Contacts of the helix formed by residues 9 - 24 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6L PRO* 6.0 0.7 - - - -
8L LEU* 1.3 76.2 - - - +
10L ALA* 1.3 64.4 + - - +
11L GLU* 3.3 14.8 + - - +
12L GLN* 2.6 41.8 + - - +
13L LYS* 3.0 23.4 + - - +
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Residues in contact with ALA 10 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L SER* 1.3 73.2 - - - +
11L GLU* 1.3 67.7 + - + +
13L LYS* 3.4 12.6 + - - +
14L LYS* 3.1 23.2 + - - +
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Residues in contact with GLU 11 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L SER* 3.6 13.9 - - - +
10L ALA* 1.3 78.4 - - + +
12L GLN* 1.3 63.4 - - + +
14L LYS* 3.1 10.4 - - - +
15L GLU* 3.0 21.4 + - - +
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Residues in contact with GLN 12 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L ALA 4.2 2.6 - - - +
8L LEU* 3.3 27.7 - - + +
9L SER* 2.6 42.7 + - - +
11L GLU* 1.3 76.5 - - + +
13L LYS* 1.3 66.4 + - - +
15L GLU* 3.2 12.5 + - - +
16L LEU* 3.0 29.0 + - + +
179L GLN 5.4 1.1 + - - +
180L GLN* 4.8 11.1 + - - +
182L GLY* 6.0 1.9 - - - +
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Residues in contact with LYS 13 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259I ARG* 4.6 15.3 - - - +
8L LEU* 3.8 32.3 - - + +
9L SER 3.0 19.4 + - - +
10L ALA* 3.7 9.9 - - - +
12L GLN* 1.3 75.8 - - - +
14L LYS* 1.3 64.8 + - - +
16L LEU* 3.3 1.0 + - - -
17L SER* 2.9 22.2 + - - -
223L TYR* 3.3 52.7 - - + +
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Residues in contact with LYS 14 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10L ALA 3.1 13.4 + - - +
11L GLU* 3.1 13.9 + - - +
13L LYS* 1.3 75.5 - - - +
15L GLU* 1.3 64.5 + - - +
17L SER* 3.0 12.7 + - - -
18L ASP* 2.8 56.4 + - - +
223L TYR* 6.0 0.4 + - - -
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Residues in contact with GLU 15 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L GLU 3.0 9.9 + - - +
12L GLN* 3.6 13.8 - - - +
14L LYS* 1.3 77.9 - - - +
16L LEU* 1.3 62.4 + - + +
18L ASP* 3.5 8.0 + - - +
19L ILE* 2.9 44.6 + - + +
139L LYS* 2.9 30.8 + - - -
182L GLY* 4.1 15.8 - - - +
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Residues in contact with LEU 16 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L LEU* 3.5 33.9 - - + -
12L GLN* 3.0 16.7 + - + +
13L LYS 3.6 5.4 - - - +
15L GLU* 1.3 77.8 - - + +
17L SER* 1.3 64.4 + - - +
19L ILE* 3.2 2.8 + - + -
20L ALA* 2.9 20.8 + - - +
179L GLN* 3.8 29.4 - - + +
182L GLY* 3.7 11.4 - - - +
183L ILE 3.6 42.6 - - - +
184L VAL* 3.2 18.2 - - + +
223L TYR* 4.3 3.1 - - + -
226L GLY* 4.0 13.9 - - - -
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Residues in contact with SER 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L LYS 2.9 17.8 + - - -
14L LYS* 3.5 12.7 + - - -
16L LEU* 1.3 75.1 - - - +
18L ASP* 1.3 66.2 + - - +
20L ALA* 3.2 2.5 + - - +
21L LEU* 3.0 40.5 + - - +
223L TYR* 4.2 11.0 - - - -
225L GLU* 3.5 27.2 + - - +
226L GLY* 4.3 0.4 - - - -
