Contacts of the helix formed by residues 28 - 41 (chain A) in PDB entry 3AA6
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 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ALA* 4.4 1.6 - - - -
25A PRO* 3.1 24.8 + - + +
26A PRO 3.8 4.0 - - - +
27A GLY* 1.3 79.5 - - - +
29A PHE* 1.3 65.0 + - - +
30A ASN 3.3 2.5 - - - -
31A GLU* 3.4 12.0 + - - +
32A VAL* 3.1 24.8 + - - +
165A PRO* 6.1 1.1 - - + -
170A ASN* 2.8 31.2 + - - +
197A HIS* 2.6 41.1 + - - +
199A TYR* 3.3 5.6 - - - +
15B ARG* 2.8 39.2 + - - +
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Residues in contact with PHE 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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21A ILE* 3.3 31.6 - - + -
24A ALA* 4.1 8.3 - - + -
25A PRO 4.2 2.0 + - - -
27A GLY* 3.6 2.2 - - - -
28A GLU* 1.3 77.4 - - - +
30A ASN* 1.3 70.5 - - - +
32A VAL* 3.4 2.1 + - + +
33A PHE* 2.8 41.4 + + + +
54A PHE* 3.8 30.5 - + + -
57A TYR* 3.6 47.0 + + + +
101A LEU* 3.9 17.7 - - + -
103A LYS* 3.4 35.0 - - - -
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Residues in contact with ASN 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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27A GLY 5.5 0.2 + - - -
28A GLU 3.3 0.6 - - - -
29A PHE* 1.3 99.0 - - - +
31A GLU* 1.3 67.1 + - - +
33A PHE* 3.4 5.1 + - - +
34A ASN* 2.9 42.4 + - - +
101A LEU 5.0 4.6 + - - -
103A LYS* 4.8 8.5 - - - +
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Residues in contact with GLU 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 GLY 4.0 4.8 - - - +
28A GLU* 3.4 24.1 - - - +
29A PHE 3.3 0.2 - - - -
30A ASN* 1.3 80.8 + - - +
32A VAL* 1.3 62.4 + - - +
34A ASN* 3.4 7.4 + - - +
35A ASP* 2.9 35.2 + - - +
165A PRO* 5.8 4.9 - - - +
11B ASP* 4.4 1.6 - - - +
15B ARG* 3.6 44.6 - - - +
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Residues in contact with VAL 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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20A PHE 3.7 24.7 - - - +
21A ILE* 4.1 11.4 - - - -
24A ALA* 3.7 23.8 - - + -
25A PRO* 4.2 1.8 - - + -
28A GLU 3.1 18.1 + - - +
29A PHE 3.9 1.3 - - - +
31A GLU* 1.3 76.5 - - - +
33A PHE* 1.3 64.4 + - - +
35A ASP* 3.3 6.8 + - - +
36A VAL* 3.0 26.9 + - + +
12B LEU* 3.9 20.0 - - + -
15B ARG* 4.0 29.4 - - + -
16B LEU* 5.1 2.9 - - + -
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Residues in contact with PHE 33 (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 ILE* 4.0 17.5 - - + -
29A PHE* 2.8 35.6 + + + +
30A ASN* 3.6 6.3 - - - +
32A VAL* 1.3 77.7 - - - +
34A ASN* 1.3 72.8 + - - +
36A VAL* 3.3 1.7 + - - +
37A ARG* 2.9 45.6 + - - +
46A LEU* 3.6 29.4 - - + -
54A PHE* 3.8 32.8 - + - -
101A LEU* 4.3 22.7 - - + -
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Residues in contact with ASN 34 (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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30A ASN* 2.9 27.0 + - - +
31A GLU* 3.7 7.1 - - - +
33A PHE* 1.3 93.9 - - - +
35A ASP* 1.3 64.7 + - - +
37A ARG* 3.6 9.8 - - - +
38A LEU* 3.2 33.3 + - + +
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Residues in contact with ASP 35 (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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31A GLU 2.9 19.7 + - - +
32A VAL* 3.5 4.6 - - - +
34A ASN* 1.3 79.7 - - - +
36A VAL* 1.3 57.1 + - - +
38A LEU* 3.3 2.8 + - - +
39A LEU* 3.0 33.2 + - - +
8B CYS* 3.5 36.3 - - + +
11B ASP* 2.4 33.0 - - - +
12B LEU* 3.5 32.8 + - + +
15B ARG* 4.5 1.0 + - - -
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Residues in contact with VAL 36 (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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17A ALA* 3.4 34.1 - - + +
20A PHE* 3.9 31.4 - - + -
21A ILE* 3.9 17.0 - - + -
32A VAL* 3.0 23.0 + - + +
33A PHE 3.3 3.1 + - - +
35A ASP* 1.3 73.0 - - - +
37A ARG* 1.3 57.6 + - - +
39A LEU* 3.2 7.3 + - - +
40A LEU* 2.8 34.0 + - - +
46A LEU* 4.3 5.8 - - + -
12B LEU* 4.1 16.2 - - + -
31B LEU* 5.1 3.9 - - + +
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Residues in contact with ARG 37 (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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33A PHE* 2.9 38.0 + - + +
34A ASN* 3.6 10.1 - - - +
36A VAL* 1.3 77.6 - - - +
38A LEU* 1.3 65.5 - - + +
40A LEU* 3.6 2.3 + - - +
41A ASN* 3.0 25.3 + - - -
42A ASN 4.5 1.9 + - - -
43A ASP* 2.5 43.7 + - - +
46A LEU* 4.1 22.2 - - + +
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Residues in contact with LEU 38 (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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34A ASN* 3.2 19.9 + - + +
35A ASP 3.9 3.4 - - - +
37A ARG* 1.3 87.6 - - + +
39A LEU* 1.3 65.3 + - - +
41A ASN* 3.7 11.2 - - - +
4B GLN* 3.7 33.4 - - + +
5B GLN* 3.3 20.8 + - + +
8B CYS* 3.5 28.5 - - - -
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Residues in contact with LEU 39 (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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13A LYS* 6.1 0.2 - - - +
35A ASP 3.0 17.7 + - - +
36A VAL 3.2 4.0 + - - +
38A LEU* 1.3 75.2 - - - +
40A LEU* 1.3 64.5 + - - +
5B GLN* 3.1 57.1 + - + +
8B CYS* 4.1 3.8 - - + -
9B ALA* 3.9 11.2 - - + +
12B LEU* 3.5 32.3 - - + -
28B LEU* 3.7 19.1 - - + -
31B LEU* 3.8 18.3 - - + +
32B VAL* 3.5 30.2 - - + +
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Residues in contact with LEU 40 (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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13A LYS* 3.6 43.1 - - + +
14A VAL* 4.0 10.8 - - + -
17A ALA* 4.2 4.0 - - + -
36A VAL 2.8 20.4 + - - +
37A ARG* 4.1 2.7 - - - +
39A LEU* 1.3 75.0 - - - +
41A ASN* 1.3 70.1 + - - +
42A ASN* 3.3 11.2 + - + +
45A LEU* 3.7 19.0 - - + +
46A LEU* 3.6 50.3 - - + +
31B LEU* 3.8 14.1 - - + +
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Residues in contact with ASN 41 (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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37A ARG 3.0 15.9 + - - -
38A LEU* 3.7 14.7 + - - +
39A LEU 3.3 0.2 - - - -
40A LEU* 1.3 79.2 - - - +
42A ASN* 1.3 61.2 + - - +
43A ASP* 5.7 0.4 - - - -
5B GLN* 4.2 11.7 - - - +
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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