Contacts of the helix formed by residues 9 - 24 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A PRO* 6.0 0.4 - - - -
8A LEU* 1.3 76.1 - - - +
10A ALA* 1.3 63.9 + - - +
11A GLU* 3.3 14.4 + - - +
12A GLN* 2.6 41.7 + - - +
13A LYS* 3.0 23.3 + - - +
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Residues in contact with ALA 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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9A SER* 1.3 74.1 - - - +
11A GLU* 1.3 70.0 + - + +
13A LYS* 3.4 12.1 + - - +
14A LYS* 3.1 22.7 + - - +
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Residues in contact with GLU 11 (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 SER* 3.6 13.7 - - - +
10A ALA* 1.3 80.0 - - + +
12A GLN* 1.3 62.9 + - + +
14A LYS* 3.1 10.4 - - - +
15A GLU* 3.0 21.5 + - - +
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Residues in contact with GLN 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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7A ALA 4.2 2.6 + - - +
8A LEU* 3.3 27.1 - - + +
9A SER* 2.6 43.2 + - - +
11A GLU* 1.3 75.4 - - + +
13A LYS* 1.3 66.7 + - - +
15A GLU* 3.2 13.2 + - - +
16A LEU* 3.0 29.8 + - + +
179A GLN 5.4 1.3 + - - +
180A GLN* 4.8 11.1 + - - +
182A GLY* 6.0 1.9 - - - +
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Residues in contact with LYS 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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8A LEU* 3.8 33.7 - - + +
9A SER 3.0 19.2 + - - +
10A ALA* 3.7 9.2 - - - +
12A GLN* 1.3 75.9 - - - +
14A LYS* 1.3 64.2 + - - +
16A LEU* 3.3 0.8 + - - -
17A SER* 2.9 21.8 + - - -
223A TYR* 3.3 53.3 - - + +
259D ARG* 4.5 15.1 - - - +
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Residues in contact with LYS 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 ALA 3.1 13.2 + - - +
11A GLU* 3.1 13.9 - - - +
13A LYS* 1.3 76.7 - - - +
15A GLU* 1.3 64.6 + - - +
17A SER* 3.0 13.4 + - - -
18A ASP* 2.8 55.3 + - - +
223A TYR* 5.2 0.8 + - - -
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Residues in contact with GLU 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 GLU 3.0 8.4 + - - +
12A GLN* 3.2 14.4 + - - +
14A LYS* 1.3 79.0 - - - +
16A LEU* 1.3 63.7 + - + +
18A ASP* 3.5 7.9 + - - +
19A ILE* 2.9 43.9 + - + +
139A LYS* 2.9 30.9 + - - -
182A GLY* 4.1 15.1 - - - +
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Residues in contact with LEU 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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8A LEU* 3.5 33.9 - - + -
12A GLN* 3.0 17.6 + - + +
13A LYS 3.6 5.6 - - - +
15A GLU* 1.3 76.4 - - + +
17A SER* 1.3 64.4 + - - +
19A ILE* 3.2 2.8 + - + -
20A ALA* 2.9 20.6 + - - +
179A GLN* 3.8 28.9 - - + +
182A GLY* 3.7 11.4 - - - +
183A ILE 3.6 42.0 - - - +
184A VAL* 3.2 17.9 - - + +
223A TYR* 4.3 2.9 - - + -
226A GLY* 4.0 14.8 - - - +
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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 LYS 2.9 17.2 + - - -
14A LYS* 3.5 13.0 + - - -
16A LEU* 1.3 75.9 - - - +
18A ASP* 1.3 66.6 + - - +
20A ALA* 3.2 2.6 + - - +
21A LEU* 3.0 40.4 + - - +
