Contacts of the helix formed by residues 24 - 34 (chain N) in PDB entry 1FQV
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 24 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20N ILE 4.3 0.4 + - - -
21N ALA* 2.9 13.2 + - - +
22N LYS 3.8 1.6 - - - -
23N GLN* 1.3 77.6 - - - +
25N VAL* 1.3 52.8 + - - +
27N ILE* 3.2 26.3 + - - +
28N LYS* 2.6 36.7 + - - +
62N CYS* 6.2 0.2 - - - -
110N LEU* 2.5 37.1 + - - +
112N ILE* 3.8 17.0 - - - -
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Residues in contact with VAL 25 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22N LYS 4.4 1.1 + - - +
23N GLN 3.8 3.0 + - - +
24N SER* 1.3 70.5 - - - +
26N THR* 1.3 58.3 + - - +
28N LYS* 3.4 13.7 - - + +
29N THR* 2.9 32.7 + - + +
110N LEU 3.1 4.2 + - - -
111N ASP* 2.7 41.5 + - + +
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Residues in contact with THR 26 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24N SER 3.1 0.6 - - - -
25N VAL* 1.3 77.7 - - - +
27N ILE* 1.3 62.4 + - + +
29N THR* 2.8 30.4 - - + +
30N MET* 3.3 32.8 + - + +
47N LEU* 5.2 0.2 - - + -
109N TYR* 2.4 48.7 + - + +
110N LEU* 3.1 19.2 + - + -
111N ASP* 3.8 4.7 + - - +
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Residues in contact with ILE 27 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6N LEU* 3.7 41.1 - - + -
21N ALA* 3.8 16.2 - - + +
24N SER* 3.1 28.0 + - - +
26N THR* 1.3 77.6 - - - +
28N LYS* 1.3 60.1 + - - +
30N MET* 4.0 7.5 - - - +
31N LEU* 3.2 37.4 + - + +
45N VAL* 4.3 4.9 - - + -
47N LEU* 3.7 34.5 - - + -
55N LEU* 5.5 0.4 - - + -
110N LEU* 3.8 12.8 - - + -
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Residues in contact with LYS 28 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21N ALA 4.6 0.2 + - - -
22N LYS* 3.1 59.7 - - + +
24N SER 2.6 20.7 + - - +
25N VAL* 3.4 16.4 - - + +
27N ILE* 1.3 71.8 - - - +
29N THR* 1.3 67.7 + - - +
31N LEU* 3.1 16.3 + - - +
32N GLU* 3.1 38.4 + - - +
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Residues in contact with THR 29 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25N VAL* 2.9 18.0 + - + +
26N THR* 2.8 30.3 - - + +
28N LYS* 1.3 76.8 - - - +
30N MET* 1.3 59.3 - - + +
32N GLU* 3.2 4.9 + - - -
33N ASP* 2.7 55.9 + - - +
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Residues in contact with MET 30 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26N THR* 3.4 35.9 - - + +
27N ILE* 4.0 6.1 - - - +
28N LYS 3.2 1.0 - - - -
29N THR* 1.3 82.1 - - + +
31N LEU* 1.3 55.1 + - - +
32N GLU 2.7 15.6 + - - -
33N ASP* 5.2 0.2 - - - -
34N LEU* 3.0 42.3 + - + +
35N GLY 3.2 2.1 + - - -
36N MET* 3.5 21.8 - - + +
45N VAL* 3.8 24.7 - - + -
46N PRO* 3.9 18.8 - - - +
47N LEU* 4.7 2.0 - - + -
48N PRO* 5.8 0.2 - - + -
109N TYR* 4.1 11.9 - - + +
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Residues in contact with LEU 31 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4N ILE* 3.7 38.8 - - + -
18N VAL* 5.1 7.0 - - + +
21N ALA* 4.6 8.1 - - + -
22N LYS* 5.3 3.1 - - + +
27N ILE* 3.2 30.0 + - + +
28N LYS* 3.1 9.2 + - - +
30N MET* 1.3 77.4 - - - +
32N GLU* 1.3 60.7 + - + +
35N GLY* 3.9 15.7 - - - +
36N MET 3.7 14.8 - - - +
45N VAL* 3.4 29.8 - - + -
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Residues in contact with GLU 32 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28N LYS* 3.1 50.0 + - + +
29N THR* 3.6 7.9 + - - +
30N MET 2.7 2.4 + - - -
31N LEU* 1.3 83.6 - - + +
33N ASP* 1.3 61.8 + - - +
34N LEU* 2.6 15.8 + - - -
35N GLY* 3.4 7.6 + - - -
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Residues in contact with ASP 33 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29N THR* 2.7 36.7 + - - +
32N GLU* 1.3 76.7 - - - +
34N LEU* 1.3 75.1 + - + +
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Residues in contact with LEU 34 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30N MET* 3.0 28.0 + - + +
32N GLU 2.6 8.4 + - - -
33N ASP* 1.3 93.4 - - + +
35N GLY* 1.3 66.3 + - - +
36N MET* 3.3 42.0 + - + +
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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