Contacts of the helix formed by residues 9 - 24 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6F PRO* 6.0 0.7 - - - -
8F LEU* 1.3 76.0 - - - +
10F ALA* 1.3 64.4 + - - +
11F GLU* 3.3 15.0 + - - +
12F GLN* 2.6 41.8 + - - +
13F LYS* 3.0 23.3 + - - +
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Residues in contact with ALA 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F SER* 1.3 73.8 - - - +
11F GLU* 1.3 68.6 + - + +
13F LYS* 3.4 12.8 + - - +
14F LYS* 3.1 22.9 + - - +
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Residues in contact with GLU 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F SER* 3.6 13.7 - - - +
10F ALA* 1.3 78.3 - - + +
12F GLN* 1.3 63.3 - - + +
14F LYS* 3.1 10.3 - - - +
15F GLU* 3.0 21.6 + - - +
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Residues in contact with GLN 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F ALA 4.2 2.6 - - - +
8F LEU* 3.3 27.7 - - + +
9F SER* 2.6 42.6 + - - +
11F GLU* 1.3 76.1 - - + +
13F LYS* 1.3 66.2 + - - +
15F GLU* 3.2 12.5 + - - +
16F LEU* 3.0 28.8 + - + +
179F GLN 5.4 1.1 + - - +
180F GLN* 4.8 11.1 + - - +
182F GLY* 6.0 1.7 - - - +
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Residues in contact with LYS 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F LEU* 3.8 32.7 - - + +
9F SER 3.0 18.9 + - - +
10F ALA* 3.7 9.9 - - - +
12F GLN* 1.3 76.0 - - - +
14F LYS* 1.3 64.8 + - - +
16F LEU* 3.3 1.0 + - - -
17F SER* 2.9 21.8 + - - -
223F TYR* 3.3 53.1 - - + +
259G ARG* 4.5 15.9 - - - +
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Residues in contact with LYS 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ALA 3.1 13.7 + - - +
11F GLU* 3.1 13.9 + - - +
13F LYS* 1.3 75.9 - - - +
15F GLU* 1.3 65.2 + - - +
17F SER* 3.0 12.9 + - - -
18F ASP* 2.8 56.2 + - - +
223F TYR* 6.0 0.4 + - - -
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Residues in contact with GLU 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F GLU 3.0 9.9 + - - +
12F GLN* 3.6 13.7 - - - +
14F LYS* 1.3 77.5 - - - +
16F LEU* 1.3 64.1 + - + +
18F ASP* 3.5 8.0 + - - +
19F ILE* 2.9 42.4 + - + +
139F LYS* 2.9 31.0 + - - -
182F GLY* 4.1 16.1 - - - +
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Residues in contact with LEU 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F LEU* 3.5 33.7 - - + -
12F GLN* 3.0 17.4 + - + +
13F LYS 3.6 5.2 - - - +
15F GLU* 1.3 78.2 - - + +
17F SER* 1.3 64.3 + - - +
19F ILE* 3.2 2.8 + - + -
20F ALA* 2.9 20.6 + - - +
179F GLN* 3.8 29.6 - - + +
182F GLY* 3.7 11.0 - - - +
183F ILE 3.6 42.8 - - - +
184F VAL* 3.2 18.2 - - + +
223F TYR* 4.3 3.4 - - + -
226F GLY* 4.0 13.9 - - - -
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Residues in contact with SER 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F LYS 2.9 17.8 + - - -
14F LYS* 3.5 13.0 + - - -
16F LEU* 1.3 75.5 - - - +
18F ASP* 1.3 66.2 + - - +
20F ALA* 3.2 2.5 + - - +
21F LEU* 3.0 40.3 + - - +
223F TYR* 4.2 10.8 - - - -
225F GLU* 3.5 27.2 + - - +
226F GLY* 4.3 0.4 - - - -
