Contacts of the helix formed by residues 9 - 24 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C PRO* 6.0 0.4 - - - -
8C LEU* 1.3 76.3 - - - +
10C ALA* 1.3 65.3 + - - +
11C GLU* 3.3 13.8 + - - +
12C GLN* 2.6 42.3 + - - +
13C LYS* 3.0 23.3 + - - +
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Residues in contact with ALA 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C SER* 1.3 74.0 - - - +
11C GLU* 1.3 70.7 + - + +
13C LYS* 3.4 11.9 + - - +
14C LYS* 3.1 22.5 + - - +
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Residues in contact with GLU 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C SER* 3.6 13.9 - - - +
10C ALA* 1.3 78.8 - - + +
12C GLN* 1.3 64.4 + - + +
14C LYS* 3.1 10.1 - - - +
15C GLU* 3.0 21.6 + - - +
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Residues in contact with GLN 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ALA 4.2 2.3 + - - +
8C LEU* 3.3 27.5 - - + +
9C SER* 2.6 43.8 + - - +
11C GLU* 1.3 75.5 - - + +
13C LYS* 1.3 66.6 + - - +
15C GLU* 3.2 12.4 + - - +
16C LEU* 3.0 29.1 + - + +
179C GLN 5.4 1.5 + - - +
180C GLN* 4.8 10.9 + - - +
182C GLY* 6.0 2.2 - - - +
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Residues in contact with LYS 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B ARG* 4.3 17.9 - - - +
8C LEU* 3.8 32.7 - - + +
9C SER 3.0 19.4 + - - +
10C ALA* 3.7 10.3 - - - +
12C GLN* 1.3 76.5 - - - +
14C LYS* 1.3 64.4 + - - +
16C LEU* 3.3 0.8 + - - -
17C SER* 2.9 21.3 + - - -
223C TYR* 3.3 55.1 - - + +
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Residues in contact with LYS 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ALA 3.1 14.5 + - - +
11C GLU* 3.1 14.1 - - - +
13C LYS* 1.3 74.9 - - - +
15C GLU* 1.3 65.7 + - - +
17C SER* 3.0 13.3 + - - -
18C ASP* 2.8 55.3 + - - +
223C TYR* 5.2 0.6 + - - -
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Residues in contact with GLU 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C GLU 3.0 8.8 + - - +
12C GLN* 3.2 14.3 + - - +
14C LYS* 1.3 79.0 - - - +
16C LEU* 1.3 62.2 + - + +
18C ASP* 3.5 7.9 + - - +
19C ILE* 2.9 44.0 + - + +
139C LYS* 2.9 31.1 + - - -
182C GLY* 4.1 16.3 - - - +
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Residues in contact with LEU 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 3.5 33.2 - - + -
12C GLN* 3.0 17.5 + - + +
13C LYS 3.6 5.8 - - - +
15C GLU* 1.3 76.9 - - + +
17C SER* 1.3 64.8 + - - +
19C ILE* 3.2 3.0 + - + -
20C ALA* 2.9 21.3 + - - +
179C GLN* 3.8 28.7 - - + +
182C GLY* 3.7 11.7 - - - +
183C ILE 3.6 42.2 - - - +
184C VAL* 3.2 18.5 - - + +
223C TYR* 4.3 3.1 - - + -
226C GLY* 4.0 13.7 - - - +
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Residues in contact with SER 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LYS 2.9 17.9 + - - -
14C LYS* 3.5 12.7 + - - -
16C LEU* 1.3 76.7 - - - +
18C ASP* 1.3 65.7 + - - +
20C ALA* 3.2 2.1 + - - +
21C LEU* 3.0 40.6 + - - +
223C TYR* 4.2 9.6 - - - -
225C GLU* 3.5 27.2 + - - +
226C GLY* 4.3 0.4 - - - -
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Residues in contact with ASP 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LYS* 2.8 50.1 + - - +
15C GLU* 3.8 6.7 + - - +
17C SER* 1.3 76.0 + - - +
19C ILE* 1.3 66.3 + - + +
21C LEU* 2.9 13.4 + - - +
22C ARG* 2.9 33.2 + - + +
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Residues in contact with ILE 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C GLU* 2.9 29.8 + - + +
16C LEU* 3.5 4.5 - - - +
18C ASP* 1.3 77.5 - - + +
20C ALA* 1.3 64.3 + - - +
22C ARG* 3.3 16.9 + - - +
23C ILE* 3.1 40.2 + - + +
104C VAL* 4.2 5.4 - - + -
139C LYS* 3.7 20.0 - - - +
144C ASP* 3.5 53.2 - - + +
182C GLY 4.1 3.1 - - - +
184C VAL* 3.6 11.0 - - + -
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Residues in contact with ALA 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LEU 2.9 14.0 + - - +
17C SER 3.4 9.0 - - - +
19C ILE* 1.3 75.4 - - - +
21C LEU* 1.3 62.7 + - - +
23C ILE* 3.2 17.5 + - - +
24C VAL* 3.2 17.6 + - - +
184C VAL* 3.9 22.0 - - + +
225C GLU 4.1 7.0 - - - +
226C GLY* 4.6 0.9 - - - -
227C THR 4.4 2.0 - - - +
228C LEU* 4.5 4.8 - - + +
266C PRO* 3.8 24.9 - - + -
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Residues in contact with LEU 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C SER* 3.0 33.4 + - - +
18C ASP* 2.9 10.6 + - - +
20C ALA* 1.3 73.4 - - - +
22C ARG* 1.3 65.9 + - - +
24C VAL* 3.6 7.1 - - + -
25C ALA* 2.9 25.3 + - - +
266C PRO* 3.8 26.0 - - + +
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Residues in contact with ARG 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ASP* 2.9 24.3 + - + +
19C ILE* 3.7 18.8 - - - +
21C LEU* 1.3 77.1 - - - +
23C ILE* 1.3 64.7 + - - +
25C ALA* 3.3 16.8 + - - +
28C LYS* 4.2 6.8 - - - +
75C GLY* 4.3 3.5 - - - +
102C GLY* 3.0 32.5 + - - -
103C ILE 4.6 1.8 + - - -
104C VAL* 3.8 28.4 - - + +
144C ASP* 5.2 5.5 + - - -
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Residues in contact with ILE 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ILE* 3.1 24.5 - - + +
20C ALA* 3.2 7.6 + - - +
22C ARG* 1.3 80.4 - - - +
24C VAL* 1.3 59.1 + - + +
25C ALA 3.4 1.9 + - - -
28C LYS* 3.9 9.0 - - - +
29C GLY* 4.5 2.4 - - - +
30C ILE* 3.6 36.3 - - + +
75C GLY* 3.6 19.9 + - - -
76C GLY* 4.4 7.4 - - - +
104C VAL* 3.7 18.6 - - + -
145C PHE* 3.6 43.1 - - + -
184C VAL* 5.2 0.9 - - + -
228C LEU* 4.0 16.2 - - + -
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Residues in contact with VAL 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ALA 3.2 14.1 + - - +
21C LEU* 3.6 12.6 - - + +
23C ILE* 1.3 76.6 - - + +
25C ALA* 1.3 69.3 + - - +
26C PRO* 3.5 2.3 - - - +
28C LYS 4.5 5.2 - - - -
30C ILE* 6.0 0.4 - - + -
228C LEU* 3.7 25.1 - - + -
266C PRO* 4.2 17.5 - - + +
267C GLY* 4.2 6.7 - - - -
268C VAL 5.0 0.4 - - - +
269C THR* 3.8 22.2 - - + -
297C ALA* 3.7 31.0 - - + +
299C 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