Contacts of the helix formed by residues 9 - 24 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6G PRO* 6.0 0.4 - - - -
8G LEU* 1.3 75.9 - - - +
10G ALA* 1.3 63.7 + - - +
11G GLU* 3.3 14.0 + - - +
12G GLN* 2.6 43.0 + - - +
13G LYS* 3.0 23.3 + - - +
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Residues in contact with ALA 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G SER* 1.3 74.7 - - - +
11G GLU* 1.3 68.3 + - + +
13G LYS* 3.4 11.3 + - - +
14G LYS* 3.1 23.3 + - - +
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Residues in contact with GLU 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G SER* 3.6 13.2 - - - +
10G ALA* 1.3 77.8 - - + +
12G GLN* 1.3 64.0 + - + +
14G LYS* 3.1 10.3 - - - +
15G GLU* 3.0 21.0 + - - +
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Residues in contact with GLN 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G ALA 4.2 2.6 + - - +
8G LEU* 3.3 27.8 - - + +
9G SER* 2.6 42.1 + - - +
11G GLU* 1.3 75.0 - - + +
13G LYS* 1.3 66.3 + - - +
15G GLU* 3.2 12.8 + - - +
16G LEU* 3.0 29.4 + - + +
179G GLN 5.4 1.3 + - - +
180G GLN* 4.8 11.1 + - - +
182G GLY* 6.0 2.5 - - - +
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Residues in contact with LYS 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259F ARG* 4.4 16.3 - - - +
8G LEU* 3.8 33.2 - - + +
9G SER 3.0 18.6 + - - +
10G ALA* 3.7 10.5 - - - +
12G GLN* 1.3 77.3 - - - +
14G LYS* 1.3 64.3 + - - +
16G LEU* 3.3 0.8 + - - -
17G SER* 2.9 21.3 + - - -
223G TYR* 3.3 53.9 - - + +
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Residues in contact with LYS 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G ALA 3.1 13.6 + - - +
11G GLU* 3.1 13.2 + - - +
13G LYS* 1.3 75.9 - - - +
15G GLU* 1.3 64.4 + - - +
17G SER* 3.0 12.3 + - - -
18G ASP* 2.8 55.6 + - - +
223G TYR* 5.2 0.8 + - - -
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Residues in contact with GLU 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G GLU 3.0 8.6 + - - +
12G GLN* 3.2 14.5 + - - +
14G LYS* 1.3 79.5 - - - +
16G LEU* 1.3 62.4 + - + +
18G ASP* 3.5 7.7 + - - +
19G ILE* 2.9 44.6 + - + +
139G LYS* 2.9 31.1 + - - -
182G GLY* 4.1 15.9 - - - +
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Residues in contact with LEU 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G LEU* 3.5 33.9 - - + -
12G GLN* 3.0 17.6 + - + +
13G LYS 3.6 4.9 - - - +
15G GLU* 1.3 76.9 - - + +
17G SER* 1.3 63.9 + - - +
19G ILE* 3.2 2.6 + - + -
20G ALA* 2.9 21.0 + - - +
179G GLN* 3.8 28.7 - - + +
182G GLY* 3.7 11.4 - - - +
183G ILE 3.6 42.6 - - - +
184G VAL* 3.2 18.7 - - + +
223G TYR* 4.3 2.9 - - + -
226G GLY* 4.0 13.5 - - - -
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Residues in contact with SER 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G LYS 2.9 17.2 + - - -
14G LYS* 3.5 12.2 + - - -
16G LEU* 1.3 75.2 - - - +
18G ASP* 1.3 66.0 + - - +
20G ALA* 3.2 2.3 + - - +
21G LEU* 3.0 40.6 + - - +
223G TYR* 4.2 10.3 - - - -
225G GLU* 3.5 27.1 + - - +
226G GLY* 4.3 0.4 - - - -
