Contacts of the helix formed by residues 15 - 36 (chain A) in PDB entry 1BA4
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 GLN 15 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A VAL* 3.2 19.2 - - + +
14A HIS* 1.3 79.9 + - - +
16A LYS* 1.3 61.6 + - - +
18A VAL* 3.1 31.3 + - + +
19A PHE* 2.9 58.1 + - + -
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Residues in contact with LYS 16 (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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1A ASP 6.1 1.8 - - - +
3A GLU* 3.2 33.6 + - - +
9A GLY 3.9 12.9 + - - -
10A TYR 3.6 19.3 - - - +
11A GLU* 3.2 45.8 + - - +
12A VAL* 3.1 12.1 - - + +
13A HIS 5.1 1.1 - - - +
14A HIS* 4.6 2.5 - - - -
15A GLN* 1.3 77.8 - - - +
17A LEU* 1.3 62.4 + - - +
19A PHE* 3.4 5.1 + - + +
20A PHE* 3.0 22.4 + - + +
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Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A HIS* 2.9 29.5 + - + +
16A LYS* 1.3 78.9 - - - +
18A VAL* 1.3 79.8 + - + +
20A PHE* 3.0 28.7 + - + -
21A ALA* 2.9 25.4 + - + -
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Residues in contact with VAL 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A HIS* 3.7 12.6 - - + +
15A GLN* 3.1 33.6 + - + +
17A LEU* 1.3 95.7 - - + +
19A PHE* 1.3 62.9 + - + +
21A ALA* 3.1 7.1 + - - +
22A GLU* 2.8 36.6 + - - +
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Residues in contact with PHE 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU* 3.3 37.2 - - - +
12A VAL* 4.9 2.0 - - + -
15A GLN* 2.9 59.4 + - + -
16A LYS* 3.6 6.5 - - + +
18A VAL* 1.3 76.2 - - + +
20A PHE* 1.3 64.7 + - - +
22A GLU* 3.0 26.6 + - - +
23A ASP* 3.0 21.2 + - - +
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Residues in contact with PHE 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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1A ASP 5.5 12.1 - - - +
16A LYS* 3.0 16.8 + - + +
17A LEU* 3.1 34.1 - - + +
19A PHE* 1.3 75.4 - - - +
21A ALA* 1.3 72.2 + - + +
23A ASP* 3.0 10.7 + - + +
24A VAL* 2.9 51.3 + - + +
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Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 2.9 17.0 + - + +
18A VAL* 3.3 12.8 - - - +
20A PHE* 1.3 88.0 - - + +
22A GLU* 1.3 63.4 + - + +
24A VAL* 3.2 9.7 + - - +
25A GLY* 2.9 20.6 + - - -
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Residues in contact with GLU 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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18A VAL* 2.8 40.1 + - - +
19A PHE* 3.0 26.6 + - - +
21A ALA* 1.3 76.9 - - + +
23A ASP* 1.3 66.5 + - - +
25A GLY* 3.1 3.3 + - - -
26A SER* 3.0 24.0 + - - -
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Residues in contact with ASP 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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1A ASP* 3.0 38.1 - - - +
19A PHE 3.0 12.3 + - - +
20A PHE* 3.1 13.7 - - + +
22A GLU* 1.3 74.5 - - - +
24A VAL* 1.3 61.7 + - + +
26A SER* 2.6 22.0 + - - -
27A ASN* 2.8 51.0 + - - +
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Residues in contact with VAL 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PHE* 2.9 49.6 - - + +
21A ALA* 3.2 9.9 - - - +
23A ASP* 1.3 78.1 - - + +
25A GLY* 1.3 64.1 + - - +
27A ASN* 3.2 8.7 + - - +
28A LYS* 3.1 22.7 + - - +
31A ILE* 5.0 3.4 - - + +
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Residues in contact with GLY 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 ALA 2.9 14.0 + - - -
22A GLU* 3.1 4.5 + - - -
24A VAL* 1.3 80.2 - - - +
26A SER* 1.3 61.7 + - - +
28A LYS* 3.3 17.9 - - - +
29A GLY 4.6 0.2 + - - -
