Contacts of the helix formed by residues 16 - 32 (chain A) in PDB entry 4D87
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 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A LEU 4.3 2.3 - - - +
15A THR* 1.3 80.1 + - - -
17A THR* 1.3 57.9 - - - +
18A GLU 1.9 23.3 + - - -
19A LYS* 2.1 34.9 + - + +
20A ARG* 2.9 8.6 + - + +
112A ASP* 5.4 8.3 - - - +
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Residues in contact with THR 17 (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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15A THR* 3.0 19.3 - - + +
16A ASP* 1.3 76.8 - - - +
18A GLU* 1.3 49.1 + - - +
20A ARG* 3.6 16.6 - - - +
21A ASP* 1.4 57.6 + - - +
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Residues in contact with GLU 18 (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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9A LYS* 2.9 26.6 + - - +
13A HIS 4.3 3.1 - - - +
14A LEU* 3.4 27.6 - - + +
15A THR* 1.9 54.9 + - + +
16A ASP 1.9 11.3 + - - -
17A THR* 1.3 73.5 + - - +
19A LYS* 1.3 59.9 + - - -
21A ASP* 3.4 7.4 - - + +
22A PHE* 3.2 21.8 + - - +
86A GLU 5.8 3.6 - - - +
87A VAL* 5.7 0.9 - - - +
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Residues in contact with LYS 19 (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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11A VAL* 4.2 21.8 + - - +
12A LEU* 5.3 3.2 - - - +
14A LEU* 3.9 22.3 + - + -
15A THR 3.6 10.8 - - - +
16A ASP* 2.1 35.7 + - + +
18A GLU* 1.3 66.6 - - - +
20A ARG* 1.3 59.8 + - - +
21A ASP 3.1 0.2 - - - -
22A PHE* 3.2 2.3 + - - +
23A VAL* 3.0 35.7 + - - +
107A GLN* 3.6 28.0 + - - +
110A SER* 4.8 1.3 + - - -
112A ASP* 4.4 18.4 - - - +
113A PHE* 3.3 42.2 - - + -
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Residues in contact with ARG 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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16A ASP* 2.9 8.4 + - + +
17A THR* 3.6 18.6 - - - +
19A LYS* 1.3 80.4 - - - +
21A ASP* 1.3 57.0 - - - +
23A VAL* 4.1 4.7 - - - -
24A ARG* 2.2 89.4 + - + +
112A ASP 5.2 4.3 - - - +
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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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17A THR* 1.4 55.6 + - - +
18A GLU* 3.2 8.7 + - + +
19A LYS 3.1 0.2 - - - -
20A ARG* 1.3 83.4 - - - +
22A PHE* 1.3 60.9 + - - +
24A ARG* 3.6 6.3 + - - +
25A THR* 3.0 27.4 + - - -
84A ASN* 4.7 10.7 - - - +
87A VAL* 3.8 17.1 - - + +
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Residues in contact with PHE 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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14A LEU* 5.3 1.1 - - + -
18A GLU 3.2 18.1 + - - +
19A LYS* 3.2 6.1 + - - +
21A ASP* 1.3 76.7 - - - +
23A VAL* 1.3 68.2 + - + +
25A THR* 3.4 2.6 + - - -
26A VAL* 3.2 43.6 + - + +
76A PHE* 5.3 3.8 - + - -
80A LEU* 3.9 19.6 - - + +
87A VAL* 3.9 16.5 - - + +
88A THR 3.4 19.5 - - - -
89A LEU* 4.0 6.7 - - + -
90A PRO* 2.9 38.4 - - + -
113A PHE* 5.1 7.2 - + + -
114A MET* 4.5 14.1 - - + -
225A PRO* 5.8 1.8 - - + -
228A PHE* 5.9 1.6 - - + -
229A LEU* 4.0 18.2 - - + -
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Residues in contact with VAL 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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19A LYS 3.0 20.9 + - - +
20A ARG* 4.5 4.3 - - - +
22A PHE* 1.3 76.8 - - + +
24A ARG* 1.3 69.9 + - - +
25A THR 3.2 1.0 + - - -
26A VAL* 3.7 5.6 + - - +
27A LEU* 3.1 26.1 + - + +
112A ASP 4.1 8.5 - - - +
113A PHE* 3.2 35.9 - - + +
