Contacts of the helix formed by residues 56 - 62 (chain V) in PDB entry 5FLX
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 CYS 56 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17V CYS* 3.3 30.7 - - + +
20V SER* 4.4 9.9 - - - -
22V ARG* 3.4 37.2 - - - +
24V ILE* 4.4 7.9 - - + -
31V SER* 4.1 7.2 - - - -
55V ILE* 1.3 80.0 - - - +
57V GLY* 1.3 66.7 + - - +
58V ALA* 3.2 2.2 + - - -
59V ILE* 3.4 37.9 + - - -
60V ARG* 3.4 9.0 + - - +
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Residues in contact with GLY 57 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22V ARG* 3.2 5.7 - - - +
28V ASP* 3.6 16.8 + - - -
30V ALA* 3.6 26.4 - - - +
31V SER* 3.8 5.6 - - - -
56V CYS* 1.3 76.2 - - - +
58V ALA* 1.3 58.4 + - - +
60V ARG* 3.2 3.4 + - - +
61V ARG* 2.9 37.1 + - - +
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Residues in contact with ALA 58 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22V ARG* 3.1 29.8 - - - +
56V CYS* 4.7 2.0 - - - -
57V GLY* 1.3 78.1 - - - +
59V ILE* 1.3 58.6 + - + +
61V ARG* 3.2 10.0 + - - +
62V MET* 2.9 46.2 + - + +
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Residues in contact with ILE 59 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19V ALA* 4.9 8.1 - - + -
20V SER* 4.4 18.2 - - - +
55V ILE* 4.3 7.0 - - + -
56V CYS* 3.4 29.7 + - - +
57V GLY 3.4 0.4 - - - -
58V ALA* 1.3 77.8 - - + +
60V ARG* 1.3 59.8 - - - +
62V MET* 3.6 20.8 + - + -
63V GLY 3.1 2.6 + - - -
64V GLU* 2.8 49.7 + - + +
65V SER* 3.3 25.4 + - - +
68V SER* 4.1 12.1 - - - +
21W GLY* 5.2 10.5 - - - +
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Residues in contact with ARG 60 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ALA* 4.5 10.1 + - - +
138A SER* 5.3 1.6 - - - +
142A LEU 3.9 13.3 + - - -
144A THR* 3.1 22.2 + - - +
156A TYR* 2.9 79.6 + - + +
157A VAL 4.5 1.3 + - - +
158A ASP* 2.6 50.0 + - - +
30V ALA 3.2 25.7 + - - +
32V ILE* 4.7 6.2 - - - +
55V ILE* 4.5 4.9 - - + +
56V CYS 3.4 9.1 + - - +
57V GLY 3.2 8.4 + - - +
58V ALA 3.2 0.6 - - - -
59V ILE* 1.3 77.7 - - - +
61V ARG* 1.3 63.2 + - - +
63V GLY* 3.2 8.7 + - - -
65V SER* 4.2 13.7 - - - +
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Residues in contact with ARG 61 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11381 C 2.9 57.0 + - - +
11391 C 4.4 7.0 + - - +
155A ARG* 3.8 21.1 + - - +
156A TYR* 3.5 36.3 + - + +
28V ASP* 3.9 18.5 + - - -
30V ALA* 4.1 11.5 - - + +
57V GLY 2.9 22.9 + - - +
58V ALA* 3.2 8.0 + - - +
60V ARG* 1.3 78.6 - - - +
62V MET* 1.3 60.8 + - + +
63V GLY 3.1 1.1 + - - -
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Residues in contact with MET 62 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11391 C 4.3 22.2 - - - +
32A PHE* 5.2 4.7 - - - -
33A GLN* 3.3 12.3 + - - -
155A ARG* 5.6 0.2 - - - -
58V ALA* 2.9 32.9 + - + +
59V ILE* 3.7 28.9 - - + +
61V ARG* 1.3 77.3 - - + +
63V GLY* 1.3 60.7 + - - +
64V GLU* 3.3 8.6 + - + +
19W LYS 5.4 3.6 - - - +
20W ARG* 3.4 58.1 + - - +
21W GLY* 5.4 0.4 - - - -
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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