Contacts of the helix formed by residues 27 - 38 (chain R) 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 ASP 27 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25R GLY* 3.3 1.7 - - - -
26R ASN* 1.3 79.5 - - - +
28R PHE* 1.3 62.9 + - - +
29R HIS* 3.1 30.2 + - - +
30R THR* 3.2 22.6 + - - +
31R ASN* 2.9 27.3 + - - +
17g TRP* 3.4 33.8 - - + -
36g ARG* 3.5 18.9 + - - -
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Residues in contact with PHE 28 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14521 A 5.2 6.3 - - - -
14531 C 3.0 40.4 - + - -
14551 A 4.5 13.2 - - - +
14561 G 5.1 3.5 + - - +
26R ASN 3.7 2.2 + - - -
27R ASP* 1.3 73.2 + - - +
29R HIS* 1.3 78.6 + + + +
30R THR 3.1 2.5 - - - -
31R ASN* 2.9 17.4 + - - -
32R LYS* 2.9 40.7 + - + -
48R ASN* 4.0 8.1 - - + -
51R ALA* 3.4 17.7 - - + -
52R GLY* 3.3 28.9 - - - -
55R THR* 3.3 31.8 - - + +
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Residues in contact with HIS 29 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14521 A 5.5 5.6 - - - -
27R ASP* 3.1 12.8 + - - +
28R PHE* 1.3 88.6 - + + +
30R THR* 1.3 60.7 + - - +
32R LYS* 3.3 47.2 + - - +
33R ARG* 4.0 7.4 + - - +
17g TRP* 6.5 0.2 - + - -
36g ARG* 3.7 22.4 - - - +
64g HIS* 5.8 1.3 - - + -
65g PHE* 3.3 43.8 - + + -
83g TRP* 5.1 12.9 - - + -
125g ARG* 4.6 3.1 + - - -
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Residues in contact with THR 30 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23R ARG 5.4 2.2 - - - +
25R GLY* 5.4 7.4 - - - +
27R ASP* 3.2 22.2 + - - +
28R PHE 3.1 0.6 - - - -
29R HIS* 1.3 77.2 - - - +
31R ASN* 1.3 63.6 + - - +
32R LYS 3.2 0.6 + - - -
33R ARG* 3.3 4.0 + - - +
34R VAL* 2.9 45.6 + - + +
36g ARG* 5.9 0.3 + - - -
83g TRP* 5.2 4.8 - - - -
125g ARG* 4.8 19.2 + - - +
150g TRP* 4.8 3.1 - - + -
170g TRP* 5.2 10.8 - - + -
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Residues in contact with ASN 31 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24R LEU* 3.4 19.0 - - + -
25R GLY* 2.4 49.4 + - - -
26R ASN 4.2 1.8 + - - -
27R ASP 2.9 16.2 + - - +
28R PHE 2.9 6.7 + - - +
30R THR* 1.3 79.5 - - - +
32R LYS* 1.3 56.9 + - - +
34R VAL* 3.6 6.5 - - - +
35R CYS* 2.9 34.8 + - - -
51R ALA* 4.4 4.9 - - + +
54R VAL* 5.1 4.9 - - + +
55R THR* 3.8 20.6 + - - +
58R MET* 4.0 10.3 - - - +
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Residues in contact with LYS 32 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14511 G 3.1 27.5 + - - +
14521 A 3.8 14.1 + - - +
28R PHE* 2.9 31.0 + - + +
29R HIS* 3.3 47.4 + - - +
31R ASN* 1.3 78.6 - - - +
33R ARG* 1.3 61.8 + - + +
35R CYS* 3.4 4.3 + - - +
36R GLU* 2.9 24.7 + - - +
47R ARG* 4.1 7.5 - - + +
48R ASN* 4.5 16.2 - - - +
51R ALA* 3.6 24.4 - - + +
64g HIS* 4.2 11.3 + - - -
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Residues in contact with ARG 33 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29R HIS 4.3 4.3 - - - +
30R THR 3.3 3.4 + - - +
32R LYS* 1.3 80.7 - - + +
34R VAL* 1.3 60.9 + - - +
36R GLU* 3.1 29.2 + - - +
37R GLU* 2.9 53.6 + - - +
106g LYS* 3.5 33.9 - - - +
107g ASP* 3.9 7.7 + - - +
125g ARG* 3.3 51.8 + - - +
126g ASP* 5.5 2.6 - - - +
127g LYS* 5.7 1.8 - - - +
150g TRP* 3.3 25.4 - - + +
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Residues in contact with VAL 34 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23R ARG* 3.6 42.0 - - + +
24R LEU* 3.7 20.9 - - + -
30R THR* 2.9 34.3 + - + +
31R ASN* 3.6 8.7 - - - +
33R ARG* 1.3 75.9 - - - +
35R CYS* 1.3 58.3 + - - +
37R GLU* 3.0 4.9 + - - +
38R ILE* 2.9 40.7 + - + +
150g TRP* 3.5 23.8 - - + -
170g TRP* 5.6 1.8 - - + -
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Residues in contact with CYS 35 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16R ILE* 4.0 27.4 - - + +
24R LEU* 4.4 10.8 - - - -
31R ASN 2.9 25.4 + - - +
32R LYS* 3.7 6.5 - - - +
34R VAL* 1.3 74.2 - - - +
36R GLU* 1.3 61.2 + - - +
38R ILE* 3.9 8.6 - - - +
39R ALA* 3.2 24.6 + - - +
41R ILE* 4.9 3.8 - - + +
47R ARG* 4.3 12.0 + - + +
50R ILE* 4.6 7.2 - - + -
51R ALA* 4.4 10.5 - - + +
54R VAL* 4.1 23.3 - - - -
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Residues in contact with GLU 36 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14501 G 4.9 3.4 + - - -
32R LYS 2.9 10.3 + - - +
33R ARG* 3.1 35.5 + - - +
35R CYS* 1.3 79.0 - - - +
37R GLU* 1.3 57.8 + - - +
39R ALA 3.0 16.3 - - - +
40R ILE* 5.6 1.6 - - - +
44R LYS* 5.1 7.1 - - - -
47R ARG* 3.4 39.3 + - - +
106g LYS* 3.3 31.2 + - - +
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Residues in contact with GLU 37 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D VAL* 5.0 4.3 - - - +
23R ARG* 3.6 25.6 - - - +
33R ARG* 2.9 33.1 + - - +
34R VAL 3.0 4.9 + - - +
36R GLU* 1.3 75.2 - - - +
38R ILE* 1.3 66.5 + - - +
39R ALA 4.7 0.9 - - - +
40R ILE* 6.1 0.5 - - - +
127g LYS* 3.9 19.0 + - - +
149g GLU* 5.4 1.6 - - - +
150g TRP* 3.4 21.4 + - + +
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Residues in contact with ILE 38 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D ILE* 5.0 4.9 - - + -
211D VAL* 3.1 41.4 + - + +
16R ILE* 3.8 37.5 - - + -
20R TYR* 3.6 46.9 - - + -
23R ARG* 4.6 9.9 - - - +
34R VAL* 2.9 40.6 + - + +
35R CYS* 3.9 8.7 - - - +
36R GLU 3.4 0.2 - - - -
37R GLU* 1.3 79.9 - - - +
39R ALA* 1.3 65.4 + - + +
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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