Contacts of the helix formed by residues 16 - 31 (chain N) in PDB entry 3BBX
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 HIS 16 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1273B U 5.3 2.5 - - - -
1274B A 4.1 19.1 + - - -
1275B A 1.3 121.4 - + + +
1296B G 4.6 4.2 + - - -
1297B C 5.8 0.6 - - - -
2710B C 4.1 19.8 + - - -
2711B A 6.0 2.9 - - - -
13N ASN* 2.9 19.9 + - + +
15N SER* 1.3 98.3 - - - +
17N ARG* 1.3 65.2 + - - +
18N GLN 2.9 5.3 + - - -
19N ALA 2.9 13.1 + - - +
20N MET* 3.3 8.4 - - + +
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Residues in contact with ARG 17 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8N ARG 4.1 10.8 + - - -
9N GLN* 3.0 34.1 - - - +
10N LEU* 2.6 46.0 + - + +
12N ARG* 3.4 31.6 + - - +
13N ASN 2.5 15.8 + - - +
14N SER* 3.3 33.0 + - - +
15N SER 3.7 0.4 - - - -
16N HIS* 1.3 71.0 - - - +
18N GLN* 1.3 63.6 + - - +
20N MET* 3.4 8.8 + - - +
21N PHE* 3.1 50.9 + - + +
43N GLU* 5.3 1.8 - - - -
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Residues in contact with GLN 18 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2690B U 5.8 2.7 - - - -
2709B G 3.6 21.2 + - - -
2710B C 5.4 1.6 + - - -
14N SER 4.4 12.6 - - - +
15N SER* 4.1 12.5 - - - +
16N HIS 2.9 2.5 + - - +
17N ARG* 1.3 77.4 - - + +
19N ALA* 1.3 51.3 + - - +
21N PHE* 3.6 2.5 - - - +
22N ARG* 2.7 47.8 + - - +
69N ARG* 4.8 18.1 + - - +
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Residues in contact with ALA 19 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1275B A 3.2 33.9 - - + +
1276B A 5.1 0.9 - - - +
1295B C 3.9 11.9 - - - +
16N HIS* 2.9 13.2 + - - +
18N GLN* 1.3 70.2 - - - +
20N MET* 1.3 54.6 + - - +
21N PHE 2.5 16.0 + - - -
22N ARG* 2.8 21.8 + - + +
23N ASN* 3.1 27.7 + - - +
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Residues in contact with MET 20 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1275B A 1.9 52.9 - - + +
1276B A 2.3 70.4 + - - +
1277B G 3.0 22.5 - - - +
12N ARG* 3.2 53.7 + - - +
16N HIS 3.3 18.3 + - - +
17N ARG* 3.9 4.0 - - - +
19N ALA* 1.3 68.5 - - - +
21N PHE* 1.3 67.0 + - + +
24N MET* 4.2 1.6 - - - +
40N LYS* 5.6 1.4 - - - +
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Residues in contact with PHE 21 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10N LEU* 3.9 25.6 - - + -
12N ARG* 6.4 0.9 - - - -
17N ARG* 3.1 36.7 + - + +
18N GLN* 3.6 2.9 - - - +
19N ALA 2.5 10.9 + - - -
20N MET* 1.3 83.1 - - + +
22N ARG* 1.3 57.6 + - - +
23N ASN 3.6 0.4 - - - -
24N MET* 3.4 33.3 - - + +
25N ALA* 3.1 25.8 + - - +
40N LYS* 3.5 17.9 - - + -
43N GLU* 3.4 42.4 - - + -
44N LEU* 4.2 9.3 - - + +
47N VAL* 4.0 20.7 - - + +
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Residues in contact with ARG 22 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1295B C 4.9 16.4 + - - -
2708B G 4.4 24.9 + - - -
2709B G 5.0 7.4 + - - -
18N GLN* 2.7 33.3 + - - +
19N ALA* 2.8 18.4 + - - +
21N PHE* 1.3 69.9 - - - +
23N ASN* 1.3 85.3 + - - +
24N MET 3.1 1.6 - - - -
25N ALA* 2.8 17.4 + - - +
26N GLY* 2.8 12.6 + - - -
47N VAL* 5.6 1.1 - - - -
65N LEU* 5.1 2.0 - - - +
68N ALA* 2.6 30.9 + - - +
69N ARG* 2.8 78.0 - - - +
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Residues in contact with ASN 23 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1276B A 2.5 39.3 + - - -
1277B G 2.5 42.7 + - + +
1294B U 3.2 18.7 + - - +
1295B C 3.3 14.7 - - - +
19N ALA* 3.1 25.0 + - - +
22N ARG* 1.3 85.9 - - - +
24N MET* 1.3 60.6 + - - +
26N GLY* 3.1 10.3 + - - +
27N SER* 3.2 10.4 + - - -
69N ARG 5.5 1.9 - - - +
