Contacts of the helix formed by residues 8 - 28 (chain A) in PDB entry 2FBH
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 TYR 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A PHE* 1.3 68.7 + - - +
10A GLY 3.2 3.1 - - - -
11A THR* 3.1 20.8 + - - +
12A LEU* 3.0 21.4 + - - +
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Residues in contact with PHE 9 (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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8A TYR* 1.3 76.0 - - - +
10A GLY* 1.3 67.9 + - - +
12A LEU* 3.2 13.6 + - + +
13A LEU* 3.1 32.7 + - + +
133A VAL* 4.5 13.5 - - + -
134A LEU* 5.3 4.9 - - + -
137A ILE* 3.6 32.8 - - + -
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Residues in contact with GLY 10 (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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8A TYR* 3.2 0.8 - - - +
9A PHE* 1.3 84.8 - - - +
11A THR* 1.3 56.1 + - - +
13A LEU* 3.3 10.3 + - - +
14A ALA* 2.9 28.5 + - - +
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Residues in contact with THR 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A TYR* 3.1 25.3 + - + +
10A GLY* 1.3 74.9 - - - +
12A LEU* 1.3 59.3 + - - +
14A ALA* 3.2 5.9 + - + +
15A GLN* 2.9 55.6 + - + +
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Residues in contact with LEU 12 (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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8A TYR 3.0 12.0 + - - +
9A PHE* 3.2 15.2 + - + +
11A THR* 1.3 76.5 - - - +
13A LEU* 1.3 62.9 + - - +
15A GLN* 3.4 11.4 + - + +
16A THR* 2.8 41.5 + - - +
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Residues in contact with LEU 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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9A PHE* 3.1 26.7 + - + +
10A GLY* 3.6 12.1 - - - +
12A LEU* 1.3 77.5 - - - +
14A ALA* 1.3 64.4 + - - +
16A THR* 3.8 5.4 - - - -
17A SER* 3.0 30.8 + - - -
134A LEU* 4.0 32.1 - - + -
137A ILE* 5.2 11.9 - - + -
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Residues in contact with ALA 14 (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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10A GLY 2.9 17.4 + - - +
11A THR* 3.2 7.6 + - + +
13A LEU* 1.3 78.7 - - - +
15A GLN* 1.3 60.6 + - + +
17A SER* 3.5 5.0 + - - -
18A ARG* 2.8 48.9 + - - +
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Residues in contact with GLN 15 (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 THR* 2.9 40.3 + - + +
12A LEU* 3.8 12.3 - - + +
14A ALA* 1.3 76.3 - - + +
16A THR* 1.3 59.4 + - - +
18A ARG* 3.5 11.5 + - - +
19A ALA* 2.9 30.7 + - - +
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Residues in contact with THR 16 (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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12A LEU* 2.8 36.8 + - - +
13A LEU* 3.8 7.4 - - - -
15A GLN* 1.3 73.6 - - - +
17A SER* 1.3 65.5 + - - +
19A ALA* 3.3 7.4 + - + +
20A TRP* 3.0 33.4 + - + +
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Residues in contact with SER 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 LEU* 3.0 23.3 + - - -
14A ALA* 3.8 5.6 - - - -
16A THR* 1.3 78.6 - - - +
18A ARG* 1.3 60.5 + - - +
20A TRP* 3.2 7.6 + - - +
21A ARG* 3.0 38.3 + - - +
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Residues in contact with ARG 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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14A ALA* 2.8 37.6 + - - +
15A GLN* 3.7 10.8 - - - +
17A SER* 1.3 72.9 - - - +
19A ALA* 1.3 58.8 + - - +
21A ARG* 3.5 5.1 + - - +
22A ALA* 2.9 30.6 + - + +
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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 GLN 2.9 18.7 + - - +
