Contacts of the helix formed by residues 9 - 24 (chain E) in PDB entry 1XFB
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 SER 9 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E PRO* 6.0 0.2 - - - -
8E LEU* 1.3 76.7 - - - +
10E ALA* 1.3 65.4 + - - +
11E GLU* 3.3 14.3 + - - +
12E GLN* 2.6 41.5 + - - +
13E LYS* 3.0 23.2 + - - +
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Residues in contact with ALA 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E SER* 1.3 73.6 - - - +
11E GLU* 1.3 68.4 + - + +
13E LYS* 3.4 12.5 + - - +
14E LYS* 3.1 22.9 + - - +
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Residues in contact with GLU 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E SER* 3.6 13.7 - - - +
10E ALA* 1.3 78.3 - - + +
12E GLN* 1.3 63.6 + - + +
14E LYS* 3.1 11.1 - - - +
15E GLU* 3.0 21.7 + - - +
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Residues in contact with GLN 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ALA 4.2 2.3 - - - +
8E LEU* 3.3 28.0 - - + +
9E SER* 2.6 41.9 + - - +
11E GLU* 1.3 75.8 - - + +
13E LYS* 1.3 65.4 + - - +
15E GLU* 3.2 12.7 + - - +
16E LEU* 3.0 29.8 + - + +
179E GLN 5.4 1.1 + - - +
180E GLN* 4.8 11.3 + - - +
182E GLY* 6.0 1.9 - - - +
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Residues in contact with LYS 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E LEU* 3.8 33.4 - - + +
9E SER 3.0 18.9 + - - +
10E ALA* 3.7 10.3 - - - +
12E GLN* 1.3 77.0 - - - +
14E LYS* 1.3 63.5 + - - +
16E LEU* 3.3 1.1 + - - -
17E SER* 2.9 21.1 + - - -
223E TYR* 3.3 54.8 - - + +
259H ARG* 4.2 18.5 - - - +
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Residues in contact with LYS 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLU* 5.1 10.6 + - - +
10E ALA 3.1 13.0 + - - +
11E GLU* 3.1 13.4 + - - +
13E LYS* 1.3 75.6 - - - +
15E GLU* 1.3 65.5 + - - +
17E SER* 3.0 13.1 + - - -
18E ASP* 2.8 55.5 + - - +
223E TYR* 6.0 0.4 + - - -
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Residues in contact with GLU 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E GLU 3.0 8.2 + - - +
12E GLN* 3.2 14.3 + - - +
14E LYS* 1.3 79.0 - - - +
16E LEU* 1.3 63.4 + - + +
18E ASP* 3.5 7.9 + - - +
19E ILE* 2.9 43.7 + - + +
139E LYS* 2.9 31.3 + - - -
182E GLY* 4.1 16.3 - - - +
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Residues in contact with LEU 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E LEU* 3.5 33.2 - - + -
12E GLN* 3.0 16.7 + - + +
13E LYS 3.6 5.6 - - - +
15E GLU* 1.3 75.8 - - + +
17E SER* 1.3 64.3 + - - +
19E ILE* 3.2 2.9 + - + -
20E ALA* 2.9 21.0 + - - +
179E GLN* 3.8 28.9 - - + +
182E GLY* 3.7 11.2 - - - +
183E ILE 3.6 43.1 - - - +
184E VAL* 3.2 18.4 - - + +
223E TYR* 4.3 2.5 - - + -
226E GLY* 4.0 14.1 - - - -
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Residues in contact with SER 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E LYS 2.9 17.9 + - - -
14E LYS* 3.5 12.3 + - - -
16E LEU* 1.3 76.1 - - - +
18E ASP* 1.3 66.7 + - - +
20E ALA* 3.2 2.3 + - - +
21E LEU* 3.0 40.5 + - - +
223E TYR* 4.2 10.1 - - - -
225E GLU* 3.5 27.2 + - - +
226E GLY* 4.3 0.6 - - - -
