Contacts of the helix formed by residues 38 - 56 (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 LEU 38 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2817A U 5.1 2.5 - - - +
36O THR 3.7 2.0 + - - -
37O THR* 1.3 69.8 - - - +
39O PRO* 1.3 65.6 - - + +
41O ALA* 3.3 3.4 + - - +
42O LYS* 2.9 48.5 + - + +
97O ILE* 4.2 12.1 - - + -
99O LYS* 3.5 30.7 - - + -
109O PRO* 3.0 31.9 + - + +
110O MET* 4.2 8.7 - - - +
111O ALA* 3.6 22.0 - - + -
42b HIS* 5.9 2.7 - - + -
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Residues in contact with PRO 39 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1650A A 5.4 1.8 - - - +
1651A G 3.6 37.9 - - - +
1652A A 4.0 16.8 - - - +
8O ARG* 4.0 16.2 + - - +
10O LEU* 4.5 4.0 - - + -
37O THR* 3.3 15.7 - - - +
38O LEU* 1.3 90.7 - - + +
40O LYS* 1.3 64.3 + - - +
42O LYS* 3.2 6.9 + - + +
43O GLU* 2.9 27.8 + - - +
109O PRO* 4.8 4.7 - - + +
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Residues in contact with LYS 40 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1277A G 3.9 28.2 + - - -
1278A C 5.1 0.4 - - - +
1650A A 3.7 25.7 + - - -
1651A G 3.3 30.4 + - - +
10O LEU* 4.8 10.0 - - + +
12O ARG* 4.1 18.1 - - - +
20O MET* 4.3 12.3 - - + -
21O PHE* 3.9 8.8 - - + -
24O MET* 3.5 27.1 - - + +
36O THR* 3.9 5.8 - - - +
37O THR* 2.9 31.6 + - + +
39O PRO* 1.3 78.1 - - - +
41O ALA* 1.3 57.4 + - - +
43O GLU* 3.4 7.8 + - - +
44O LEU* 3.0 26.0 + - - +
103O ARG* 5.0 0.2 - - - +
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Residues in contact with ALA 41 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36O THR* 3.6 26.2 - - + +
37O THR 2.9 8.6 + - - +
38O LEU* 3.4 13.5 - - - +
40O LYS* 1.3 72.6 - - - +
42O LYS* 1.3 59.2 + - - +
43O GLU 3.0 1.3 - - - -
44O LEU* 2.7 32.4 + - - +
45O ARG 3.4 3.3 + - - -
97O ILE* 4.0 14.8 - - + +
111O ALA* 4.5 9.6 - - + -
113O ILE* 3.7 14.8 - - + +
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Residues in contact with LYS 42 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2817A U 3.1 30.9 + - - -
2818A U 2.6 37.5 + - - +
8O ARG* 3.6 29.4 - - - +
38O LEU* 2.9 39.6 + - + +
39O PRO* 3.2 2.7 + - + +
41O ALA* 1.3 72.7 - - - +
43O GLU* 1.3 61.7 + - - +
45O ARG* 3.3 37.7 + - - +
46O ARG* 4.2 7.3 - - - +
97O ILE* 3.9 17.9 - - + +
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Residues in contact with GLU 43 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7O GLY* 3.7 10.6 + - - -
8O ARG* 3.1 62.3 + - + +
10O LEU* 4.2 4.3 - - + -
21O PHE* 3.6 27.9 - - + -
39O PRO 2.9 12.6 + - - +
40O LYS* 3.5 5.6 - - - +
42O LYS* 1.3 71.8 - - - +
44O LEU* 1.3 67.1 + - - +
45O ARG 3.1 2.4 + - - -
46O ARG* 3.5 32.2 + - - +
47O VAL* 3.8 13.0 + - - +
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Residues in contact with LEU 44 (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* 3.9 30.7 - - + +
24O MET* 3.7 43.5 - - + +
25O ALA* 4.0 3.8 - - + +
28O LEU* 3.8 30.1 - - + -
34O ILE* 4.5 9.2 - - + -
36O THR* 6.1 0.2 - - + -
40O LYS 3.0 11.3 + - - +
