Contacts of the helix formed by residues 13 - 31 (chain O) in PDB entry 5GAG
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 ASN 13 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1273A U 5.4 3.8 + - - -
1275A A 4.9 12.2 + - - +
2001A C 5.1 2.9 - - - +
2002A G 3.5 38.1 + - - +
2003A A 5.1 0.2 + - - -
12O ARG* 1.3 77.5 - - - +
14O SER* 1.3 69.7 + - - +
15O SER* 3.6 7.6 + - - -
16O HIS* 3.3 21.7 + - - +
17O ARG* 3.2 15.7 + - - +
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Residues in contact with SER 14 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2001A C 4.9 1.9 + - - -
2002A G 3.7 2.0 + - - -
2689A U 3.8 22.7 + - - -
2690A U 3.1 25.8 + - - -
13O ASN* 1.3 75.3 - - - +
15O SER* 1.3 66.2 + - - +
17O ARG* 3.0 27.0 + - - +
18O GLN* 3.0 26.3 + - - +
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Residues in contact with SER 15 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1275A A 3.6 12.3 + - - -
2710A C 3.5 25.2 + - - -
3064A MG 4.7 10.5 - - - -
13O ASN* 3.6 9.6 + - - -
14O SER* 1.3 77.6 - - - +
16O HIS* 1.3 76.4 + - - +
18O GLN* 3.0 13.7 + - - +
19O ALA* 2.9 24.3 + - - +
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Residues in contact with HIS 16 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1275A A 3.2 61.6 + + + +
1276A A 2.8 33.0 + - - -
12O ARG* 2.9 50.1 + - + +
13O ASN* 3.3 20.6 + - - +
14O SER 3.3 0.2 - - - -
15O SER* 1.3 84.8 + - - +
17O ARG* 1.3 63.2 + - - +
19O ALA* 3.9 0.7 - - - +
20O MET* 2.9 26.7 + - + +
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Residues in contact with ARG 17 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2002A G 2.5 26.8 + - - -
2689A U 5.3 0.8 + - - -
8O ARG 3.4 18.3 + - - -
9O GLN* 2.7 47.0 + - - +
10O LEU* 4.2 11.2 - - + -
12O ARG* 3.1 23.3 + - + +
13O ASN 3.2 3.8 + - - +
14O SER* 3.0 32.6 + - - +
16O HIS* 1.3 77.7 + - - +
18O GLN* 1.3 65.8 + - - +
20O MET* 3.1 6.6 + - - +
21O PHE* 3.0 48.4 + - + -
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Residues in contact with GLN 18 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2690A U 4.0 17.7 + - - +
2691A C 5.3 4.3 + - - -
2709A G 3.3 25.1 + - - -
2710A C 5.9 0.2 + - - -
14O SER* 3.0 14.0 + - - +
15O SER* 3.2 14.1 + - - +
17O ARG* 1.3 79.1 - - - +
19O ALA* 1.3 63.3 + - - +
21O PHE* 3.3 5.6 + - - +
22O ARG* 3.0 36.6 + - - +
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Residues in contact with ALA 19 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1275A A 4.1 11.2 - - - +
1295A C 3.7 29.8 - - - +
1296A G 5.6 0.7 - - - +
2709A G 6.4 2.7 - - - -
15O SER 2.9 12.0 + - - +
16O HIS 4.1 2.5 - - - +
18O GLN* 1.3 78.7 - - - +
20O MET* 1.3 63.8 + - - +
22O ARG* 3.1 18.2 + - - +
23O ASN* 2.9 28.8 + - - +
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Residues in contact with MET 20 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1275A A 5.9 0.9 - - - -
1276A A 3.7 16.8 - - - +
1277A G 4.0 22.5 + - - +
10O LEU* 4.6 3.4 - - + -
12O ARG* 3.0 47.1 - - - +
16O HIS* 2.9 19.9 + - + +
17O ARG* 3.3 4.7 - - - +
19O ALA* 1.3 75.6 - - - +
21O PHE* 1.3 93.3 + - + +
23O ASN* 3.1 12.3 + - - +
24O MET* 2.9 31.1 + - + +
40O LYS* 4.3 20.4 - - + -
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Residues in contact with PHE 21 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10O LEU* 3.4 26.5 - - + -
17O ARG* 3.0 32.6 + - + +
18O GLN* 3.9 4.9 - - - +
20O MET* 1.3 98.1 - - + +
22O ARG* 1.3 67.1 + - - +
24O MET* 3.8 6.0 - - - +
25O ALA* 2.9 27.4 + - - +
40O LYS 3.9 18.6 - - - -
43O GLU* 3.6 25.6 - - + -
44O LEU* 3.9 16.7 - - + +
47O VAL* 4.1 30.1 - - + -
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Residues in contact with ARG 22 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1295A C 6.4 2.0 - - - -
2708A G 3.2 34.2 + - - -
2709A G 3.6 24.2 + - - -
18O GLN* 3.0 33.1 + - - +
19O ALA* 3.1 18.2 + - - +
21O PHE* 1.3 76.2 - - - +
23O ASN* 1.3 65.7 + - - +
25O ALA* 3.6 5.6 - - - +
26O GLY* 3.0 18.0 + - - -
47O VAL* 5.7 1.8 - - - -
68O ALA 4.6 5.2 + - - -
