Contacts of the helix formed by residues 14 - 23 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12J VAL 3.3 3.5 - - - +
13J ILE* 1.3 87.7 - - + +
15J ALA* 1.3 71.6 + - - +
16J ALA* 3.2 7.7 + - + +
17J ARG* 3.2 15.0 + - + +
18J LEU* 3.0 16.5 + - - +
106J ALA* 5.9 1.8 - - + -
110J GLY* 3.2 24.2 - - - +
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Residues in contact with ALA 15 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J ILE 3.3 2.0 + - - -
14J PRO* 1.3 70.1 - - - +
16J ALA* 1.3 71.4 + - - +
18J LEU* 3.0 1.8 + - - +
19J PHE* 2.7 21.9 + - - +
79J PHE* 4.0 10.1 - - + -
104J ILE* 3.3 35.6 - - + +
105J VAL 3.9 1.3 - - - -
106J ALA* 3.7 34.5 - - + +
111J GLY 3.9 2.0 + - - -
112J SER* 3.5 8.7 - - - -
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Residues in contact with ALA 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J PRO* 4.5 6.7 - - + +
15J ALA* 1.3 80.9 - - - +
17J ARG* 1.3 63.6 + - - +
19J PHE* 3.0 15.4 + - - +
20J LYS* 3.2 15.4 + - + +
79J PHE* 3.4 27.7 - - + -
106J ALA* 5.5 0.4 - - - +
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Residues in contact with ARG 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J ILE* 3.8 18.7 - - + +
14J PRO* 3.2 16.6 + - + +
16J ALA* 1.3 78.8 - - - +
18J LEU* 1.3 65.8 + - - +
19J PHE 3.0 0.7 + - - -
20J LYS* 3.1 15.4 + - - +
21J ALA* 2.9 21.5 + - - +
151J LEU* 2.5 57.2 + - + +
152J LEU* 4.8 1.6 - - - +
154J HIS 4.0 1.6 + - - -
155J SER* 2.9 32.9 + - - +
157J ALA 3.3 15.5 + - - -
158J TYR* 3.5 20.2 - - + +
159J ASN* 4.1 12.0 + - + -
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Residues in contact with LEU 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J SER* 4.3 6.3 - - - -
13J ILE* 3.8 19.7 - - + +
14J PRO 3.0 15.9 + - - +
15J ALA 3.6 6.5 - - - +
17J ARG* 1.3 75.4 - - - +
19J PHE* 1.3 57.9 - - - +
21J ALA* 4.3 3.4 - - - -
22J PHE* 2.8 46.2 + - + +
104J ILE* 4.0 15.7 - - + -
112J SER* 3.8 17.5 - - - +
114J LEU* 3.9 25.8 - - + -
144J LEU* 4.0 20.2 - - + -
147J VAL* 4.3 3.6 - - + -
148J GLU* 5.3 0.2 - - + -
151J LEU* 4.0 17.9 - - + -
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Residues in contact with PHE 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J ALA 2.7 15.3 + - - +
16J ALA 3.2 10.3 - - - +
18J LEU* 1.3 70.1 - - - +
20J LYS* 1.3 72.9 + - + +
23J ILE* 2.9 54.5 + - + +
24J LEU* 3.3 33.3 + - + -
74J VAL* 4.5 4.7 - - + -
75J ASP 3.8 13.7 - - - -
76J HIS* 4.1 11.4 - - - -
79J PHE* 3.2 64.6 - + + -
80J LYS 4.3 4.5 - - - -
81J TYR* 4.1 7.9 - - + -
102J ILE 5.4 0.2 - - - -
104J ILE* 4.0 12.1 - - + +
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Residues in contact with LYS 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J ALA* 3.6 16.4 - - + +
17J ARG* 3.1 13.4 + - - +
19J PHE* 1.3 84.1 - - + +
21J ALA* 1.3 68.3 + - - +
24J LEU* 3.1 26.9 + - + +
25J ASP* 3.0 21.3 + - - +
79J PHE* 6.0 1.1 - - + -
158J TYR* 3.8 22.1 + - + +
159J ASN* 2.8 44.4 - - + +
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Residues in contact with ALA 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J ARG 2.9 16.2 + - - +
18J LEU 3.7 0.9 - - - +
20J LYS* 1.3 78.9 - - - +
22J PHE* 1.3 54.7 + - - +
25J ASP* 3.6 2.3 + - - +
26J GLY* 2.8 34.0 + - - -
29J LEU* 4.3 8.2 - - + +
147J VAL* 4.5 2.5 - - + -
151J LEU* 3.6 31.0 - - + -
158J TYR* 3.7 30.2 - - + -
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Residues in contact with PHE 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J LEU* 2.8 34.9 + - + +
21J ALA* 1.3 75.5 - - - +
23J ILE* 1.3 78.4 + - + +
26J GLY* 3.4 6.4 - - - -
27J ASP* 5.3 0.5 - - - +
30J PHE* 3.3 51.6 - + - -
102J ILE* 4.8 11.7 - - + -
104J ILE* 5.0 3.1 - - + -
114J LEU* 4.2 26.2 - - + -
116J ILE* 6.0 2.9 - - + -
140J GLY* 4.5 7.2 - - - -
143J LEU* 3.9 9.6 - - + -
144J LEU* 3.7 32.1 - - + -
147J VAL* 3.9 19.0 - - + +
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Residues in contact with ILE 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J PHE* 2.9 42.1 + - + +
22J PHE* 1.3 103.5 - - + +
24J LEU* 1.3 77.7 + - + +
25J ASP 3.4 0.4 - - - -
26J GLY 3.1 8.1 + - - -
27J ASP* 3.5 15.6 - - - +
81J TYR* 3.5 54.6 - - + -
102J ILE* 4.3 18.8 - - + -
104J ILE* 4.6 7.2 - - + -
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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