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Residues in contact with ASP 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F LYS* 2.8 49.4 + - - +
15F GLU* 3.8 7.4 + - - +
17F SER* 1.3 77.1 + - - +
19F ILE* 1.3 66.1 + - + +
21F LEU* 2.9 13.4 + - - +
22F ARG* 2.9 32.5 + - + +
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Residues in contact with ILE 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F GLU* 2.9 28.4 + - + +
16F LEU* 3.5 4.0 - - - +
18F ASP* 1.3 78.2 - - + +
20F ALA* 1.3 64.8 + - - +
22F ARG* 3.3 17.9 + - - +
23F ILE* 3.1 39.2 + - + +
104F VAL* 4.2 5.8 - - + -
139F LYS* 3.7 19.5 - - - +
144F ASP* 3.5 51.1 - - + +
182F GLY 4.1 3.8 - - - +
184F VAL* 3.6 11.2 - - + -
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Residues in contact with ALA 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F LEU 2.9 13.1 + - - +
17F SER 3.4 9.2 - - - +
18F ASP 3.1 0.2 - - - -
19F ILE* 1.3 76.9 - - - +
21F LEU* 1.3 63.3 + - - +
23F ILE* 3.2 17.7 + - - +
24F VAL* 3.2 17.8 + - - +
184F VAL* 3.9 21.1 - - + +
225F GLU 4.1 6.7 - - - +
226F GLY* 4.6 0.9 - - - -
227F THR 4.4 2.7 - - - +
228F LEU* 4.5 4.3 - - + +
266F PRO* 3.8 24.9 - - + -
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Residues in contact with LEU 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F SER* 3.0 35.1 + - - +
18F ASP* 2.9 11.4 + - - +
20F ALA* 1.3 71.7 - - - +
22F ARG* 1.3 66.6 + - + +
24F VAL* 3.4 8.3 + - + +
25F ALA* 2.9 24.9 + - - +
225F GLU 5.8 0.2 - - - +
266F PRO* 3.8 26.9 - - + +
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Residues in contact with ARG 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F ASP* 2.9 23.7 + - + +
19F ILE* 3.7 19.1 - - - +
21F LEU* 1.3 78.6 - - + +
23F ILE* 1.3 65.6 + - - +
25F ALA* 3.3 16.8 + - - +
28F LYS* 4.2 7.1 + - - +
75F GLY* 4.3 3.5 - - - +
102F GLY* 3.0 32.7 + - - -
103F ILE 4.6 1.8 + - - -
104F VAL* 3.8 28.9 - - + +
144F ASP* 5.2 5.5 + - - -
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Residues in contact with ILE 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F ILE* 3.1 23.8 - - + +
20F ALA* 3.2 8.0 + - - +
22F ARG* 1.3 78.5 - - - +
24F VAL* 1.3 59.6 + - + +
25F ALA 3.4 1.9 + - - -
28F LYS* 3.9 9.4 - - - +
29F GLY 4.5 1.9 - - - +
30F ILE* 3.6 35.9 - - + -
75F GLY* 3.6 21.5 + - - -
76F GLY* 4.4 7.6 - - - +
104F VAL* 3.7 17.9 - - + -
145F PHE* 3.6 42.2 - - + -
184F VAL* 5.2 1.1 - - + -
228F LEU* 4.0 16.8 - - + -
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Residues in contact with VAL 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F ALA 3.4 14.6 - - - +
21F LEU* 4.0 12.6 - - + +
22F ARG 3.4 0.2 - - - -
23F ILE* 1.3 77.6 - - + +
25F ALA* 1.3 68.9 + - - +
26F PRO* 3.5 2.4 - - - +
28F LYS 4.5 4.9 - - - -
30F ILE* 5.7 0.4 - - + -
228F LEU* 3.7 26.5 - - + -
266F PRO* 4.2 17.5 - - + +
267F GLY* 4.2 6.3 - - - -
268F VAL 5.0 0.4 - - - +
269F THR* 3.8 22.0 - - + -
297F ALA* 3.7 31.5 - - + +
299F THR* 4.3 11.9 - - + +
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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