Contacts of the helix formed by residues 9 - 24 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6J PRO* 6.0 0.2 - - - -
8J LEU* 1.3 76.8 - - - +
10J ALA* 1.3 65.6 + - - +
11J GLU* 3.3 13.9 + - - +
12J GLN* 2.6 42.2 + - - +
13J LYS* 3.0 22.6 + - - +
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Residues in contact with ALA 10 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J SER* 1.3 74.0 - - - +
11J GLU* 1.3 68.3 + - + +
13J LYS* 3.4 11.9 + - - +
14J LYS* 3.1 23.0 + - - +
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Residues in contact with GLU 11 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J SER* 3.6 14.4 - - - +
10J ALA* 1.3 78.4 - - + +
12J GLN* 1.3 63.1 + - + +
14J LYS* 3.1 10.1 - - - +
15J GLU* 3.0 21.8 + - - +
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Residues in contact with GLN 12 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J ALA 4.2 2.6 + - - +
8J LEU* 3.3 26.6 - - + +
9J SER* 2.6 41.5 + - - +
11J GLU* 1.3 75.6 - - + +
13J LYS* 1.3 66.2 + - - +
15J GLU* 3.2 13.6 + - - +
16J LEU* 3.0 29.6 + - + +
179J GLN 5.4 1.3 + - - +
180J GLN* 4.8 11.5 + - - +
182J GLY* 6.0 1.9 - - - +
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Residues in contact with LYS 13 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J LEU* 3.8 33.6 - - + +
9J SER 3.0 19.4 + - - +
10J ALA* 3.7 9.9 - - - +
12J GLN* 1.3 76.2 - - - +
14J LYS* 1.3 64.3 + - - +
16J LEU* 3.3 0.8 + - - -
17J SER* 2.9 21.5 + - - -
223J TYR* 3.3 53.0 - - + +
259K ARG* 4.3 18.1 - - - +
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Residues in contact with LYS 14 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J ALA 3.1 13.4 + - - +
11J GLU* 3.1 13.2 - - - +
13J LYS* 1.3 76.4 - - - +
15J GLU* 1.3 65.4 + - - +
17J SER* 3.0 12.3 + - - -
18J ASP* 2.8 55.1 + - - +
223J TYR* 5.2 0.8 + - - -
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Residues in contact with GLU 15 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J GLU 3.0 8.8 + - - +
12J GLN* 3.2 13.8 + - - +
14J LYS* 1.3 78.6 - - - +
16J LEU* 1.3 62.8 + - + +
18J ASP* 3.5 8.1 + - - +
19J ILE* 2.9 43.5 + - + +
139J LYS* 2.9 31.1 + - - -
182J GLY* 4.1 16.0 - - - +
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Residues in contact with LEU 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J LEU* 3.5 33.9 - - + -
12J GLN* 3.0 17.0 + - + +
13J LYS 3.6 5.6 - - - +
15J GLU* 1.3 76.7 - - + +
17J SER* 1.3 64.4 + - - +
19J ILE* 3.2 3.4 + - + -
20J ALA* 2.9 20.8 + - - +
179J GLN* 3.8 29.2 - - + +
182J GLY* 3.7 10.3 - - - +
183J ILE 3.6 43.5 - - - +
184J VAL* 3.2 16.9 - - + +
223J TYR* 4.3 3.1 - - + -
226J GLY* 4.0 14.8 - - - +
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Residues in contact with SER 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J LYS 2.9 18.0 + - - -
14J LYS* 3.5 13.1 + - - -
16J LEU* 1.3 75.7 - - - +
18J ASP* 1.3 65.8 + - - +
20J ALA* 3.2 2.6 + - - +
21J LEU* 3.0 40.5 + - - +
223J TYR* 4.2 10.1 - - - -
225J GLU* 3.5 26.6 + - - +
226J GLY* 4.3 0.6 - - - -