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Residues in contact with MET 24 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1277B G 1.5 61.9 + - - +
1278B C 3.5 8.6 - - - +
20N MET 4.2 2.2 - - - +
21N PHE* 3.4 28.0 - - + +
22N ARG 3.1 0.2 - - - -
23N ASN* 1.3 72.3 - - - +
25N ALA* 1.3 58.6 + - - +
27N SER* 3.2 12.0 + - - -
28N LEU* 3.0 18.4 - - - +
34N ILE* 5.1 0.2 - - + -
36N THR* 3.5 22.2 - - + -
40N LYS* 3.3 40.2 - - + +
44N LEU* 3.4 28.0 - - + -
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Residues in contact with ALA 25 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21N PHE 3.1 18.2 + - - +
22N ARG* 2.8 13.5 + - - +
24N MET* 1.3 72.9 - - - +
26N GLY* 1.3 60.1 + - - +
27N SER 3.0 4.7 - - - -
28N LEU* 3.1 26.4 + - - +
29N VAL* 4.0 5.2 + - - +
44N LEU* 3.9 2.9 - - - -
47N VAL* 3.3 28.7 - - + +
48N VAL* 3.8 14.1 - - + +
51N LEU* 6.0 4.5 - - + -
69N ARG* 6.2 1.3 - - - -
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Residues in contact with GLY 26 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22N ARG 2.8 12.5 + - - -
23N ASN* 3.1 5.1 + - - -
25N ALA* 1.3 75.5 - - - +
27N SER* 1.3 59.8 + - - +
29N VAL 4.1 0.9 - - - -
30N ARG* 3.3 16.2 + - - +
69N ARG 6.0 1.6 - - - -
75N ILE* 3.2 41.3 - - - +
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Residues in contact with SER 27 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1278B C 2.1 74.4 + - - -
23N ASN 3.2 4.8 + - - -
24N MET 3.2 8.9 + - - -
25N ALA 3.0 0.6 - - - -
26N GLY* 1.3 76.1 - - - +
28N LEU* 1.3 56.5 + - - +
29N VAL 3.0 1.6 - - - -
30N ARG* 2.7 8.7 + - - +
31N HIS* 2.6 34.3 + - - +
34N ILE* 3.2 4.9 - - - +
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Residues in contact with LEU 28 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24N MET 3.0 29.4 - - - +
25N ALA* 3.1 21.3 - - - +
27N SER* 1.3 77.3 + - - +
29N VAL* 1.3 55.8 + - - +
31N HIS 2.6 31.2 - - - +
32N GLU* 3.4 8.0 + - - +
34N ILE* 3.5 20.2 - - + -
44N LEU* 3.5 19.1 - - + -
48N VAL* 3.8 28.7 - - + -
95N THR* 3.9 9.9 - - + -
113N ILE* 3.4 32.3 - - + -
114N GLU 4.8 1.1 - - - +
115N LEU* 3.9 14.5 - - + +
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Residues in contact with VAL 29 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25N ALA 4.1 11.0 - - - +
26N GLY 3.8 0.2 - - - +
27N SER 3.0 0.6 - - - -
28N LEU* 1.3 75.2 - - - +
30N ARG* 1.3 65.9 + - - +
31N HIS 3.8 3.7 - - - +
48N VAL* 4.7 10.5 - - + -
52N ILE* 4.9 0.7 - - + -
75N ILE* 3.3 44.0 - - + +
78N LYS* 3.4 36.9 - - + +
79N LEU* 4.0 9.9 - - + -
83N LEU* 3.4 34.8 - - + +
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Residues in contact with ARG 30 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1277B G 5.2 4.4 - - - +
1278B C 4.6 12.5 + - - -
1279B G 5.6 0.2 - - - -
1292B G 5.2 5.4 - - - +
1293B C 4.3 22.5 + - - -
1294B U 5.6 2.0 + - - -
26N GLY 3.3 13.4 + - - +
27N SER* 2.7 11.9 + - - +
29N VAL* 1.3 77.6 - - - +
31N HIS* 1.3 89.4 + - + +
70N THR* 4.9 7.9 + - - -
72N ASP* 5.8 0.4 - - - +
74N GLU* 2.7 43.5 + - - +
75N ILE* 4.7 12.7 - - + +
78N LYS* 5.4 7.7 - - - +
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Residues in contact with HIS 31 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1278B C 3.1 10.0 + - - -
1279B G 1.4 111.9 + - + +
27N SER* 2.6 13.5 + - - +
28N LEU* 2.6 16.3 - - - +
29N VAL 3.8 3.6 - - - +
30N ARG* 1.3 108.0 - - + +
32N GLU* 1.3 64.9 + - - +
33N ILE* 4.5 6.7 - - + +
34N ILE* 5.3 0.2 - - + -
115N LEU* 4.3 2.1 - - - +
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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