Contacts of the helix formed by residues 12 - 30 (chain A) in PDB entry 2FC3
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 PRO 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A GLU 4.4 0.7 - - - +
11A VAL* 1.3 89.6 - - + +
13A GLU* 1.3 67.7 + - - +
14A ASP* 3.3 13.7 - - - +
15A LEU* 3.0 27.5 + - + -
16A ALA 3.1 10.0 + - - -
117A LYS* 4.8 10.3 - - - -
121A LEU* 3.7 31.6 - - + -
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Residues in contact with GLU 13 (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 3.6 2.5 + - - -
12A PRO* 1.3 71.6 - - - +
14A ASP* 1.3 63.4 + - - +
16A ALA* 3.2 10.3 + - + +
17A GLU* 3.1 35.3 + - + +
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Residues in contact with ASP 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PRO* 3.8 16.6 - - - +
13A GLU* 1.3 76.8 + - - +
15A LEU* 1.3 68.4 + - - +
17A GLU* 3.4 11.0 + - + +
18A LYS* 3.1 28.4 + - - +
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Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 4.1 10.8 - - + -
12A PRO* 3.0 19.1 + - + +
14A ASP* 1.3 81.4 + - - +
16A ALA* 1.3 66.4 + - - +
18A LYS* 3.1 17.8 + - + +
19A ALA* 2.9 21.8 + - - +
78A VAL* 4.4 5.8 - - + -
113A GLU 4.8 0.4 - - - +
114A ILE* 4.0 25.1 - - + +
117A LYS* 3.7 39.5 - - + -
118A VAL* 4.0 16.2 - - + -
121A LEU* 3.7 25.4 - - + -
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Residues in contact with ALA 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 3.9 14.8 - - + +
12A PRO 3.1 11.3 + - - +
13A GLU* 3.5 13.2 - - + +
15A LEU* 1.3 75.5 - - - +
17A GLU* 1.3 58.3 + - + +
19A ALA* 3.1 10.1 + - - +
20A TYR* 3.0 34.7 + - + -
79A TYR 4.3 4.0 - - - +
80A VAL* 3.7 3.8 - - + +
81A PRO* 3.8 29.8 - - + -
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Residues in contact with GLU 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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13A GLU* 3.1 29.9 + - + +
14A ASP* 3.5 12.8 - - - +
15A LEU 3.1 0.2 - - - -
16A ALA* 1.3 73.8 - - + +
18A LYS* 1.3 65.0 + - + +
20A TYR* 3.3 7.6 + - - +
21A GLU* 3.0 23.0 + - - +
85A ARG* 2.8 45.1 + - - -
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Residues in contact with LYS 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASP* 3.1 19.8 + - - +
15A LEU* 3.1 23.6 + - + +
17A GLU* 1.3 76.4 - - + +
19A ALA* 1.3 53.5 + - - +
21A GLU* 3.3 4.7 + - - +
22A ALA* 2.8 35.0 + - - +
110A LEU* 4.1 21.7 - - + +
113A GLU* 2.8 44.5 + - + +
114A ILE* 3.7 14.0 - - + +
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Residues in contact with ALA 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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15A LEU 2.9 12.5 + - - +
16A ALA* 3.1 10.3 + - - +
18A LYS* 1.3 73.6 - - - +
20A TYR* 1.3 66.9 + - - +
22A ALA* 3.3 2.0 + - - +
23A VAL* 3.0 30.0 + - - +
52A VAL* 4.4 5.6 - - + +
78A VAL* 4.0 25.1 - - + -
80A VAL* 3.6 20.2 - - + -
114A ILE* 3.6 13.2 - - + +
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Residues in contact with TYR 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 ALA* 3.0 30.7 + - + -
17A GLU* 3.3 8.9 + - - +
19A ALA* 1.3 76.4 - - - +
21A GLU* 1.3 57.4 + - - +
23A VAL* 3.3 1.9 + - - -
24A LYS* 3.0 25.5 + - - +
80A VAL* 3.6 26.5 - - + -
81A PRO* 3.4 13.8 - - + +
82A SER* 3.1 33.8 + - - -
85A ARG* 3.4 72.4 + - + +
86A LEU* 3.7 15.7 - - + -
89A ALA* 3.4 17.2 - - + +
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Residues in contact with GLU 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 GLU 3.0 17.0 + - - +
