Contacts of the helix formed by residues 25 - 34 (chain G) 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 ASP 25 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20G LYS 3.0 11.0 + - - +
21G ALA 3.6 0.9 - - - -
24G LEU* 1.3 73.0 - - + +
26G GLY* 1.3 66.2 + - - +
27G ASP* 3.0 3.6 + - - -
28G ASN* 2.3 55.3 + - - +
29G LEU* 3.5 3.1 + - - +
158G TYR* 3.1 40.1 + - + -
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Residues in contact with GLY 26 (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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21G ALA 2.8 17.4 + - - -
22G PHE* 3.4 17.5 - - - -
23G ILE 3.1 5.0 + - - -
25G ASP* 1.3 78.3 - - - +
27G ASP* 1.3 56.7 + - - +
28G ASN 2.8 8.1 + - - -
29G LEU* 2.9 17.7 + - - -
30G PHE* 2.9 27.8 + - - -
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Residues in contact with ASP 27 (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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22G PHE 5.3 0.2 - - - +
23G ILE* 3.5 14.6 - - - +
24G LEU 4.8 1.4 - - - +
25G ASP 3.0 2.4 + - - -
26G GLY* 1.3 72.9 - - - +
28G ASN* 1.3 57.8 + - - +
30G PHE* 4.0 17.1 - - - -
31G PRO* 4.3 4.1 - - - +
41G VAL* 3.2 44.1 - - + +
54G LYS* 3.8 37.2 + - + +
56G ILE* 4.3 13.7 - - - +
81G TYR* 4.6 12.2 + - - -
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Residues in contact with ASN 28 (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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25G ASP* 2.3 51.9 + - - +
26G GLY 2.8 1.6 + - - -
27G ASP* 1.3 77.0 - - - +
29G LEU* 1.3 69.3 + - - +
30G PHE 3.4 1.1 - - - -
31G PRO* 3.4 14.8 - - - +
32G LYS* 3.8 21.1 + - - +
158G TYR* 4.9 0.5 + - - -
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Residues in contact with LEU 29 (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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21G ALA* 4.3 17.9 - - + +
25G ASP 3.8 7.0 - - - +
26G GLY* 3.3 10.1 - - - +
28G ASN* 1.3 86.3 + - - +
30G PHE* 1.3 60.4 + - + +
32G LYS* 2.9 29.8 + - + +
33G VAL* 2.9 41.3 + - + +
147G VAL* 4.5 23.6 - - + -
150G TYR* 4.6 14.4 - - + -
151G LEU* 5.9 0.4 - - + -
158G TYR* 3.3 36.3 - - + +
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Residues in contact with PHE 30 (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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22G PHE* 3.3 58.3 - + - -
26G GLY* 2.9 28.3 + - - -
27G ASP* 4.0 17.7 - - - -
29G LEU* 1.3 72.8 - - - +
31G PRO* 1.3 63.8 - - + +
32G LYS 2.9 4.9 - - - -
33G VAL* 4.1 5.4 - - + -
34G ALA* 2.7 33.1 + - - -
38G ILE* 3.2 35.4 - - + -
41G VAL* 5.5 1.6 - - + -
56G ILE* 6.3 0.7 - - + -
143G LEU* 4.4 20.4 - - + -
147G VAL* 3.8 18.4 - - + -
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Residues in contact with PRO 31 (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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27G ASP 4.3 3.6 - - - +
28G ASN* 3.4 24.9 - - - +
30G PHE* 1.3 93.1 - - + +
32G LYS* 1.3 57.9 + - - +
35G PRO* 3.3 19.3 - - - +
38G ILE* 3.4 26.0 - - + +
39G SER 3.1 26.9 - - - +
40G SER* 4.0 9.9 - - - -
41G VAL* 4.4 6.1 - - + +
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Residues in contact with LYS 32 (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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28G ASN* 3.8 20.1 + - - +
29G LEU* 3.0 28.1 - - + +
30G PHE 2.9 1.6 - - - -
31G PRO* 1.3 79.7 - - - +
33G VAL* 1.3 62.0 + - + +
35G PRO* 3.2 19.1 - - - +
150G TYR* 3.9 23.3 - - + +
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Residues in contact with VAL 33 (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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29G LEU* 2.9 33.2 + - + +
30G PHE* 4.0 9.4 - - + +
32G LYS* 1.3 70.7 - - + +
34G ALA* 1.3 60.9 + - + +
35G PRO* 3.0 11.1 - - - +
36G GLN* 4.8 1.2 + - - +
146G ALA* 3.8 36.3 - - + +
147G VAL* 4.2 12.8 - - + -
150G TYR* 3.4 43.1 - - + -
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Residues in contact with ALA 34 (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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30G PHE* 2.7 22.2 + - + +
33G VAL* 1.3 78.9 - - + +
35G PRO* 1.3 50.8 - - - +
36G GLN* 2.8 21.0 + - - +
37G ALA* 2.8 27.2 + - + -
38G ILE 3.3 7.3 + - - +
142G THR* 5.1 1.3 - - - +
143G LEU* 3.7 29.4 - - + -
146G ALA* 4.1 12.8 - - + -
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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