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Residues in contact with ASP 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLU* 3.9 19.2 - - - +
14E LYS* 2.8 48.5 + - - +
15E GLU* 3.8 6.9 + - - +
17E SER* 1.3 76.8 + - - +
19E ILE* 1.3 66.3 + - + +
21E LEU* 2.9 12.0 + - - +
22E ARG* 2.9 32.6 + - + +
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Residues in contact with ILE 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E GLU* 2.9 28.2 + - + +
16E LEU* 3.5 4.7 - - - +
18E ASP* 1.3 78.5 - - + +
20E ALA* 1.3 63.0 + - - +
22E ARG* 3.3 17.3 + - - +
23E ILE* 3.1 39.2 + - + +
104E VAL* 4.2 5.4 - - + -
139E LYS* 3.7 20.2 - - - +
144E ASP* 3.5 51.1 - - + +
182E GLY 4.1 3.4 - - - +
184E VAL* 3.6 10.8 - - + -
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Residues in contact with ALA 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E LEU 2.9 13.4 + - - +
17E SER 3.4 9.0 - - - +
18E ASP 3.1 0.2 - - - -
19E ILE* 1.3 77.1 - - - +
21E LEU* 1.3 62.7 + - - +
23E ILE* 3.2 17.1 + - - +
24E VAL* 3.2 18.6 + - - +
184E VAL* 3.9 21.5 - - + +
225E GLU 4.1 6.5 - - - +
226E GLY* 4.6 0.9 - - - -
227E THR 4.4 2.7 - - - +
228E LEU* 4.5 4.3 - - + +
266E PRO* 3.8 24.7 - - + -
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Residues in contact with LEU 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLU* 5.1 13.9 - - + +
17E SER* 3.0 34.5 + - - +
18E ASP* 2.9 10.6 + - - +
20E ALA* 1.3 71.9 - - - +
22E ARG* 1.3 66.3 + - + +
24E VAL* 3.4 7.9 + - + +
25E ALA* 2.9 25.1 + - - +
266E PRO* 3.8 26.0 - - + +
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Residues in contact with ARG 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E ASP* 2.9 23.6 + - + +
19E ILE* 3.7 18.9 - - - +
20E ALA 3.3 0.2 - - - -
21E LEU* 1.3 77.2 - - - +
23E ILE* 1.3 64.9 + - - +
25E ALA* 3.3 16.8 + - - +
28E LYS* 4.2 7.1 - - - +
75E GLY* 4.3 3.5 - - - +
102E GLY* 3.0 32.5 + - - -
103E ILE 4.6 1.8 + - - -
104E VAL* 3.8 28.0 - - + +
144E ASP* 5.2 5.9 + - - -
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Residues in contact with ILE 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E ILE* 3.1 24.5 - - + +
20E ALA* 3.2 7.8 + - - +
22E ARG* 1.3 78.8 - - - +
24E VAL* 1.3 59.5 + - + +
25E ALA 3.4 1.9 + - - -
28E LYS* 3.9 9.4 - - - +
29E GLY* 4.5 2.3 - - - +
30E ILE* 3.6 36.3 - - + -
75E GLY* 3.6 21.3 + - - -
76E GLY* 4.4 8.1 - - - +
104E VAL* 3.7 17.9 - - + -
145E PHE* 3.6 42.6 - - + -
184E VAL* 5.2 0.9 - - + -
228E LEU* 4.0 16.6 - - + -
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Residues in contact with VAL 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ALA 3.4 14.4 - - - +
21E LEU* 4.0 12.6 - - + +
22E ARG 3.4 0.2 - - - -
23E ILE* 1.3 76.8 - - + +
25E ALA* 1.3 69.4 + - - +
26E PRO* 3.5 1.7 - - - +
28E LYS 4.5 5.2 - - - -
30E ILE* 6.0 0.2 - - + -
228E LEU* 3.7 25.6 - - + -
266E PRO* 4.2 17.3 - - + +
267E GLY* 4.2 6.5 - - - -
268E VAL 5.0 0.2 - - - +
269E THR* 3.8 22.2 - - + -
297E ALA* 3.7 31.2 - - + +
299E THR* 4.3 11.3 - - + +
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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