18A LYS* 3.7 6.1 - - - +
20A TYR* 1.3 76.7 - - - +
22A ALA* 1.3 56.1 + - - +
24A LYS* 3.3 25.2 + - - +
25A ARG* 2.8 73.8 + - - +
110A LEU* 3.6 20.4 - - + -
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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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18A LYS 2.8 20.9 + - - +
19A ALA 3.7 4.5 - - - +
21A GLU* 1.3 69.9 - - - +
23A VAL* 1.3 60.5 + - - +
26A ALA* 2.9 31.9 + - - +
50A LEU* 5.1 0.4 - - + -
101A ILE* 3.9 16.3 - - + +
107A ALA* 3.4 6.8 - - + +
110A LEU* 3.7 19.9 - - + +
111A VAL* 4.2 7.6 - - + -
114A ILE* 3.7 19.3 - - + -
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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 ALA 3.0 17.8 + - - +
20A TYR 3.6 7.6 - - - +
22A ALA* 1.3 77.6 - - - +
24A LYS* 1.3 57.3 + - - +
26A ALA* 3.9 1.2 - - - +
27A ARG* 2.8 29.1 + - - +
32A ILE* 4.2 4.0 - - + +
52A VAL* 3.7 25.4 - - + -
86A LEU* 4.0 13.9 - - + -
89A ALA* 3.7 26.0 - - + +
90A ALA* 3.9 12.1 - - + +
99A VAL* 4.0 26.5 - - + -
101A ILE* 4.3 10.3 - - + -
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Residues in contact with LYS 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 TYR 3.0 14.0 + - - +
21A GLU* 3.6 31.7 + - - +
23A VAL* 1.3 76.7 - - - +
25A ARG* 1.3 59.2 + - - +
27A ARG* 3.2 15.4 + - - +
28A GLU* 2.8 69.4 + - - +
89A ALA* 3.3 21.0 + - + +
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Residues in contact with ARG 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 GLU* 2.8 54.0 + - - +
24A LYS* 1.3 75.2 - - + +
26A ALA* 1.3 53.4 + - - +
28A GLU* 3.3 11.6 + - - +
29A THR* 2.6 40.9 + - + +
106A ASP* 4.0 29.5 + - + +
107A ALA* 3.8 16.4 - - + +
110A LEU* 4.0 17.6 - - - +
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Residues in contact with ALA 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 2.9 19.3 + - - +
23A VAL 3.9 0.4 - - - +
25A ARG* 1.3 77.0 - - - +
27A ARG* 1.3 58.6 + - - +
30A GLY* 2.7 36.1 + - - +
31A ARG 3.3 0.7 + - - -
32A ILE* 3.7 18.6 - - + -
101A ILE* 3.8 22.4 - - + -
103A GLU 3.9 4.5 - - - +
104A PRO 3.4 19.7 - - - +
107A ALA* 3.7 2.6 - - + +
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Residues in contact with ARG 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 2.8 19.4 + - - +
24A LYS* 3.5 20.1 + - - +
26A ALA* 1.3 79.1 - - - +
28A GLU* 1.3 82.5 + - - +
30A GLY 4.4 6.0 - - - +
32A ILE* 3.7 24.8 - - + +
34A LYS* 6.1 0.9 - - - +
88A GLU 3.4 13.7 + - - -
89A ALA* 3.0 22.6 + - - +
90A ALA 3.5 19.7 - - - +
91A GLY* 3.4 17.3 - - - -
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Residues in contact with GLU 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 LYS* 2.8 59.5 + - - +
25A ARG* 3.8 11.3 - - - +
27A ARG* 1.3 101.8 + - - +
29A THR* 1.3 68.2 + - + +
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Residues in contact with THR 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 ARG* 2.6 22.0 + - - +
28A GLU* 1.3 90.9 - - + +
30A GLY* 1.3 60.0 + - - +
103A GLU* 4.3 5.5 - - - +
105A GLY* 3.7 7.8 - - - -
106A ASP* 2.9 49.7 + - + +
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Residues in contact with GLY 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 ALA 2.7 21.0 + - - +
27A ARG 4.4 6.1 - - - +
29A THR* 1.3 77.3 + - - +
31A ARG* 1.3 68.8 + - - +
103A GLU* 3.2 25.4 - - - -
105A GLY 4.3 3.6 - - - -
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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