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Residues in contact with ASP 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14L LYS* 2.8 48.7 + - - +
15L GLU* 3.8 7.1 + - - +
17L SER* 1.3 77.3 + - - +
19L ILE* 1.3 66.1 + - + +
21L LEU* 2.9 13.3 + - - +
22L ARG* 2.9 32.8 + - + +
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Residues in contact with ILE 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L GLU* 2.9 28.4 + - + +
16L LEU* 3.5 4.5 - - - +
18L ASP* 1.3 78.1 - - + +
20L ALA* 1.3 64.5 + - - +
22L ARG* 3.3 18.1 + - - +
23L ILE* 3.1 39.7 + - + +
104L VAL* 4.2 5.6 - - + -
139L LYS* 3.7 19.1 - - - +
144L ASP* 3.5 50.9 - - + +
182L GLY 4.1 3.8 - - - +
184L VAL* 3.6 11.2 - - + -
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Residues in contact with ALA 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L LEU 2.9 12.9 + - - +
17L SER 3.4 9.2 - - - +
18L ASP 3.1 0.2 - - - -
19L ILE* 1.3 77.7 - - - +
21L LEU* 1.3 62.6 + - - +
23L ILE* 3.2 17.7 + - - +
24L VAL* 3.2 17.6 + - - +
184L VAL* 3.9 21.1 - - + +
225L GLU 4.1 6.7 - - - +
226L GLY* 4.6 0.9 - - - -
227L THR 4.4 2.7 - - - +
228L LEU* 4.5 4.3 - - + +
266L PRO* 3.8 24.9 - - + -
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Residues in contact with LEU 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L SER* 3.0 34.9 + - - +
18L ASP* 2.9 11.2 + - - +
20L ALA* 1.3 71.3 - - - +
22L ARG* 1.3 67.0 + - + +
24L VAL* 3.4 8.8 + - + +
25L ALA* 2.9 24.8 + - - +
266L PRO* 3.8 26.7 - - + +
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Residues in contact with ARG 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L ASP* 2.9 23.5 + - + +
19L ILE* 3.7 19.1 - - - +
21L LEU* 1.3 78.8 - - + +
23L ILE* 1.3 65.2 + - - +
25L ALA* 3.3 17.2 + - - +
28L LYS* 4.2 6.9 + - - +
75L GLY* 4.3 3.5 - - - +
102L GLY* 3.0 32.9 + - - -
103L ILE 4.6 2.0 + - - -
104L VAL* 3.8 28.7 - - + +
144L ASP* 5.2 5.5 + - - -
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Residues in contact with ILE 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L ILE* 3.1 23.6 - - + +
20L ALA* 3.2 8.4 + - - +
22L ARG* 1.3 78.5 - - - +
24L VAL* 1.3 59.4 + - + +
25L ALA 3.4 1.9 + - - -
28L LYS* 3.9 9.2 - - - +
29L GLY 4.5 2.1 - - - +
30L ILE* 3.6 36.1 - - + -
75L GLY* 3.6 21.5 + - - -
76L GLY* 4.4 7.2 - - - +
104L VAL* 3.7 17.9 - - + -
145L PHE* 3.6 42.2 - - + -
184L VAL* 5.2 1.1 - - + -
228L LEU* 4.0 17.0 - - + -
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Residues in contact with VAL 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L ALA 3.4 14.4 - - - +
21L LEU* 4.0 12.8 - - + +
22L ARG 3.4 0.2 - - - -
23L ILE* 1.3 77.6 - - + +
25L ALA* 1.3 69.2 + - - +
26L PRO* 3.5 2.6 - - - +
28L LYS 4.5 4.9 - - - -
30L ILE* 5.7 0.4 - - + -
228L LEU* 3.7 26.0 - - + -
266L PRO* 4.2 17.7 - - + +
267L GLY* 4.2 6.1 - - - -
268L VAL 5.0 0.4 - - - +
269L THR* 3.8 22.0 - - + -
297L ALA* 3.7 31.5 - - + +
299L THR* 4.3 11.2 - - + +
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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