Contacts of the helix formed by residues 19 - 32 (chain A) in PDB entry 3GG0
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 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A PRO 3.7 3.6 + - - -
18A VAL* 1.3 73.0 - - - +
20A LEU* 1.3 61.2 + - - +
21A ASP* 3.9 13.3 + - - +
22A ALA* 3.4 24.3 + - + +
23A LEU* 3.2 22.5 + - - +
70A ARG* 5.6 0.7 + - - -
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Residues in contact with LEU 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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18A VAL* 3.0 20.9 + - + +
19A ASP* 1.3 70.7 + - - +
21A ASP* 1.3 58.3 + - - +
22A ALA 3.2 1.8 - - - -
23A LEU* 3.8 27.1 - - + -
24A VAL* 2.8 38.8 + - - +
40A LEU* 4.6 5.4 - - + -
42A PHE* 3.7 35.9 - - + -
47A PHE* 3.7 32.1 - - + -
94A ILE* 3.7 24.2 - - + -
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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
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19A ASP* 3.4 9.5 + - - +
20A LEU* 1.3 78.1 - - - +
22A ALA* 1.3 59.8 + - - +
24A VAL* 4.2 3.2 - - - +
25A HIS* 3.1 26.7 + - - +
94A ILE* 5.3 9.0 - - - +
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Residues in contact with ALA 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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19A ASP* 3.4 30.0 + - + +
20A LEU 3.2 0.4 - - - -
21A ASP* 1.3 76.8 - - - +
23A LEU* 1.3 64.9 + - - +
25A HIS* 4.2 4.0 - - - +
26A ARG* 3.0 29.4 + - - +
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Residues in contact with LEU 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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18A VAL* 4.0 11.0 - - + -
19A ASP 3.2 10.9 + - - +
20A LEU* 3.2 28.8 + - + +
22A ALA* 1.3 80.0 - - - +
24A VAL* 1.3 62.1 + - + +
26A ARG* 3.8 4.3 - - - +
27A ALA* 2.9 31.4 + - + +
40A LEU* 4.6 11.7 - - + -
47A PHE* 5.8 0.4 - - + -
70A ARG* 3.5 31.4 - - - +
92A MET* 6.2 0.2 - - + -
504A FMN 3.7 61.6 - - + +
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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
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20A LEU* 2.8 23.5 + - + +
21A ASP* 4.2 3.8 - - - +
23A LEU* 1.3 73.6 - - + +
25A HIS* 1.3 62.5 + - - +
27A ALA* 3.2 6.2 + - - +
28A SER* 2.8 28.1 + - - -
40A LEU* 4.1 20.4 - - + -
92A MET* 3.9 8.6 - - + +
93A ARG* 3.8 14.6 - - - +
94A ILE* 3.6 50.9 - - + +
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Residues in contact with HIS 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 3.1 19.5 + - - +
22A ALA* 4.2 3.8 - - - +
24A VAL* 1.3 79.5 - - - +
26A ARG* 1.3 62.1 + - + +
28A SER* 3.4 5.9 + - - -
29A SER* 3.0 38.4 + - - -
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Residues in contact with ARG 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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22A ALA 3.0 21.3 + - - +
23A LEU* 3.8 4.9 - - - +
25A HIS* 1.3 83.6 - - + +
27A ALA* 1.3 56.4 + - - +
29A SER* 3.6 6.4 + - - -
30A LYS* 3.1 30.7 + - + +
504A FMN 2.7 33.4 + - - +
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Residues in contact with ALA 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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23A LEU* 2.9 21.7 + - + +
24A VAL* 3.5 5.8 - - - +
25A HIS 3.2 0.2 - - - -
26A ARG* 1.3 75.2 - - - +
28A SER* 1.3 55.0 + - - +
30A LYS* 3.1 1.6 + - - -
31A ASN* 2.7 41.2 + - - +
92A MET* 3.9 11.4 - - + -
504A FMN 3.4 44.4 - - + +
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Residues in contact with SER 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 VAL* 2.8 20.8 + - - -
25A HIS* 3.8 6.7 - - - -
27A ALA* 1.3 72.5 - - - +
29A SER* 1.3 62.2 + - - +
30A LYS 3.4 0.2 + - - -
32A LEU* 3.4 27.0 + - - +
91A GLY* 3.5 8.5 + - - -
92A MET* 2.9 39.4 + - - +
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Residues in contact with SER 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 HIS* 3.0 29.3 + - - -
26A ARG* 3.7 8.5 - - - -
28A SER* 1.3 78.6 - - - +
30A LYS* 1.3 55.8 + - - +
33A PRO* 3.2 24.6 - - - +
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Residues in contact with LYS 30 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ARG* 3.1 17.7 + - + +
27A ALA 3.1 4.5 + - - +
29A SER* 1.3 78.3 - - - +
31A ASN* 1.3 64.0 + - - +
33A PRO* 3.5 8.5 - - - +
34A LEU* 3.5 33.2 - - + +
61A LEU* 5.2 2.3 - - - +
64A GLU* 3.1 27.5 + - - -
504A FMN 2.8 65.1 + - - +
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Residues in contact with ASN 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 ALA 2.7 22.7 + - - +
29A SER 3.5 0.2 - - - -
30A LYS* 1.3 75.0 - - - +
32A LEU* 1.3 58.9 + - - +
34A LEU* 3.1 9.4 + - - +
36A ILE* 2.8 61.9 + - + +
61A LEU* 3.9 8.0 - - - +
91A GLY* 3.0 26.1 + - - +
92A MET* 3.6 9.9 - - - +
504A FMN 2.7 45.2 + - - +
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Residues in contact with LEU 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 SER* 3.4 12.5 + - - +
31A ASN* 1.3 75.8 - - - +
33A PRO* 1.4 72.1 - - + +
35A GLY* 3.0 13.4 + - - -
36A ILE 3.8 1.6 - - - +
37A THR* 3.8 19.5 - - + -
89A GLY* 4.4 15.7 - - - +
90A THR 4.2 5.2 - - - +
91A GLY* 3.5 26.5 - - - +
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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