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Residues in contact with SER 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLU 3.0 11.9 + - - -
23A ASP* 2.6 26.5 + - - -
25A GLY* 1.3 72.8 - - - +
27A ASN* 1.3 70.0 + - - +
28A LYS 3.0 1.2 + - - -
29A GLY* 3.0 14.2 + - - -
30A ALA 4.3 0.7 + - - -
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Residues in contact with ASN 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASP* 2.8 51.1 + - - +
24A VAL* 3.4 9.2 - - - +
26A SER* 1.3 77.1 + - - +
28A LYS* 1.3 66.1 + - - +
29A GLY 2.8 2.4 + - - -
30A ALA* 2.8 21.5 + - - +
31A ILE* 2.9 28.6 + - + +
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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
----------------------------------------------------------
24A VAL 3.1 8.3 + - - +
25A GLY* 3.3 17.3 - - - +
27A ASN* 1.3 77.7 - - - +
29A GLY* 1.3 61.9 + - - +
31A ILE* 3.3 16.4 - - + +
32A ILE* 3.0 48.1 + - + +
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Residues in contact with GLY 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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25A GLY 4.6 0.2 + - - -
26A SER 3.0 9.5 + - - -
27A ASN 2.8 5.9 + - - -
28A LYS* 1.3 79.1 - - - +
30A ALA* 1.3 61.9 + - - +
32A ILE* 3.2 11.1 + - - +
33A GLY* 3.2 15.9 + - - -
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Residues in contact with ALA 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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26A SER 4.3 1.4 + - - +
27A ASN* 2.8 15.9 + - + +
29A GLY* 1.3 71.4 - - - -
31A ILE* 1.3 65.0 + - + +
33A GLY* 3.1 4.1 + - - +
34A LEU* 2.9 35.3 + - + +
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Residues in contact with ILE 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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24A VAL* 5.0 3.6 - - + +
27A ASN* 2.9 38.1 + - + +
28A LYS* 3.3 20.4 - - + +
30A ALA* 1.3 76.2 - - + +
32A ILE* 1.3 65.7 + - + +
34A LEU* 3.1 16.0 + - + +
35A MET* 2.9 43.2 + - + +
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Residues in contact with ILE 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 40.8 + - + +
29A GLY* 3.5 9.6 - - - +
31A ILE* 1.3 76.0 - - + +
33A GLY* 1.3 64.8 + - - +
35A MET* 3.1 25.1 + - + +
36A VAL* 3.0 36.5 + - + +
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Residues in contact with GLY 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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29A GLY 3.2 6.5 + - - -
30A ALA* 3.1 8.9 + - - -
32A ILE* 1.3 82.0 - - - +
34A LEU* 1.3 62.4 + - - +
36A VAL* 3.2 8.5 + - - +
37A GLY 2.9 25.4 + - - +
38A GLY* 5.8 0.9 - - - -
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Residues in contact with LEU 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 ALA* 2.9 31.5 + - + +
31A ILE* 3.4 14.1 - - + +
33A GLY* 1.3 75.9 - - - +
35A MET* 1.3 66.1 + - + +
37A GLY* 3.1 17.5 + - - +
38A GLY* 5.2 3.4 - - - +
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Residues in contact with MET 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 ILE* 2.9 42.1 + - + +
32A ILE* 3.1 24.7 + - + +
34A LEU* 1.3 77.2 - - + +
36A VAL* 1.3 66.0 + - + +
37A GLY* 4.4 0.2 - - - -
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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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32A ILE* 3.0 29.0 + - + +
33A GLY* 3.4 10.5 - - - +
35A MET* 1.3 81.6 - - + +
37A GLY* 1.3 58.3 + - - +
40A VAL* 3.4 52.1 - - + +
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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