Contacts of the helix formed by residues 22 - 34 (chain H) in PDB entry 5FUR
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 22 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780G GLU* 6.1 1.6 - - + -
781G THR* 4.1 16.8 - - + -
20H LEU 3.5 3.1 - - - +
21H PRO* 1.3 83.3 - - + +
23H GLU* 1.3 73.3 + - + +
25H ALA* 3.6 8.8 - - + +
26H SER* 3.1 27.6 + - - -
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Residues in contact with GLU 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H PRO* 3.2 24.9 - - - +
22H PRO* 1.3 85.1 - - + +
24H TYR* 1.3 85.4 + - + +
26H SER* 3.6 6.9 + - - -
27H THR* 3.5 20.4 + - - -
99H VAL* 4.6 7.6 - - - +
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Residues in contact with TYR 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H LEU* 4.2 4.9 - - + -
21H PRO* 2.8 28.8 + - + +
23H GLU* 1.3 98.8 - - + +
25H ALA* 1.3 67.0 + - - +
26H SER 3.2 0.2 - - - -
27H THR* 3.2 9.5 + - - -
28H VAL* 3.0 26.3 + - - +
58H VAL* 4.0 28.5 - - + -
61H VAL* 3.7 34.5 - - + +
63H LEU* 3.9 27.8 - - + +
99H VAL* 4.0 17.7 - - + +
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Residues in contact with ALA 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780G GLU* 3.5 24.5 - - + +
781G THR* 3.8 16.8 - - - +
783G PHE* 3.4 7.0 - - + -
20H LEU* 3.9 18.7 - - + +
21H PRO 2.9 11.7 + - - +
22H PRO* 3.6 11.7 - - + +
24H TYR* 1.3 78.2 - - - +
26H SER* 1.3 56.6 + - - +
28H VAL 3.5 0.2 + - - -
29H ARG* 2.8 32.2 + - - +
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Residues in contact with SER 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H PRO 3.1 16.4 + - - -
23H GLU* 3.7 8.0 - - - -
24H TYR 3.2 0.2 - - - -
25H ALA* 1.3 73.4 - - - +
27H THR* 1.3 65.9 + - - +
29H ARG* 3.4 6.1 + - - +
30H ARG* 3.2 45.6 + - - +
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Residues in contact with THR 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H GLU 3.5 11.6 + - - -
24H TYR* 3.2 13.3 + - - -
26H SER* 1.3 80.6 - - - +
28H VAL* 1.3 63.5 + - + +
30H ARG* 3.5 24.7 + - - +
31H ALA* 3.3 18.4 + - - +
42H ARG* 3.4 27.7 + - - +
58H VAL* 4.1 15.5 - - + -
59H ASP* 3.9 9.9 - - - +
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Residues in contact with VAL 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783G PHE* 3.8 22.7 - - + -
794G ILE* 4.3 8.3 - - + -
20H LEU* 3.7 17.7 - - + -
24H TYR 3.0 15.3 + - - +
25H ALA 3.9 2.9 - - - +
27H THR* 1.3 78.8 - - + +
29H ARG* 1.3 60.0 + - - +
31H ALA* 3.0 9.4 + - - +
32H VAL* 2.8 29.4 + - + +
39H LEU* 5.0 4.9 - - + -
42H ARG 5.6 0.7 - - - +
43H LEU* 4.2 29.6 - - + -
58H VAL* 3.8 25.1 - - + -
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Residues in contact with ARG 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779G PRO 3.9 1.6 + - - -
780G GLU* 2.8 51.3 + - - +
782G ASP 3.3 24.5 + - - -
783G PHE* 3.7 25.1 - - + -
796G GLU* 3.0 53.0 + - - +
797G LEU 5.0 3.0 + - - +
798G VAL* 5.2 4.0 - - - +
25H ALA 2.8 21.6 + - - +
26H SER* 3.9 6.0 - - - +
28H VAL* 1.3 72.9 - - - +
30H ARG* 1.3 63.5 + - + +
32H VAL* 3.2 5.1 + - + +
33H GLN* 2.9 34.9 + - - +
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Residues in contact with ARG 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H SER* 3.2 36.7 + - - +
27H THR* 3.5 31.6 + - - +
28H VAL 3.3 0.2 - - - -
29H ARG* 1.3 75.6 - - + +
31H ALA* 1.3 57.8 + - - +
33H GLN* 3.3 14.7 + - - +
34H SER* 2.9 30.4 + - - -
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Residues in contact with ALA 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H THR 3.3 8.9 + - - +
28H VAL* 3.0 11.3 + - - +
30H ARG* 1.3 75.6 - - - +
32H VAL* 1.3 65.9 + - - +
34H SER* 3.0 21.8 + - - -
35H GLY* 3.2 7.6 + - - -
36H HIS* 4.1 4.1 + - + +
39H LEU* 3.9 29.6 - - + +
42H ARG* 3.8 28.2 - - - +
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Residues in contact with VAL 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659G PRO* 5.5 3.6 - - + +
660G LEU 6.2 1.3 - - - +
661G LEU* 4.3 11.6 + - + +
783G PHE* 4.6 6.5 - - + -
794G ILE* 4.2 31.6 - - + +
795G ARG* 4.6 2.0 - - - -
796G GLU* 3.9 34.3 - - + +
28H VAL* 2.8 25.0 + - + +
29H ARG* 3.6 8.7 - - + +
31H ALA* 1.3 71.6 - - - +
33H GLN* 1.3 63.4 + - - +
35H GLY* 3.2 15.1 + - - -
39H LEU* 3.8 23.3 - - + -
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Residues in contact with GLN 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661G LEU* 3.5 17.6 - - - +
796G GLU* 3.0 39.6 + - - +
29H ARG* 2.9 28.9 + - - +
30H ARG* 3.6 14.5 - - - +
32H VAL* 1.3 76.5 - - - +
34H SER* 1.3 62.3 + - - +
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Residues in contact with SER 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661G LEU* 4.0 5.9 - - - +
662G LYS* 5.6 1.9 + - - -
30H ARG 2.9 14.2 + - - -
31H ALA* 3.0 19.8 + - - -
33H GLN* 1.3 77.4 - - - +
35H GLY* 1.3 59.0 + - - +
36H HIS* 3.1 42.3 + - - +
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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