16A THR* 3.6 7.6 - - - +
18A ARG* 1.3 78.0 - - - +
20A TRP* 1.3 58.7 + - - +
22A ALA* 3.3 6.9 + - - +
23A GLU* 3.0 29.0 + - - +
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Residues in contact with TRP 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 THR* 3.0 26.7 + - + +
17A SER* 3.7 7.4 - - - +
19A ALA* 1.3 76.8 - - - +
21A ARG* 1.3 78.6 + - - +
23A GLU* 3.1 6.3 + - - +
24A LEU* 2.9 29.9 + - + +
111A ALA 5.4 0.8 + - - -
114A VAL* 3.5 24.6 - - + +
115A ARG* 4.0 20.4 - - + +
118A VAL* 3.6 37.2 - - + -
119A LEU* 4.7 14.1 - - + -
205A SO4 3.4 34.5 + - - -
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Residues in contact with ARG 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 SER* 3.0 28.2 + - - +
18A ARG* 4.0 4.7 - - - +
20A TRP* 1.3 94.9 - - - +
22A ALA* 1.3 55.1 + - - +
24A LEU* 3.4 23.2 + - - +
25A ASP* 2.8 30.5 + - - +
38A TRP* 4.0 15.8 - - + -
39A LEU* 4.4 19.2 - - - +
42A LEU* 5.1 3.2 - - - +
46A ARG* 5.7 0.2 - - - +
205A SO4 2.7 37.7 + - - -
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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 ARG* 2.9 22.0 + - + +
19A ALA* 3.5 8.5 - - - +
20A TRP 3.2 0.2 - - - -
21A ARG* 1.3 77.4 - - - +
23A GLU* 1.3 58.0 + - - +
25A ASP* 3.3 6.0 + - - +
26A ARG* 2.8 29.5 + - - +
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Residues in contact with GLU 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 13.6 + - - +
20A TRP* 3.1 9.8 + - - +
22A ALA* 1.3 74.5 - - - +
24A LEU* 1.3 66.0 + - - +
26A ARG* 3.3 26.5 + - - +
27A ARG* 2.7 66.8 + - - +
114A VAL* 4.0 15.9 - - + -
118A VAL* 5.3 6.3 - - + -
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Residues in contact with LEU 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 TRP* 2.9 21.2 + - + +
21A ARG* 3.4 34.8 - - - +
23A GLU* 1.3 76.4 - - - +
25A ASP* 1.3 58.2 + - - +
27A ARG 3.1 1.8 + - - +
28A LEU* 2.9 55.9 + - + +
38A TRP* 3.5 24.9 - - + -
42A LEU* 4.8 3.1 - - + -
107A ILE* 5.8 0.2 - - + -
110A ILE* 4.1 6.7 - - + -
111A ALA* 3.7 42.0 - - + +
114A VAL* 4.1 12.7 - - + +
205A SO4 4.6 4.3 - - - +
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Residues in contact with ASP 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 ARG 2.8 19.9 + - - +
22A ALA* 3.6 7.4 - - - +
24A LEU* 1.3 75.2 - - - +
26A ARG* 1.3 62.6 + - - +
28A LEU* 3.3 3.0 + - - -
29A SER* 3.1 25.2 + - - -
33A LEU 5.0 1.6 - - - +
34A SER* 5.9 1.2 - - - -
35A GLN 4.8 4.0 - - - +
38A TRP* 2.9 37.6 + - + +
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Residues in contact with ARG 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 2.8 14.6 + - - +
23A GLU* 3.4 34.3 + - - +
25A ASP* 1.3 77.2 + - - +
27A ARG* 1.3 66.4 + - + +
29A SER* 2.8 27.4 + - - -
203A ZN 3.7 2.4 - - - -
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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 GLU* 2.7 54.6 + - - +
24A LEU 3.1 1.5 + - - +
26A ARG* 1.3 78.4 - - + +
28A LEU* 1.3 58.8 + - - +
29A SER 3.4 0.2 - - - -
30A HIS* 3.4 11.3 - - - -
110A ILE* 3.4 26.4 - - + +
113A SER* 3.2 26.6 + - - -
114A VAL* 3.6 23.5 - - + +
117A ASP* 2.8 38.1 + - - +
118A VAL* 5.8 0.8 - - - +
203A ZN 3.2 12.4 - - - -
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Residues in contact with LEU 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 LEU* 2.9 33.6 + - + +
25A ASP 3.7 3.6 - - - +
26A ARG 3.2 0.2 - - - -
27A ARG* 1.3 77.2 - - - +
29A SER* 1.3 53.9 + - - +
30A HIS* 3.1 9.0 - - - -
31A LEU* 2.9 44.0 + - + +
32A GLY 4.3 1.0 + - - -
33A LEU* 5.1 3.3 + - + +
38A TRP* 3.4 54.9 - - + -
107A ILE* 3.9 20.6 - - + +
110A ILE* 3.7 34.8 - - + -
203A ZN 3.5 0.9 - - - -
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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