Contacts of the helix formed by residues 9 - 24 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6I PRO* 6.0 0.4 - - - -
8I LEU* 1.3 76.1 - - - +
10I ALA* 1.3 64.0 + - - +
11I GLU* 3.3 14.4 + - - +
12I GLN* 2.6 43.0 + - - +
13I LYS* 3.0 23.3 + - - +
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Residues in contact with ALA 10 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I SER* 1.3 74.5 - - - +
11I GLU* 1.3 68.8 + - + +
13I LYS* 3.4 11.7 + - - +
14I LYS* 3.1 23.3 + - - +
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Residues in contact with GLU 11 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I SER* 3.6 13.5 - - - +
10I ALA* 1.3 77.4 - - + +
12I GLN* 1.3 63.6 + - + +
14I LYS* 3.1 10.4 - - - +
15I GLU* 3.0 21.0 + - - +
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Residues in contact with GLN 12 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I ALA 4.2 2.6 + - - +
8I LEU* 3.3 26.8 - - + +
9I SER* 2.6 41.9 + - - +
11I GLU* 1.3 75.4 - - + +
13I LYS* 1.3 66.3 + - - +
15I GLU* 3.2 13.0 + - - +
16I LEU* 3.0 29.2 + - + +
179I GLN 5.4 1.1 + - - +
180I GLN* 4.8 11.1 + - - +
182I GLY* 6.0 2.5 - - - +
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Residues in contact with LYS 13 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I LEU* 3.8 33.0 - - + +
9I SER 3.0 19.0 + - - +
10I ALA* 3.7 10.5 - - - +
12I GLN* 1.3 77.1 - - - +
14I LYS* 1.3 64.5 + - - +
16I LEU* 3.3 1.0 + - - -
17I SER* 2.9 21.5 + - - -
223I TYR* 3.3 54.1 - - + +
259L ARG* 4.5 15.3 - - - +
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Residues in contact with LYS 14 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I ALA 3.1 13.4 + - - +
11I GLU* 3.1 13.2 + - - +
13I LYS* 1.3 75.9 - - - +
15I GLU* 1.3 64.4 + - - +
17I SER* 3.0 12.4 + - - -
18I ASP* 2.8 55.3 + - - +
223I TYR* 5.2 0.6 + - - -
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Residues in contact with GLU 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I GLU 3.0 8.8 + - - +
12I GLN* 3.6 14.6 - - - +
14I LYS* 1.3 80.1 - - - +
16I LEU* 1.3 61.9 + - + +
18I ASP* 3.5 8.1 + - - +
19I ILE* 2.9 44.3 + - + +
139I LYS* 2.9 31.1 + - - -
182I GLY* 4.1 15.7 - - - +
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Residues in contact with LEU 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I LEU* 3.5 33.9 - - + -
12I GLN* 3.0 16.9 + - + +
13I LYS 3.6 4.9 - - - +
15I GLU* 1.3 77.3 - - + +
17I SER* 1.3 64.2 + - - +
19I ILE* 3.2 2.6 + - + -
20I ALA* 2.9 21.0 + - - +
179I GLN* 3.8 28.7 - - + +
182I GLY* 3.7 11.2 - - - +
183I ILE 3.6 42.4 - - - +
184I VAL* 3.2 18.7 - - + +
223I TYR* 4.3 2.7 - - + -
226I GLY* 4.0 13.5 - - - -
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Residues in contact with SER 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I LYS 2.9 17.4 + - - -
14I LYS* 3.5 12.0 + - - -
16I LEU* 1.3 75.7 - - - +
18I ASP* 1.3 66.2 + - - +
20I ALA* 3.2 2.1 + - - +
21I LEU* 3.0 40.8 + - - +
223I TYR* 4.2 10.3 - - - -
225I GLU* 3.5 26.9 + - - +
226I GLY* 4.3 0.4 - - - -
