Contacts of the helix formed by residues 25 - 37 (chain E) in PDB entry 3AG2
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 ASP 25 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23E ASP 3.3 5.3 + - - +
24E ILE* 1.3 77.9 - - - +
26E ALA* 1.3 65.4 + - - +
27E TRP* 3.4 11.0 + - - +
28E GLU* 2.8 42.1 + - - +
29E LEU* 3.0 21.1 + - - +
58E LEU* 3.8 6.6 - - - +
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Residues in contact with ALA 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E ASP* 1.3 76.2 - - - +
27E TRP* 1.3 63.9 + - - +
29E LEU* 3.2 6.6 + - + +
30E ARG* 3.0 42.9 + - + +
58E LEU* 3.7 22.6 - - + +
60E ASP* 6.2 0.4 - - - +
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Residues in contact with TRP 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E TYR* 5.1 1.3 - - - -
25E ASP* 3.4 11.6 + - - +
26E ALA* 1.3 80.8 - - - +
28E GLU* 1.3 74.7 + - + +
30E ARG* 3.4 27.4 + - - +
31E LYS* 2.9 65.7 + - + -
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Residues in contact with GLU 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E TYR* 2.6 36.2 + - + +
21E LYS* 3.2 33.7 + - - -
23E ASP 4.4 0.5 - - - +
24E ILE* 3.6 13.8 - - + -
25E ASP* 2.8 41.5 + - - +
27E TRP* 1.3 88.0 - - + +
29E LEU* 1.3 61.2 + - - +
31E LYS* 4.3 0.2 - - - -
32E GLY 2.9 14.7 + - - -
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Residues in contact with LEU 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D LEU* 4.3 9.9 - - + -
19E PHE* 4.0 19.0 - - + -
24E ILE* 3.9 7.2 - - + +
25E ASP 3.0 12.8 + - - +
26E ALA* 3.2 11.0 + - + +
28E GLU* 1.3 76.4 - - - +
30E ARG* 1.3 65.0 + - + +
32E GLY* 3.8 0.5 - - - -
33E MET* 3.0 22.5 + - + +
51E ALA 4.1 9.2 - - - +
54E ALA* 4.1 21.8 - - + -
55E CYS* 4.0 23.6 - - - -
58E LEU* 3.9 20.9 - - + -
60E ASP* 4.6 5.6 - - - +
63E SER* 4.3 15.9 - - - +
67E ILE* 4.6 7.6 - - + -
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Residues in contact with ARG 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D LEU* 3.6 38.3 + - + +
25D PRO 3.3 25.9 + - - -
26D ASP* 4.0 24.5 + - - +
63D LYS* 6.2 1.8 - - - +
26E ALA* 3.0 38.9 + - + +
27E TRP* 3.7 32.5 - - - +
29E LEU* 1.3 75.3 - - + +
31E LYS* 1.3 58.7 + - - +
33E MET 3.2 0.3 + - - -
34E ASN* 2.7 44.2 + - - +
63E SER* 5.9 1.1 - - - +
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Residues in contact with LYS 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E TYR* 4.0 6.7 - - + +
27E TRP* 2.9 58.9 + - + +
28E GLU 3.8 2.9 - - - +
30E ARG* 1.3 75.2 - - - +
32E GLY* 1.3 58.1 + - - +
34E ASN* 3.8 4.8 - - + +
35E THR* 2.8 63.7 + - - +
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Residues in contact with GLY 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E TRP* 3.4 14.4 - - - -
18E TYR* 3.5 27.1 + - - -
19E PHE* 3.8 7.4 - - - -
28E GLU 2.9 11.8 + - - -
29E LEU 3.8 1.1 - - - -
31E LYS* 1.3 77.9 - - - +
33E MET* 1.3 56.6 + - - +
35E THR* 4.7 0.2 - - - -
36E LEU* 2.9 32.1 + - - +
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Residues in contact with MET 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D PRO* 4.7 4.0 - - + -
24D LEU* 3.8 20.2 - - + -
19E PHE* 3.7 23.5 - - + -
29E LEU* 3.0 18.7 + - + +
32E GLY* 1.3 75.5 - - - +
34E ASN* 1.3 64.0 + - - +
36E LEU* 3.4 15.4 + - + +
37E VAL* 3.2 35.1 + - + +
43E PRO* 5.6 2.0 - - + -
48E ILE* 5.0 6.7 - - + -
51E ALA* 4.0 14.4 - - - -
67E ILE* 3.8 37.5 - - + -
70E VAL* 3.9 28.7 - - + -
71E VAL* 5.9 0.2 - - + -
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Residues in contact with ASN 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ASP 4.4 4.2 - - - +
22D TYR* 3.6 40.1 + - + -
23D PRO* 3.2 14.6 - - - +
24D LEU* 3.0 46.0 + - - +
30E ARG* 2.7 29.7 + - - +
31E LYS* 4.1 4.4 - - + +
33E MET* 1.3 73.2 - - - +
35E THR* 1.3 59.7 + - - +
37E VAL* 3.5 16.6 - - - +
38E GLY* 4.1 2.8 + - - -
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Residues in contact with THR 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B SER* 5.9 0.7 - - - -
15E TRP* 4.1 12.8 - - + -
31E LYS* 2.8 50.1 + - - +
32E GLY* 3.8 2.9 - - - -
34E ASN* 1.3 76.5 - - - +
36E LEU* 1.3 65.9 + - - +
38E GLY* 3.0 15.6 + - - -
39E TYR* 3.8 27.6 - - + +
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Residues in contact with LEU 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E PHE* 4.0 22.9 - - + -
15E TRP* 3.9 26.0 - - + -
19E PHE* 4.1 14.8 - - + -
32E GLY 2.9 16.7 + - - +
33E MET* 3.4 15.9 + - + +
35E THR* 1.3 79.1 - - - +
37E VAL* 1.3 61.6 + - + +
38E GLY 3.1 1.1 + - - -
39E TYR* 3.2 27.1 + - + +
41E LEU* 4.4 7.3 - - + +
43E PRO* 3.7 28.5 - - + +
47E ILE* 3.7 28.9 - - + -
48E ILE* 5.2 1.1 - - + -
74E LYS* 5.1 0.7 - - - -
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Residues in contact with VAL 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B THR* 4.0 4.0 + - - -
53B THR* 6.0 0.2 - - - +
20D ARG 5.4 0.4 - - - +
21D ASP* 3.7 26.9 - - + +
23D PRO* 3.9 12.3 - - + -
33E MET* 3.2 24.1 + - + +
34E ASN 3.5 11.9 - - - +
36E LEU* 1.3 79.4 - - + +
38E GLY* 1.3 58.1 + - - +
39E TYR 3.3 0.7 - - - -
43E PRO* 5.7 4.7 - - + -
70E VAL* 3.6 36.3 - - + -
74E LYS* 2.8 45.3 + - + +
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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