 3.1 32.4 + - - +
22W ALA* 4.1 8.3 - - - +
23W LEU 3.3 0.2 - - - -
24W ILE* 1.3 75.7 - - - +
26W LYS* 1.3 62.9 + - - +
27W LEU 3.2 0.4 - - - -
28W VAL* 3.3 24.6 + - + +
29W GLU* 3.7 12.5 + - - +
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Residues in contact with LYS 26 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22W ALA 3.4 12.9 + - - +
23W LEU* 3.1 19.5 + - + +
24W ILE 3.1 0.4 - - - -
25W GLU* 1.3 80.5 - - - +
27W LEU* 1.3 60.5 + - + +
29W GLU* 3.6 31.5 + - - +
30W LEU* 4.0 6.5 + - + +
59W SER* 4.8 12.6 - - - +
62W LEU* 3.2 36.5 + - + +
63W ASN* 3.4 27.7 + - - +
66W GLU* 3.1 25.8 + - - +
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Residues in contact with LEU 27 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8W LEU* 3.6 33.2 - - + -
12W LEU* 5.8 4.7 - - + -
19W CYS* 5.7 5.2 - - - -
23W LEU* 3.1 20.6 - - + +
24W ILE* 3.3 8.0 + - - +
25W GLU 3.2 0.4 - - - -
26W LYS* 1.3 76.7 - - + +
28W VAL* 1.3 65.7 + - - +
29W GLU 3.0 2.5 - - - -
30W LEU* 3.0 45.3 + - + +
31W CYS* 3.3 11.8 - - - -
41W MET* 4.6 8.2 - - + +
42W VAL* 6.5 0.2 - - - -
45W LEU* 4.1 13.2 - - + -
62W LEU* 3.6 37.9 - - + -
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Residues in contact with VAL 28 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2W SER* 4.0 12.3 - - - -
3W ALA* 3.6 30.3 - - + +
4W SER 4.4 2.2 - - - +
5W ALA* 3.6 27.8 - - + +
8W LEU* 4.8 4.0 - - + -
24W ILE 3.2 17.3 - - - +
25W GLU* 3.4 20.6 - - + +
26W LYS 3.3 0.2 - - - -
27W LEU* 1.3 79.6 - - - +
29W GLU* 1.3 60.1 + - + +
31W CYS* 3.3 14.8 + - - +
32W VAL* 3.2 18.3 + - + +
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Residues in contact with GLU 29 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25W GLU 3.7 12.3 - - - +
26W LYS* 3.6 31.6 - - - +
27W LEU 3.0 0.4 - - - -
28W VAL* 1.3 76.7 - - + +
30W LEU* 1.3 54.3 + - - +
31W CYS 3.1 0.7 - - - -
32W VAL* 3.0 7.5 + - - +
33W GLN* 2.8 48.4 + - + +
66W GLU* 5.4 6.0 - - - +
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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