Contacts of the helix formed by residues 9 - 24 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6K PRO* 6.0 0.2 - - - -
8K LEU* 1.3 76.9 - - - +
10K ALA* 1.3 65.2 + - - +
11K GLU* 3.3 14.1 + - - +
12K GLN* 2.6 41.4 + - - +
13K LYS* 3.0 23.0 + - - +
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Residues in contact with ALA 10 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K SER* 1.3 74.5 - - - +
11K GLU* 1.3 69.4 + - + +
13K LYS* 3.4 12.1 + - - +
14K LYS* 3.1 22.5 + - - +
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Residues in contact with GLU 11 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K SER* 3.6 13.9 - - - +
10K ALA* 1.3 78.8 - - + +
12K GLN* 1.3 63.6 + - + +
14K LYS* 3.1 10.4 - - - +
15K GLU* 3.0 21.4 + - - +
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Residues in contact with GLN 12 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K ALA 4.2 2.1 - - - +
8K LEU* 3.3 28.2 - - + +
9K SER* 2.6 42.8 + - - +
11K GLU* 1.3 75.6 - - + +
13K LYS* 1.3 65.9 + - - +
15K GLU* 3.2 12.4 + - - +
16K LEU* 3.0 29.4 + - + +
179K GLN 5.4 0.8 + - - +
180K GLN* 4.8 11.5 + - - +
182K GLY* 6.0 1.9 - - - +
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Residues in contact with LYS 13 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259J ARG* 4.3 17.5 - - - +
8K LEU* 3.8 33.4 - - + +
9K SER 3.0 19.1 + - - +
10K ALA* 3.7 9.9 - - - +
12K GLN* 1.3 76.4 - - - +
14K LYS* 1.3 62.9 + - - +
16K LEU* 3.3 1.1 + - - -
17K SER* 2.9 21.3 + - - -
223K TYR* 3.3 54.3 - - + +
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Residues in contact with LYS 14 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K ALA 3.1 13.8 + - - +
11K GLU* 3.1 13.7 + - - +
13K LYS* 1.3 75.3 - - - +
15K GLU* 1.3 64.9 + - - +
17K SER* 3.0 13.9 + - - -
18K ASP* 2.8 54.7 + - - +
223K TYR* 5.2 0.6 + - - -
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Residues in contact with GLU 15 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K GLU 3.0 8.7 + - - +
12K GLN* 3.2 14.0 + - - +
14K LYS* 1.3 79.4 - - - +
16K LEU* 1.3 63.9 + - + +
18K ASP* 3.5 7.7 + - - +
19K ILE* 3.0 41.2 + - + +
139K LYS* 2.9 31.3 + - - -
182K GLY* 4.1 16.1 - - - +
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Residues in contact with LEU 16 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8K LEU* 3.5 33.4 - - + -
12K GLN* 3.0 16.5 + - + +
13K LYS 3.6 5.6 - - - +
15K GLU* 1.3 76.4 - - + +
17K SER* 1.3 63.9 + - - +
19K ILE* 3.2 3.0 + - + -
20K ALA* 2.9 21.1 + - - +
179K GLN* 3.8 28.5 - - + +
182K GLY* 3.7 11.9 - - - +
183K ILE 3.6 43.1 - - - +
184K VAL* 3.2 18.4 - - + +
223K TYR* 4.3 2.5 - - + -
226K GLY* 4.0 14.6 - - - +
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Residues in contact with SER 17 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K LYS 2.9 18.3 + - - -
14K LYS* 3.5 12.2 + - - -
16K LEU* 1.3 76.1 - - - +
18K ASP* 1.3 66.0 + - - +
20K ALA* 3.2 2.3 + - - +
21K LEU* 3.0 40.2 + - - +
223K TYR* 4.2 9.9 - - - -
225K GLU* 3.5 26.9 + - - +
226K GLY* 4.3 0.4 - - - -