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Residues in contact with ASP 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G LYS* 2.8 49.5 + - - +
15G GLU* 3.8 6.9 + - - +
17G SER* 1.3 76.7 + - - +
19G ILE* 1.3 66.0 + - + +
21G LEU* 2.9 12.4 + - - +
22G ARG* 2.9 32.3 + - + +
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Residues in contact with ILE 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G GLU* 2.9 29.0 + - + +
16G LEU* 3.5 4.9 - - - +
18G ASP* 1.3 76.2 - - + +
20G ALA* 1.3 63.9 + - - +
22G ARG* 3.3 16.7 + - - +
23G ILE* 3.1 40.5 + - + +
104G VAL* 4.2 4.7 - - + -
139G LYS* 3.7 19.3 - - - +
144G ASP* 3.5 50.7 - - + +
182G GLY 4.1 3.8 - - - +
184G VAL* 3.6 11.7 - - + -
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Residues in contact with ALA 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G LEU 2.9 13.4 + - - +
17G SER 3.4 9.4 - - - +
19G ILE* 1.3 76.9 - - - +
21G LEU* 1.3 61.9 + - - +
23G ILE* 3.2 17.6 + - - +
24G VAL* 3.2 18.4 + - - +
184G VAL* 3.9 21.3 - - + +
225G GLU 4.1 6.3 - - - +
226G GLY* 4.6 0.9 - - - -
227G THR 4.4 2.5 - - - +
228G LEU* 4.5 4.3 - - + +
266G PRO* 3.8 26.0 - - + -
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Residues in contact with LEU 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G SER* 3.0 34.5 + - - +
18G ASP* 2.9 10.8 + - - +
20G ALA* 1.3 72.7 - - - +
22G ARG* 1.3 65.6 + - + +
24G VAL* 3.4 8.4 + - + +
25G ALA* 2.9 24.9 + - - +
225G GLU 5.8 0.2 - - - +
266G PRO* 3.8 26.2 - - + +
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Residues in contact with ARG 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G ASP* 2.9 24.5 + - + +
19G ILE* 3.7 17.9 - - - +
20G ALA 3.3 0.2 - - - -
21G LEU* 1.3 77.8 - - + +
23G ILE* 1.3 64.8 + - - +
25G ALA* 3.3 17.6 + - - +
28G LYS* 4.2 7.1 + - - +
75G GLY* 4.3 3.3 - - - +
102G GLY* 3.0 32.9 + - - -
103G ILE 4.6 2.0 + - - -
104G VAL* 3.8 29.4 - - + +
144G ASP* 5.2 6.1 + - - -
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Residues in contact with ILE 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G ILE* 3.1 24.2 - - + +
20G ALA* 3.2 7.6 + - - +
22G ARG* 1.3 79.2 - - - +
24G VAL* 1.3 58.7 + - + +
25G ALA 3.4 2.1 + - - -
28G LYS* 3.9 9.2 - - - +
29G GLY* 4.5 2.4 - - - +
30G ILE* 3.6 36.6 - - + -
75G GLY* 3.6 20.7 + - - -
76G GLY* 4.4 7.4 - - - +
104G VAL* 3.7 18.6 - - + -
145G PHE* 3.6 42.8 - - + -
184G VAL* 5.2 0.9 - - + -
228G LEU* 4.0 16.8 - - + -
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Residues in contact with VAL 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G ALA 3.4 14.4 - - - +
21G LEU* 4.0 11.9 - - + +
22G ARG 3.4 0.2 - - - -
23G ILE* 1.3 77.8 - - + +
25G ALA* 1.3 68.9 + - - +
26G PRO* 3.5 2.4 - - - +
28G LYS 4.5 4.9 - - - -
29G GLY* 6.5 0.2 - - - -
30G ILE* 6.0 0.4 - - + -
228G LEU* 3.7 25.8 - - + -
266G PRO* 4.2 17.0 - - + +
267G GLY* 4.2 6.5 - - - -
268G VAL 5.5 0.2 - - - -
269G THR* 3.8 22.0 - - + -
297G ALA* 3.7 30.4 - - + +
299G THR* 4.3 10.7 - - + +
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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