Contacts of the helix formed by residues 24 - 34 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20L ILE 5.6 0.4 - - - -
21L ALA* 2.9 12.7 + - - +
22L LYS 2.8 2.7 - - - +
23L GLN* 1.3 78.5 - - - +
25L VAL* 1.3 52.7 + - - +
27L ILE* 3.3 24.0 + - - +
28L LYS* 2.6 36.7 + - - +
62L CYS* 6.2 0.2 - - - -
110L LEU* 2.4 41.6 + - - +
112L ILE* 3.7 17.3 - - - -
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Residues in contact with VAL 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L LYS 4.8 0.9 - - - +
23L GLN 3.8 3.9 + - - +
24L SER* 1.3 70.6 - - - +
26L THR* 1.3 57.9 - - - +
28L LYS* 3.4 14.1 - - + +
29L THR* 2.9 33.2 + - + +
111L ASP* 2.7 43.6 + - + +
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Residues in contact with THR 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L SER 3.1 0.2 - - - -
25L VAL* 1.3 78.9 - - - +
27L ILE* 1.3 64.3 + - + +
29L THR* 2.8 29.1 - - + +
30L MET* 3.3 32.1 + - + +
47L LEU* 5.2 0.4 - - + -
109L TYR* 2.4 46.3 + - + +
110L LEU* 3.2 20.7 + - + -
111L ASP* 3.7 5.7 + - - +
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Residues in contact with ILE 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L LEU* 3.6 42.6 - - + -
21L ALA* 3.7 16.2 - - + +
24L SER* 3.1 26.6 + - - +
26L THR* 1.3 76.1 - - - +
28L LYS* 1.3 60.0 + - - +
30L MET* 3.9 7.8 - - - +
31L LEU* 3.2 39.2 + - + +
45L VAL* 4.5 4.5 - - + -
47L LEU* 3.8 18.8 - - + -
55L LEU* 5.5 0.2 - - + -
110L LEU* 3.6 28.5 - - + -
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Residues in contact with LYS 28 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L LYS* 3.1 59.2 - - + +
24L SER 2.6 21.6 + - - +
25L VAL* 3.4 15.0 - - + +
26L THR 3.0 0.2 - - - -
27L ILE* 1.3 71.8 - - - +
29L THR* 1.3 67.9 + - - +
31L LEU* 3.1 16.3 + - - +
32L GLU* 3.1 39.7 + - - +
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Residues in contact with THR 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25L VAL* 2.9 19.1 + - + +
26L THR* 2.8 30.1 - - + +
28L LYS* 1.3 76.1 - - - +
30L MET* 1.3 61.6 + - + +
32L GLU* 3.1 5.2 + - - -
33L ASP* 2.7 57.5 + - - +
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Residues in contact with MET 30 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26L THR* 3.3 37.0 + - + +
27L ILE* 3.9 6.5 - - - +
28L LYS 3.1 0.6 - - - -
29L THR* 1.3 83.9 - - + +
31L LEU* 1.3 58.9 + - - +
32L GLU 2.8 11.1 + - - -
33L ASP* 5.2 0.2 - - - -
34L LEU* 3.2 41.0 + - + +
35L GLY 3.3 2.3 + - - -
36L MET* 3.6 23.2 - - + +
45L VAL* 3.9 22.7 - - + -
46L PRO* 4.0 12.3 - - - +
47L LEU* 4.8 2.0 - - - -
48L PRO* 6.0 0.2 - - + -
109L TYR* 4.2 16.8 - - + +
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Residues in contact with LEU 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4L ILE* 3.6 40.8 - - + -
18L VAL* 5.0 7.4 - - + +
21L ALA* 4.6 8.3 - - + -
22L LYS* 5.2 3.1 - - + +
27L ILE* 3.2 29.1 + - + +
28L LYS* 3.1 9.6 + - - +
30L MET* 1.3 78.1 - - - +
32L GLU* 1.3 59.6 + - + +
35L GLY* 3.9 14.9 - - - +
36L MET 3.8 14.1 - - - +
45L VAL* 3.3 30.5 - - + -
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Residues in contact with GLU 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28L LYS* 3.1 50.2 + - - +
29L THR* 3.5 7.0 + - - +
30L MET 2.8 2.2 + - - -
31L LEU* 1.3 83.4 - - + +
33L ASP* 1.3 63.2 + - - +
34L LEU 2.6 16.8 + - - -
35L GLY* 3.3 8.5 + - - -
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Residues in contact with ASP 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L THR* 2.7 36.5 + - - +
32L GLU* 1.3 76.5 - - - +
34L LEU* 1.3 76.0 + - + +
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Residues in contact with LEU 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30L MET* 3.2 26.9 + - + +
32L GLU 2.6 8.4 + - - -
33L ASP* 1.3 93.3 - - + +
35L GLY* 1.3 66.0 + - - +
36L MET* 3.4 41.3 + - + +
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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