114A MET* 4.6 7.9 - - + -
130A PRO* 3.4 34.8 - - + -
131A PHE* 4.2 9.0 - - + -
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Residues in contact with ARG 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 ARG* 2.2 81.5 - - + +
21A ASP* 3.8 8.7 - - - +
22A PHE 3.3 0.4 - - - -
23A VAL* 1.3 84.3 - - - +
25A THR* 1.3 62.0 + - - +
27A LEU* 4.0 15.3 - - - +
28A ILE* 3.7 22.2 + - - +
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Residues in contact with THR 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 3.0 16.2 + - - -
22A PHE* 3.4 5.9 + - - -
23A VAL 3.2 0.4 - - - -
24A ARG* 1.3 78.7 - - - +
26A VAL* 1.3 68.1 + - - +
27A LEU 3.0 1.6 - - - -
28A ILE* 2.9 7.4 + - - +
29A LEU* 2.9 24.2 + - + +
80A LEU* 3.1 42.2 - - + +
83A ILE* 4.4 20.4 - - + +
84A ASN* 4.0 17.5 + - + +
87A VAL* 4.2 5.2 - - + +
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Residues in contact with VAL 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 PHE* 3.2 43.8 + - + +
23A VAL* 4.0 6.7 - - - +
25A THR* 1.3 78.3 - - - +
27A LEU* 1.3 62.9 + - - +
29A LEU* 3.4 8.7 + - - +
30A LYS* 3.0 18.2 + - - +
35A TYR* 4.2 9.8 - - + -
76A PHE* 4.8 11.2 - - + -
80A LEU* 4.2 11.6 - - + +
114A MET* 5.8 0.4 - - + -
131A PHE* 4.1 14.4 - - + -
136A TRP* 3.7 29.8 - - + -
225A PRO* 4.6 10.1 - - + -
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Residues in contact with LEU 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 VAL* 3.1 20.2 + - + +
24A ARG* 4.0 16.8 - - - +
25A THR 3.0 0.4 - - - -
26A VAL* 1.3 76.4 - - - +
28A ILE* 1.3 51.8 + - - +
30A LYS* 2.5 29.3 + - + +
31A GLU* 2.5 21.2 + - + -
130A PRO* 4.3 9.4 - - + +
131A PHE* 3.7 29.4 - - + -
135A ARG 5.0 5.4 - - - +
136A TRP* 4.0 13.9 - - + -
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Residues in contact with ILE 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 ARG 3.8 12.3 - - - +
25A THR* 2.9 11.1 + - - +
27A LEU* 1.3 79.5 - - + +
29A LEU* 1.3 56.0 + - - +
31A GLU* 3.6 8.0 - - + +
32A LYS* 2.5 50.9 + - + +
83A ILE* 2.9 47.1 - - + -
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Residues in contact with LEU 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 THR 2.9 6.1 + - - +
26A VAL* 3.4 10.1 - - - +
28A ILE* 1.3 78.9 - - + +
30A LYS* 1.3 58.4 + - - +
32A LYS* 4.1 2.2 - - - -
33A GLY 3.5 0.5 + - - -
34A ILE* 2.8 39.6 + - + +
35A TYR* 2.8 28.5 + - + -
76A PHE* 4.1 22.0 - - + -
79A ASP* 4.1 12.8 - - + +
80A LEU* 2.7 47.3 - - + +
83A ILE* 3.3 33.0 - - + -
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Residues in contact with LYS 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 VAL 3.0 12.5 + - - +
27A LEU* 2.5 18.4 + - + +
29A LEU* 1.3 69.8 - - - +
31A GLU* 1.3 63.2 + - - +
33A GLY* 3.0 14.7 + - - -
35A TYR* 3.4 31.5 - - + +
36A ASP* 3.4 28.3 + - - +
39A ILE* 4.1 10.1 - - - +
136A TRP* 3.8 37.4 - - + +
137A THR* 3.3 41.2 + - + +
139A ILE* 5.1 1.4 - - - +
223A ASN* 4.9 0.4 + - - -
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Residues in contact with GLU 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 LEU* 2.5 18.1 + - + +
28A ILE* 3.6 9.6 - - - +
30A LYS* 1.3 70.1 - - - +
32A LYS* 1.3 69.8 + - - +
33A GLY* 2.8 10.9 + - - -
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Residues in contact with LYS 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 ILE* 2.5 53.6 + - + +
29A LEU* 3.9 1.8 - - - +
30A LYS 3.3 0.4 - - - -
31A GLU* 1.3 83.1 - - - +
33A GLY* 1.3 60.2 - - - +
34A ILE* 2.9 29.1 + - + +
83A ILE* 3.4 24.0 - - - -
258B PHE* 3.3 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