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Residues in contact with ASP 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I LYS* 2.8 50.1 + - - +
15I GLU* 3.8 7.1 + - - +
17I SER* 1.3 76.5 + - - +
19I ILE* 1.3 65.6 + - + +
21I LEU* 2.9 12.4 + - - +
22I ARG* 2.9 32.3 + - + +
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Residues in contact with ILE 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I GLU* 2.9 29.5 + - + +
16I LEU* 3.5 5.2 - - - +
18I ASP* 1.3 76.6 - - + +
20I ALA* 1.3 63.3 + - - +
22I ARG* 3.3 16.7 + - - +
23I ILE* 3.1 40.3 + - + +
104I VAL* 4.2 4.7 - - + -
139I LYS* 3.7 19.3 - - - +
144I ASP* 3.5 50.5 - - + +
182I GLY 4.1 3.8 - - - +
184I VAL* 3.6 11.4 - - + -
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Residues in contact with ALA 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I LEU 2.9 13.4 + - - +
17I SER 3.4 9.4 - - - +
19I ILE* 1.3 77.0 - - - +
21I LEU* 1.3 62.5 + - - +
23I ILE* 3.2 17.4 + - - +
24I VAL* 3.2 18.6 + - - +
184I VAL* 3.9 21.1 - - + +
225I GLU 4.1 6.5 - - - +
226I GLY* 4.6 0.9 - - - -
227I THR 4.4 2.5 - - - +
228I LEU* 4.5 4.3 - - + +
266I PRO* 3.8 25.8 - - + -
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Residues in contact with LEU 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I SER* 3.0 34.0 + - - +
18I ASP* 2.9 10.8 + - - +
20I ALA* 1.3 72.7 - - - +
22I ARG* 1.3 66.1 + - + +
24I VAL* 3.6 8.2 - - + +
25I ALA* 2.9 25.1 + - - +
225I GLU 5.8 0.2 - - - +
266I PRO* 3.8 25.6 - - + +
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Residues in contact with ARG 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A ASP* 5.9 0.8 + - - -
18I ASP* 2.9 24.3 + - + +
19I ILE* 3.7 17.9 - - - +
20I ALA 3.3 0.2 - - - -
21I LEU* 1.3 77.8 - - + +
23I ILE* 1.3 64.6 + - - +
25I ALA* 3.3 17.6 + - - +
28I LYS* 4.2 7.1 + - - +
75I GLY* 4.3 3.3 - - - +
102I GLY* 3.0 32.9 + - - -
103I ILE 4.6 2.0 + - - -
104I VAL* 3.8 29.2 - - + +
144I ASP* 5.2 6.1 + - - -
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Residues in contact with ILE 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I ILE* 3.1 24.0 - - + +
20I ALA* 3.2 7.6 + - - +
22I ARG* 1.3 79.4 - - - +
24I VAL* 1.3 58.7 + - + +
25I ALA 3.4 2.1 + - - -
28I LYS* 3.9 9.2 - - - +
29I GLY* 4.5 2.4 - - - +
30I ILE* 3.6 36.3 - - + -
75I GLY* 3.6 20.7 + - - -
76I GLY* 4.4 7.6 - - - +
104I VAL* 3.7 18.4 - - + -
145I PHE* 3.6 42.6 - - + -
184I VAL* 5.2 0.9 - - + -
228I LEU* 4.0 17.0 - - + -
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Residues in contact with VAL 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I ALA 3.4 14.6 - - - +
21I LEU* 4.0 11.9 - - + +
22I ARG 3.4 0.2 - - - -
23I ILE* 1.3 78.0 - - + +
25I ALA* 1.3 68.7 + - - +
26I PRO* 3.5 2.4 - - - +
28I LYS 4.5 4.9 - - - -
29I GLY* 6.5 0.2 - - - -
30I ILE* 6.0 0.4 - - + -
228I LEU* 3.7 26.0 - - + -
266I PRO* 4.2 17.0 - - + +
267I GLY* 4.2 6.3 - - - -
268I VAL 5.5 0.2 - - - -
269I THR* 3.8 21.8 - - + -
297I ALA* 3.7 31.0 - - + +
299I THR* 4.3 10.9 - - + +
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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