41O ALA* 2.7 22.0 + - - +
43O GLU* 1.3 72.8 - - - +
45O ARG* 1.3 60.8 + - - +
47O VAL* 3.1 8.2 + - + +
48O VAL* 2.9 32.5 + - + +
113O ILE* 4.6 7.4 - - + -
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Residues in contact with ARG 45 (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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2817A U 5.7 0.2 + - - -
2818A U 3.5 22.6 + - - -
2837A A 5.2 5.5 + - - -
2838A G 3.9 38.1 + - - +
2839A G 4.9 0.4 - - - +
2881A U 4.6 15.6 + - - -
2882A A 5.4 7.5 + - - -
8O ARG* 5.6 0.2 - - - +
41O ALA 3.4 0.4 + - - +
42O LYS* 3.3 38.9 + - - +
43O GLU 3.1 0.8 - - - -
44O LEU* 1.3 77.6 - - - +
46O ARG* 1.3 58.9 + - + +
47O VAL 2.9 6.1 + - - -
48O VAL* 5.0 2.2 - - - -
49O GLU* 3.0 42.1 + - - +
95O THR* 3.3 29.6 - - - +
97O ILE* 4.1 17.3 - - - +
113O ILE* 4.0 14.4 - - + -
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Residues in contact with ARG 46 (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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2690A U 4.5 7.5 + - - -
2838A G 3.6 35.2 + - - +
2839A G 3.3 36.9 + - - +
2872A A 4.3 14.5 + - - -
2873A A 4.2 14.5 + - - -
6O SER* 4.1 19.1 + - - -
7O GLY* 3.9 22.0 - - - +
42O LYS 4.2 10.1 - - - +
43O GLU* 3.5 30.1 + - - +
44O LEU 3.4 0.4 - - - -
45O ARG* 1.3 72.6 - - - +
47O VAL* 1.3 59.6 + - + +
50O PRO* 3.4 17.2 - - - +
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Residues in contact with VAL 47 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21O PHE* 4.1 35.7 - - + +
22O ARG* 5.5 1.6 - - - +
25O ALA* 4.4 17.0 - - + -
43O GLU* 3.8 13.7 - - - +
44O LEU* 3.1 8.9 + - + +
45O ARG 2.9 1.2 + - - -
46O ARG* 1.3 81.8 - - + +
48O VAL* 1.3 68.9 + - - +
49O GLU 3.4 0.2 - - - -
50O PRO* 3.1 14.0 - - - +
51O LEU* 3.5 19.1 - - + +
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Residues in contact with VAL 48 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25O ALA* 3.8 29.8 - - + +
28O LEU* 3.9 15.5 - - + -
29O VAL* 5.4 8.1 - - + -
44O LEU* 2.9 38.2 + - + +
45O ARG* 4.4 1.3 - - - +
47O VAL* 1.3 73.8 - - - +
49O GLU* 1.3 68.7 + - - +
51O LEU* 2.9 24.0 + - + +
52O ILE* 3.4 21.4 + - + +
95O THR* 4.0 24.5 - - + -
115O LEU* 4.9 2.9 - - + -
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Residues in contact with GLU 49 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2838A G 4.5 4.5 + - - +
2839A G 2.8 44.7 + - - +
2840A C 4.5 0.4 - - - -
2881A U 5.9 0.2 - - - -
45O ARG* 3.0 27.3 + - - +
48O VAL* 1.3 77.2 - - - +
50O PRO* 1.4 63.3 - - + +
52O ILE* 3.2 6.2 + - - +
53O THR* 2.7 32.0 + - - -
93O GLY* 3.7 6.8 + - - -
94O TYR* 3.8 33.8 + - + +
95O THR* 2.8 37.9 + - + +
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Residues in contact with PRO 50 (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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2839A G 4.5 8.3 - - - +
2840A C 3.8 10.1 - - - +
45O ARG 3.7 2.5 - - - +
46O ARG* 3.4 22.9 - - - +
47O VAL* 3.1 16.2 - - - +
49O GLU* 1.4 92.5 - - + +
51O LEU* 1.3 66.6 + - + +