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Residues in contact with ASP 18 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14K LYS* 2.8 49.5 + - - +
15K GLU* 3.8 7.1 + - - +
17K SER* 1.3 77.2 + - - +
19K ILE* 1.3 66.7 + - + +
21K LEU* 2.9 13.3 + - - +
22K ARG* 2.9 32.0 + - + +
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Residues in contact with ILE 19 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K GLU* 3.0 28.8 + - + +
16K LEU* 3.5 4.7 - - - +
18K ASP* 1.3 77.9 - - + +
20K ALA* 1.3 63.7 + - - +
22K ARG* 3.3 17.4 + - - +
23K ILE* 3.1 38.8 + - + +
104K VAL* 4.2 5.4 - - + -
139K LYS* 3.7 20.0 - - - +
144K ASP* 3.5 50.9 - - + +
182K GLY 4.1 3.6 - - - +
184K VAL* 3.6 10.5 - - + -
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Residues in contact with ALA 20 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K LEU 2.9 13.4 + - - +
17K SER 3.4 9.0 - - - +
18K ASP 3.1 0.2 - - - -
19K ILE* 1.3 76.7 - - - +
21K LEU* 1.3 63.6 + - - +
23K ILE* 3.2 17.2 + - - +
24K VAL* 3.2 18.1 + - - +
184K VAL* 3.9 21.5 - - + +
225K GLU 4.1 6.7 - - - +
226K GLY* 4.6 0.9 - - - -
227K THR 4.4 2.5 - - - +
228K LEU* 4.5 4.9 - - + +
266K PRO* 3.8 24.5 - - + -
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Residues in contact with LEU 21 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17K SER* 3.0 34.7 + - - +
18K ASP* 2.9 10.6 + - - +
20K ALA* 1.3 72.1 - - - +
22K ARG* 1.3 66.7 + - + +
24K VAL* 3.4 8.1 + - + +
25K ALA* 2.9 24.1 + - - +
225K GLU 5.8 0.2 - - - +
266K PRO* 3.8 26.0 - - + +
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Residues in contact with ARG 22 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K ASP* 2.9 24.1 + - + +
19K ILE* 3.7 18.9 - - - +
20K ALA 3.3 0.2 - - - -
21K LEU* 1.3 77.4 - - + +
23K ILE* 1.3 65.0 + - - +
25K ALA* 3.3 17.2 + - - +
28K LYS* 4.2 6.6 - - - +
75K GLY* 4.3 4.0 - - - +
102K GLY* 3.0 32.3 + - - -
103K ILE 4.6 1.8 + - - -
104K VAL* 3.8 28.7 - - + +
144K ASP* 5.2 6.1 + - - -
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Residues in contact with ILE 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K ILE* 3.1 24.5 - - + +
20K ALA* 3.2 8.0 + - - +
22K ARG* 1.3 78.6 - - - +
24K VAL* 1.3 59.7 + - + +
25K ALA 3.4 1.9 + - - -
28K LYS* 3.9 8.8 - - - +
29K GLY 4.5 2.3 - - - +
30K ILE* 3.6 36.6 - - + -
75K GLY* 3.6 21.2 + - - -
76K GLY* 4.4 7.6 - - - +
104K VAL* 3.7 18.4 - - + -
145K PHE* 3.6 42.6 - - + -
184K VAL* 5.2 1.1 - - + -
228K LEU* 4.0 16.2 - - + -
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Residues in contact with VAL 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K ALA 3.4 14.8 - - - +
21K LEU* 4.0 12.1 - - + +
22K ARG 3.4 0.2 - - - -
23K ILE* 1.3 76.4 - - + +
25K ALA* 1.3 68.3 + - - +
26K PRO* 3.5 2.1 - - - +
28K LYS 4.5 5.4 - - - -
30K ILE* 6.0 0.2 - - + -
228K LEU* 3.7 26.0 - - + -
266K PRO* 4.2 17.5 - - + +
267K GLY* 4.2 6.5 - - - -
268K VAL 5.0 0.2 - - - +
269K THR* 3.8 22.2 - - + -
297K ALA* 3.7 30.8 - - + +
299K THR* 4.3 11.9 - - + +
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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