Contacts of the helix formed by residues 19 - 32 (chain A) in PDB entry 4E2E
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 ARG 19 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ALA* 2.8 20.9 + - + +
17A ALA* 3.8 26.2 - - - +
18A GLU* 1.3 74.7 - - - +
20A TYR* 1.3 59.1 + - - +
21A ASP* 3.4 3.4 - - - -
22A ASP* 2.8 44.2 + - + +
23A MSE 3.1 20.3 + - - -
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Residues in contact with TYR 20 (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 GLU* 4.2 20.9 + - + +
18A GLU* 3.5 42.4 + - + +
19A ARG* 1.3 72.2 - - - +
21A ASP* 1.4 56.8 + - - +
23A MSE 3.2 29.8 + - - +
24A ALA* 2.8 29.5 + - - +
47A VAL* 4.8 2.0 - - + -
48A ALA 4.3 3.6 - - - +
51A ASN* 3.4 55.6 + - + +
52A VAL* 3.4 19.3 - - + +
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Residues in contact with ASP 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ARG 3.4 0.8 - - - -
20A TYR* 1.4 76.0 - - - +
22A ASP* 1.4 59.1 + - - +
24A ALA* 3.4 3.5 + - - +
25A ALA* 3.0 29.3 + - - +
52A VAL* 3.5 19.1 - - - +
56A ARG* 3.3 30.3 + - - -
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Residues in contact with ASP 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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10A LYS* 5.2 18.0 - - - +
14A ALA* 3.8 12.6 - - + +
19A ARG* 2.8 52.7 + - + +
21A ASP* 1.4 74.6 - - - +
23A MSE 1.3 59.7 + - - +
25A ALA* 3.4 7.2 + - - +
26A ALA* 3.0 30.3 + - - +
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Residues in contact with MSE 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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11A ALA* 3.3 22.4 - - + +
14A ALA* 3.5 10.2 - - + +
15A GLU* 3.6 35.2 - - + +
19A ARG 3.1 13.2 + - - +
20A TYR* 3.4 25.8 - - - +
22A ASP* 1.3 76.9 - - - +
24A ALA* 1.4 60.3 + - - +
26A ALA* 3.3 3.8 + - - +
27A MSE 3.1 24.6 + - - +
44A LEU* 3.4 49.1 - - + +
47A VAL* 3.9 11.4 - - + -
48A ALA* 3.8 19.1 - - + -
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Residues in contact with ALA 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 TYR 2.8 20.2 + - - +
21A ASP* 3.7 4.7 - - - +
23A MSE 1.4 71.1 - - - +
25A ALA* 1.3 57.0 + - - +
27A MSE 3.4 2.1 + - - +
28A LYS* 2.8 30.7 + - - +
48A ALA* 3.5 14.7 - - + +
49A TYR* 3.7 34.0 + - + -
52A VAL* 4.0 16.4 - - + -
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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 ASP 3.0 16.7 + - - +
22A ASP* 3.6 7.9 - - - +
24A ALA* 1.3 77.6 - - - +
26A ALA* 1.4 55.7 + - - +
28A LYS* 3.4 9.9 + - - +
29A ASN* 3.0 36.3 + - - +
49A TYR* 5.3 0.4 - - - -
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Residues in contact with ALA 26 (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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7A LEU* 3.5 28.0 - - + +
10A LYS* 4.3 15.7 - - + +
11A ALA* 3.9 14.4 - - + +
22A ASP 3.0 17.2 + - - +
23A MSE 3.7 4.7 - - - +
25A ALA* 1.4 74.2 - - - +
27A MSE 1.3 58.5 + - - +
29A ASN* 3.3 11.3 + - - +
30A VAL* 3.0 31.8 + - - +
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Residues in contact with MSE 27 (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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8A VAL* 4.5 5.4 - - + -
11A ALA* 3.6 25.4 - - + -
23A MSE 3.1 18.8 + - - +
24A ALA* 3.9 3.6 - - - +
26A ALA* 1.3 72.6 - - - +
28A LYS* 1.3 61.0 + - - +
30A VAL* 3.4 28.8 + - + +
31A THR* 2.8 32.7 + - - -
37A LEU* 5.2 2.9 - - + -
41A GLU* 3.2 46.2 - - + +
44A LEU* 3.8 19.5 - - - +
45A LEU* 3.8 37.0 - - + +
48A ALA* 4.8 0.2 - - + -
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Residues in contact with LYS 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 ALA 2.8 17.3 + - - +
25A ALA* 3.6 10.1 - - - +
26A ALA 3.3 0.2 - - - -
27A MSE 1.3 77.2 - - - +
29A ASN* 1.3 56.4 + - - +
31A THR* 3.3 3.3 + - - -
32A GLU* 3.0 61.1 + - - +
45A LEU* 4.5 0.4 - - - +
49A TYR* 3.5 20.6 - - - +
99A ASP* 2.6 29.4 + - - +
103A LEU* 4.1 22.4 - - + -
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Residues in contact with ASN 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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2A VAL* 6.2 1.1 - - - +
7A LEU* 3.9 26.0 - - + +
25A ALA* 3.0 22.4 + - - +
26A ALA* 3.3 10.6 + - - +
28A LYS* 1.3 73.7 - - - +
30A VAL* 1.3 63.2 + - - +
32A GLU* 3.3 26.1 + - - +
33A LEU* 3.4 16.8 + - - +
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Residues in contact with VAL 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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4A ARG* 3.8 39.2 + - + +
7A LEU* 3.5 24.2 - - + -
8A VAL* 4.1 15.0 - - + -
26A ALA 3.0 15.9 + - - +
27A MSE 3.6 30.7 - - + +
28A LYS 3.3 0.2 - - - -
29A ASN* 1.3 72.2 - - - +
31A THR* 1.4 65.1 + - - +
33A LEU* 3.1 28.1 + - - +
34A ASN 4.4 0.3 + - - -
35A GLU 5.1 1.0 - - - +
37A LEU* 4.1 6.0 - - + +
41A GLU* 4.2 7.0 - - - +
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Residues in contact with THR 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 MSE 2.8 20.7 + - - -
28A LYS 3.6 8.3 - - - -
30A VAL* 1.4 74.4 - - - +
32A GLU* 1.3 58.1 + - - +
34A ASN* 3.0 22.3 + - - -
35A GLU 4.3 4.4 + - - +
37A LEU* 4.1 20.5 - - - +
45A LEU* 4.1 13.0 - - - +
103A LEU* 4.0 20.6 - - + -
107A TYR* 3.7 22.8 - - + +
108A LEU* 3.8 32.3 - - + -
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Residues in contact with GLU 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 LYS* 3.0 47.7 + - - +
29A ASN* 3.7 22.1 - - - +
30A VAL 3.2 0.4 - - - -
31A THR* 1.3 71.9 - - - +
33A LEU* 1.4 55.5 + - - +
34A ASN* 3.0 12.8 + - - +
103A LEU* 4.4 8.0 - - + +
107A TYR* 3.7 32.9 + - + +
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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