53O THR* 3.2 10.3 + - - +
54O LEU* 2.9 23.1 + - - +
69O ARG* 6.2 1.6 - - - +
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Residues in contact with LEU 51 (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* 4.6 14.6 - - + -
29O VAL* 5.6 5.4 - - + -
47O VAL* 3.5 22.2 - - + +
48O VAL* 2.9 15.8 + - + +
50O PRO* 1.3 75.5 - - + +
52O ILE* 1.3 64.4 + - + +
54O LEU* 3.1 15.4 + - + +
55O ALA* 2.9 22.5 + - - +
66O ALA* 5.3 4.2 - - + +
69O ARG* 3.8 37.9 - - + +
70O THR* 3.7 27.1 - - + -
79O LEU* 3.7 22.2 - - + +
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Residues in contact with ILE 52 (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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29O VAL* 6.4 1.3 - - + -
48O VAL* 4.0 18.8 - - + +
49O GLU 3.2 7.5 + - - +
51O LEU* 1.3 74.0 - - + +
53O THR* 1.3 66.4 + - - +
55O ALA* 3.0 3.8 + - - +
56O LYS* 3.0 24.2 + - + +
79O LEU* 4.0 22.0 - - + -
83O LEU* 4.6 13.0 - - + +
84O GLY* 5.3 0.5 - - - -
87O PHE* 4.0 42.2 - - + -
94O TYR* 3.6 36.8 - - + -
115O LEU* 4.3 15.3 - - + -
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Residues in contact with THR 53 (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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2840A C 2.7 44.4 + - - +
2841A C 3.4 26.5 - - - +
49O GLU 2.7 20.4 + - - -
50O PRO 3.2 6.2 + - - -
52O ILE* 1.3 78.0 - - - +
54O LEU* 1.3 64.1 + - - +
56O LYS* 3.1 35.2 + - - +
57O THR* 4.1 3.8 + - - -
94O TYR* 4.1 3.1 - - - -
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Residues in contact with LEU 54 (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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2870A C 6.1 0.9 - - - +
50O PRO 2.9 12.4 + - - +
51O LEU* 3.1 14.8 - - + +
53O THR* 1.3 77.0 - - - +
55O ALA* 1.3 56.5 + - - +
57O THR* 2.8 29.3 + - - +
62O ASN* 3.3 39.9 - - + +
65O LEU* 4.1 22.2 - - + -
66O ALA* 3.8 38.8 - - + +
69O ARG* 4.4 9.9 - - - +
80O PHE* 4.5 1.6 - - + -
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Residues in contact with ALA 55 (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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51O LEU 2.9 14.9 + - - +
52O ILE 3.0 4.4 + - - +
54O LEU* 1.3 72.5 - - - +
56O LYS* 1.3 64.9 + - - +
57O THR 3.0 3.5 + - - +
58O ASP* 5.2 1.4 - - - +
79O LEU* 3.7 32.5 - - + +
80O PHE* 3.4 41.6 - - + +
84O GLY* 3.6 14.6 - - - -
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Residues in contact with LYS 56 (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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2840A C 4.6 7.1 + - - -
2841A C 4.9 2.2 + - - -
52O ILE* 3.0 15.2 + - + +
53O THR* 3.1 32.4 + - - +
55O ALA* 1.3 78.8 - - - +
57O THR* 1.3 60.0 + - - +
58O ASP* 4.3 1.0 + - - +
84O GLY 3.9 19.2 - - - +
87O PHE 3.3 25.1 - - - +
88O ALA* 3.7 16.7 + - - +
90O ARG 3.9 6.9 + - - -
91O ALA* 4.2 8.9 - - - +
94O TYR* 2.8 28.9 + - + -
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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