69O ARG* 3.2 22.8 + - - +
70O THR* 3.2 35.5 - - - +
71O ARG* 3.7 11.0 - - - +
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Residues in contact with ASN 23 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1275A A 5.9 0.8 - - - -
1276A A 4.5 9.1 + - - -
1277A G 4.4 22.1 + - - +
1294A U 3.0 40.6 + - - +
1295A C 3.7 27.1 + - - +
19O ALA 2.9 24.9 + - - -
20O MET* 3.4 8.7 - - - +
22O ARG* 1.3 75.4 - - - +
24O MET* 1.3 59.6 + - - +
26O GLY* 2.6 25.3 + - - -
27O SER* 2.9 12.5 + - - -
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Residues in contact with MET 24 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1277A G 3.2 44.4 + - - +
1278A C 3.8 7.2 - - - +
20O MET* 2.9 21.6 + - + +
21O PHE* 4.2 17.9 - - - -
23O ASN* 1.3 72.6 - - - +
25O ALA* 1.3 56.1 + - - +
27O SER* 3.3 9.1 + - - -
28O LEU* 2.9 29.1 + - - +
34O ILE* 4.1 6.4 - - + +
36O THR* 3.1 32.1 - - - +
40O LYS* 3.5 35.2 - - + +
44O LEU* 3.7 24.5 - - + +
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Residues in contact with ALA 25 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21O PHE 2.9 18.6 + - - +
22O ARG* 3.6 5.8 - - - +
24O MET* 1.3 74.1 - - - +
26O GLY* 1.3 65.0 + - - +
28O LEU* 3.8 1.1 - - - +
29O VAL* 2.9 31.8 + - + +
44O LEU* 4.0 2.4 - - + +
47O VAL* 4.4 13.5 - - + -
48O VAL* 3.8 27.4 - - + -
51O LEU* 4.6 13.5 - - + -
70O THR* 5.7 3.4 - - + -
75O ILE* 5.8 0.2 - - - -
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Residues in contact with GLY 26 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22O ARG 3.0 10.6 + - - -
23O ASN* 2.6 15.7 + - - -
25O ALA* 1.3 71.7 - - - +
27O SER* 1.3 60.3 + - - -
29O VAL* 3.3 3.4 + - - +
30O ARG* 3.0 32.5 + - - +
70O THR* 5.9 2.8 - - - +
75O ILE* 3.8 23.4 - - - +
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Residues in contact with SER 27 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1277A G 4.6 4.9 + - - -
1278A C 2.5 51.7 + - - -
23O ASN 2.9 9.6 + - - -
24O MET* 3.4 9.6 - - - -
26O GLY* 1.3 75.1 - - - +
28O LEU* 1.3 58.9 + - - +
30O ARG* 3.0 9.9 + - - +
31O HIS* 2.9 42.4 + - - +
34O ILE* 4.3 6.3 - - - -
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Residues in contact with LEU 28 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24O MET 2.9 19.2 + - - +
25O ALA* 3.3 4.0 + - - +
27O SER* 1.3 73.5 - - - +
29O VAL* 1.3 60.5 + - - +
32O GLU* 3.2 39.3 - - - +
33O ILE* 4.1 1.8 - - - +
34O ILE* 4.1 14.8 - - + +
44O LEU* 3.8 22.2 - - + -
48O VAL* 3.9 16.8 - - + -
95O THR* 4.2 20.4 - - + -
113O ILE* 3.8 30.7 - - + +
114O GLU* 3.9 5.6 - - - -
115O LEU* 3.8 13.8 - - + +
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Residues in contact with VAL 29 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25O ALA* 2.9 26.8 + - + +
26O GLY 3.6 3.8 - - - +
28O LEU* 1.3 81.5 - - - +
30O ARG* 1.3 63.1 + - - +
32O GLU* 3.8 4.9 - - - +
48O VAL* 5.4 9.6 - - + -
51O LEU* 5.6 4.7 - - + -
52O ILE* 6.4 1.3 - - + -
75O ILE* 4.0 39.9 - - + +
78O LYS* 3.3 30.8 + - + -
79O LEU* 4.5 12.3 - - + -
83O LEU* 4.0 26.9 - - + +
115O LEU* 5.1 0.4 - - - -
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Residues in contact with ARG 30 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1293A C 3.7 23.9 + - - -
26O GLY 3.0 26.2 + - - +
27O SER* 3.0 6.8 + - - +
29O VAL* 1.3 77.2 - - - +
31O HIS* 1.3 92.0 + - + +
32O GLU* 3.9 0.7 - - - +
72O ASP* 4.1 7.7 + - - -
74O GLU* 3.1 40.1 + - - +
75O ILE* 3.9 12.5 - - + +
78O LYS* 3.1 26.8 + - + +
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Residues in contact with HIS 31 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1278A C 3.6 19.0 + - - -
1279A G 3.5 48.0 + - - -
1292A G 5.8 1.6 - - - -
27O SER* 2.9 26.9 + - - +
30O ARG* 1.3 105.8 - - + +
32O GLU* 1.3 64.9 + - - +
33O ILE* 2.9 28.8 + - - +
34O ILE* 5.0 1.1 - - + +
118O ARG* 4.7 1.0 - - - +
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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
------------------------------------------------------------
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