Contacts of the helix formed by residues 14 - 23 (chain D) in PDB entry 1FSK
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 PRO 14 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12D VAL 3.3 3.6 - - - +
13D ILE* 1.3 87.5 - - + +
15D ALA* 1.3 70.1 + - - +
16D ALA* 3.2 7.9 + - + +
17D ARG* 3.2 15.4 + - + +
18D LEU* 3.0 16.5 + - - +
106D ALA* 5.7 2.2 - - + -
110D GLY* 3.2 24.9 - - - +
111D GLY 3.9 0.2 - - - +
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Residues in contact with ALA 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ILE 3.3 2.6 + - - -
14D PRO* 1.3 70.0 - - - +
16D ALA* 1.3 69.7 + - - +
18D LEU* 3.0 1.5 + - - +
19D PHE* 2.7 21.9 + - - +
79D PHE* 4.0 10.5 - - + -
104D ILE* 3.3 36.0 - - + +
105D VAL 3.9 1.3 - - - -
106D ALA* 3.7 35.1 - - + +
111D GLY 3.9 1.8 + - - -
112D SER* 3.5 8.7 - - - -
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Residues in contact with ALA 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D PRO* 4.5 7.0 - - + +
15D ALA* 1.3 82.1 - - - +
17D ARG* 1.3 63.1 + - + +
19D PHE* 3.1 15.6 + - - +
20D LYS* 3.2 15.2 + - + +
79D PHE* 3.4 28.5 - - + -
106D ALA* 5.5 0.2 - - - +
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Residues in contact with ARG 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ILE* 3.8 18.7 - - + +
14D PRO* 3.2 16.6 + - + +
16D ALA* 1.3 79.9 - - + +
18D LEU* 1.3 65.9 + - - +
19D PHE 3.0 0.7 + - - -
20D LYS* 3.1 14.4 + - - +
21D ALA* 2.9 21.5 + - - +
151D LEU* 2.5 56.8 + - + +
152D LEU* 4.8 1.6 - - - +
154D HIS 4.0 1.8 + - - -
155D SER* 2.9 31.9 + - - +
157D ALA 3.3 15.5 + - - -
158D TYR* 3.5 21.4 - - + +
159D ASN* 4.1 11.9 + - + -
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Residues in contact with LEU 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D SER* 4.3 5.2 - - - -
13D ILE* 3.8 19.9 - - + +
14D PRO 3.0 15.9 + - - +
15D ALA 3.6 7.2 - - - +
17D ARG* 1.3 74.4 - - - +
19D PHE* 1.3 57.6 + - - +
21D ALA* 4.3 3.6 - - - -
22D PHE* 2.8 45.1 + - + +
104D ILE* 4.0 15.5 - - + -
112D SER* 3.9 18.4 - - - +
114D LEU* 3.9 26.2 - - + -
144D LEU* 4.0 20.4 - - + -
147D VAL* 4.3 4.0 - - + -
148D GLU* 5.3 0.4 - - + -
151D LEU* 4.0 17.5 - - + -
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Residues in contact with PHE 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ALA 2.7 14.7 + - - +
16D ALA 3.2 10.1 - - - +
18D LEU* 1.3 70.7 - - - +
20D LYS* 1.3 73.3 + - + +
23D ILE* 2.9 56.0 + - + +
24D LEU* 3.3 34.0 + - + -
74D VAL* 4.5 4.0 - - + -
75D ASP 3.8 14.1 - - - -
76D HIS* 4.1 11.2 - - - -
79D PHE* 3.2 63.7 - + + -
80D LYS 4.3 4.5 - - - -
81D TYR* 4.1 7.9 - - + -
102D ILE 5.4 0.4 - - - -
104D ILE* 4.0 13.4 - - + +
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Residues in contact with LYS 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ALA* 3.6 16.4 - - + +
17D ARG* 3.4 12.3 - - - +
19D PHE* 1.3 83.0 - - + +
21D ALA* 1.3 69.0 + - - +
24D LEU* 3.1 26.1 + - + +
25D ASP* 3.0 21.4 + - - +
79D PHE* 6.0 1.1 - - + -
158D TYR* 3.8 23.0 + - + +
159D ASN* 2.8 44.2 - - + +
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Residues in contact with ALA 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ARG 2.9 15.8 + - - +
18D LEU 3.7 0.9 - - - +
20D LYS* 1.3 79.4 - - - +
22D PHE* 1.3 55.1 + - - +
25D ASP 3.6 1.7 + - - -
26D GLY* 2.8 34.0 + - - -
29D LEU* 4.3 8.0 - - + +
147D VAL* 4.5 3.1 - - + -
151D LEU* 3.6 31.4 - - + -
158D TYR* 3.7 29.7 - - + -
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Residues in contact with PHE 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 2.8 34.7 + - + +
21D ALA* 1.3 74.3 - - - +
23D ILE* 1.3 78.3 + - + +
26D GLY* 3.4 6.2 - - - -
27D ASP* 5.3 0.2 - - - +
30D PHE* 3.3 52.5 - + - -
102D ILE* 4.8 11.2 - - + -
104D ILE* 5.0 2.9 - - + -
114D LEU* 4.2 26.0 - - + -
116D ILE* 6.0 2.2 - - + -
140D GLY* 4.6 7.0 - - - -
143D LEU* 3.9 10.1 - - + -
144D LEU* 3.7 31.9 - - + -
147D VAL* 3.9 19.0 - - + +
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Residues in contact with ILE 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D PHE* 2.9 40.9 + - + +
22D PHE* 1.3 106.3 - - + +
24D LEU* 1.3 76.4 + - + +
25D ASP 3.4 0.4 - - - -
26D GLY 3.2 9.0 + - - -
27D ASP* 3.5 15.1 - - - +
81D TYR* 3.5 53.4 - - + -
102D ILE* 4.3 17.7 - - + -
104D ILE* 4.6 8.3 - - + -
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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