223A TYR* 4.2 10.5 - - - -
225A GLU* 3.5 26.5 + - - +
226A GLY* 4.3 0.4 - - - -
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Residues in contact with ASP 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 LYS* 2.8 49.4 + - - +
15A GLU* 3.8 6.7 + - - +
17A SER* 1.3 76.6 + - - +
19A ILE* 1.3 65.4 + - + +
21A LEU* 2.9 13.3 + - - +
22A ARG* 2.9 33.2 + - + +
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Residues in contact with ILE 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 GLU* 2.9 28.9 + - + +
16A LEU* 3.5 4.5 - - - +
18A ASP* 1.3 78.1 - - + +
20A ALA* 1.3 63.6 + - - +
22A ARG* 3.3 16.4 + - - +
23A ILE* 3.1 39.3 + - + +
104A VAL* 4.2 5.3 - - + +
139A LYS* 3.7 20.0 - - - +
144A ASP* 3.5 51.8 - - + +
182A GLY 4.1 3.6 - - - +
184A VAL* 3.6 10.5 - - + -
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Residues in contact with ALA 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 LEU 2.9 13.1 + - - +
17A SER 3.4 9.4 - - - +
18A ASP 3.1 0.2 - - - -
19A ILE* 1.3 77.1 - - - +
21A LEU* 1.3 63.0 + - - +
23A ILE* 3.2 17.4 + - - +
24A VAL* 3.2 18.4 + - - +
184A VAL* 3.9 21.7 - - + +
225A GLU 4.1 6.7 - - - +
226A GLY* 4.6 1.1 - - - -
227A THR 4.4 2.7 - - - +
228A LEU* 4.5 4.3 - - + +
266A PRO* 3.8 24.9 - - + -
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Residues in contact with LEU 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 35.5 + - - +
18A ASP* 2.9 10.6 + - - +
20A ALA* 1.3 72.1 - - - +
22A ARG* 1.3 65.6 + - + +
24A VAL* 3.6 6.8 - - + +
25A ALA* 2.9 25.3 + - - +
266A PRO* 3.8 26.0 - - + +
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Residues in contact with ARG 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 ASP* 2.9 24.0 + - + +
19A ILE* 3.7 18.1 - - - +
20A ALA 3.3 0.2 - - - -
21A LEU* 1.3 78.0 - - + +
23A ILE* 1.3 64.5 + - - +
25A ALA* 3.3 17.3 + - - +
28A LYS* 4.2 6.8 - - - +
75A GLY* 4.3 3.3 - - - +
102A GLY* 3.0 31.9 + - - -
103A ILE 4.6 1.6 + - - -
104A VAL* 3.8 28.5 - - + +
144A ASP* 5.2 6.1 + - - -
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Residues in contact with ILE 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 ILE* 3.1 24.0 - - + +
20A ALA* 3.2 8.2 + - - +
22A ARG* 1.3 79.1 - - - +
24A VAL* 1.3 60.2 + - + +
25A ALA 3.4 1.9 + - - -
28A LYS* 3.9 9.2 - - - +
29A GLY 4.5 1.9 + - - +
30A ILE* 3.6 36.5 - - + +
75A GLY* 3.6 20.1 + - - -
76A GLY* 4.4 7.9 - - - +
104A VAL* 3.7 18.2 - - + -
145A PHE* 3.6 43.3 - - + -
184A VAL* 5.2 0.9 - - + -
228A LEU* 4.0 15.5 - - + -
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Residues in contact with VAL 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 ALA 3.4 14.4 - - - +
21A LEU* 3.6 12.6 - - + +
23A ILE* 1.3 77.3 - - + +
25A ALA* 1.3 70.1 + - - +
26A PRO* 3.5 2.4 - - - +
28A LYS 4.5 5.4 - - - -
30A ILE* 6.0 0.2 - - + -
228A LEU* 3.7 25.4 - - + -
266A PRO* 4.2 17.0 - - + +
267A GLY* 4.2 6.5 - - - -
268A VAL 5.5 0.4 - - - -
269A THR* 3.8 22.0 - - + -
297A ALA* 3.7 30.6 - - + +
299A THR* 4.3 11.7 - - + +
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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