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Residues in contact with ASP 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J LYS* 2.8 49.6 + - - +
15J GLU* 3.8 7.1 + - - +
17J SER* 1.3 76.3 + - - +
19J ILE* 1.3 64.8 + - + +
21J LEU* 2.9 13.0 + - - +
22J ARG* 2.9 32.0 + - + +
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Residues in contact with ILE 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J GLU* 2.9 28.2 + - + +
16J LEU* 3.5 5.4 - - - +
18J ASP* 1.3 77.4 - - + +
20J ALA* 1.3 64.1 + - - +
22J ARG* 3.3 16.8 + - - +
23J ILE* 3.1 38.8 + - + +
104J VAL* 4.2 4.9 - - + -
139J LYS* 3.7 19.7 - - - +
144J ASP* 3.5 52.5 - - + +
182J GLY 4.1 3.8 - - - +
184J VAL* 3.6 10.8 - - + -
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Residues in contact with ALA 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J LEU 2.9 11.9 + - - +
17J SER 3.4 9.6 - - - +
19J ILE* 1.3 77.5 - - - +
21J LEU* 1.3 62.5 + - - +
23J ILE* 3.2 17.6 + - - +
24J VAL* 3.2 18.0 + - - +
184J VAL* 3.9 20.6 - - + +
225J GLU 4.1 6.5 - - - +
226J GLY* 4.6 1.1 - - - -
227J THR 4.4 2.5 - - - +
228J LEU* 4.5 4.7 - - + +
266J PRO* 3.8 24.5 - - + -
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Residues in contact with LEU 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J SER* 3.0 35.1 + - - +
18J ASP* 2.9 10.1 + - - +
20J ALA* 1.3 73.2 - - - +
22J ARG* 1.3 67.4 + - + +
24J VAL* 3.4 8.4 + - + -
25J ALA* 2.9 25.3 + - - +
225J GLU 5.8 0.2 - - - +
266J PRO* 3.8 25.8 - - + +
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Residues in contact with ARG 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J ASP* 2.9 24.1 + - + +
19J ILE* 3.7 18.3 - - - +
20J ALA 3.3 0.2 - - - -
21J LEU* 1.3 77.4 - - - +
23J ILE* 1.3 65.8 + - - +
25J ALA* 3.3 17.3 + - - +
28J LYS* 4.2 7.1 - - - +
75J GLY* 4.3 3.5 - - - +
102J GLY* 3.0 33.1 + - - -
103J ILE 4.6 1.8 + - - -
104J VAL* 3.8 28.7 - - + +
144J ASP* 5.2 5.7 + - - -
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Residues in contact with ILE 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J ILE* 3.1 24.0 - - + +
20J ALA* 3.2 8.0 + - - +
22J ARG* 1.3 79.5 - - - +
24J VAL* 1.3 58.8 + - + +
25J ALA 3.4 2.3 + - - -
28J LYS* 3.9 8.5 - - - +
29J GLY 4.5 2.3 - - - +
30J ILE* 3.6 37.0 - - + -
75J GLY* 3.6 21.2 + - - -
76J GLY* 4.4 7.2 - - - +
104J VAL* 3.7 18.2 - - + -
145J PHE* 3.6 43.3 - - + -
184J VAL* 5.2 0.9 - - + -
228J LEU* 4.0 16.4 - - + -
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Residues in contact with VAL 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J ALA 3.4 14.8 - - - +
21J LEU* 4.0 12.3 - - + +
22J ARG 3.4 0.2 - - - -
23J ILE* 1.3 76.8 - - + +
25J ALA* 1.3 69.3 + - - +
26J PRO* 3.5 2.1 - - - +
28J LYS 4.5 4.7 - - - -
30J ILE* 6.0 0.2 - - + -
228J LEU* 3.7 24.9 - - + -
266J PRO* 4.2 17.5 - - + +
267J GLY* 4.2 6.5 - - - -
268J VAL 5.0 0.2 - - - +
269J THR* 3.8 22.4 - - + -
297J ALA* 3.7 31.1 - - + +
299J THR* 4.3 11.6 - - + +
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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