Contacts of the helix formed by residues 21 - 36 (chain J) 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 GLU 21 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31 C 5.6 1.4 - - - +
6041 A 5.7 2.2 - - - -
208C PRO* 6.3 3.1 - - + -
18J ARG* 3.5 34.9 + - + +
20J PHE* 1.3 79.5 - - - +
22J LYS* 1.3 66.2 + - - +
23J SER 3.4 0.7 - - - +
24J ARG* 3.2 61.1 + - + +
25J LEU* 3.1 33.2 + - - +
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Residues in contact with LYS 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6041 A 5.0 22.0 + - - +
6051 A 6.0 2.0 - - - +
21J GLU* 1.3 74.6 - - - +
23J SER* 1.3 63.9 + - - +
25J LEU* 4.3 3.3 - - - +
26J ASP* 3.1 40.4 + - - +
53e LYS* 4.1 31.2 - - - +
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Residues in contact with SER 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J GLU* 3.4 1.0 - - - +
22J LYS* 1.3 79.2 + - - +
24J ARG* 1.3 60.9 + - - +
26J ASP* 3.2 9.1 + - - +
27J GLN* 2.9 29.6 + - - +
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Residues in contact with ARG 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J PRO* 3.3 26.9 - - - +
17J ARG 4.6 0.8 - - - +
18J ARG 2.3 35.7 + - - +
19J PRO 3.0 21.8 + - - -
20J PHE 3.8 0.2 - - - +
21J GLU* 3.2 49.0 + - + +
22J LYS 3.5 0.4 - - - -
23J SER* 1.3 80.1 - - - +
25J LEU* 1.3 61.1 + - - +
27J GLN* 3.3 10.8 + - + +
28J GLU* 2.9 56.9 + - + +
44J TRP* 5.9 1.8 - - - -
47J LYS* 6.4 1.8 - - - +
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Residues in contact with LEU 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6041 A 4.6 15.7 - - - +
6401 A 4.4 29.4 - - - +
6411 A 3.9 22.0 - - - +
19J PRO 4.7 10.3 - - - +
20J PHE* 4.5 8.5 - - + -
21J GLU 3.1 34.4 + - - +
22J LYS* 4.3 3.1 - - - +
24J ARG* 1.3 81.6 - - + +
26J ASP* 1.3 60.3 + - - +
28J GLU* 3.4 16.9 + - - +
29J LEU* 2.9 41.8 + - + +
40J LYS* 4.4 4.7 - - - +
44J TRP* 6.2 1.1 - - + -
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Residues in contact with ASP 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J LYS* 3.1 32.0 + - - +
23J SER* 3.2 11.1 + - - +
25J LEU* 1.3 80.7 - - - +
27J GLN* 1.3 56.7 + - - +
29J LEU* 3.3 9.1 + - - +
30J LYS* 2.9 34.8 + - + +
42e PHE* 4.4 22.4 - - + -
53e LYS* 5.8 1.4 + - - -
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Residues in contact with GLN 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J SER 2.9 16.7 + - - +
24J ARG* 3.3 10.4 + - + +
26J ASP* 1.3 75.1 - - - +
28J GLU* 1.3 59.5 + - + +
30J LYS* 3.2 30.0 - - - +
31J LEU* 2.9 35.0 + - + +
102J ILE* 5.8 5.9 - - - +
103J GLU* 5.4 5.9 + - - -
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Residues in contact with GLU 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J PRO* 6.2 0.2 - - - +
24J ARG* 2.9 42.2 + - + +
25J LEU* 3.8 14.2 - - - +
27J GLN* 1.3 77.7 - - + +
29J LEU* 1.3 58.4 + - - +
31J LEU* 3.6 8.5 - - + +
32J ILE* 2.9 37.9 + - + +
40J LYS* 3.2 34.1 - - + +
43J VAL* 4.9 11.7 - - + -
44J TRP* 2.8 34.6 + - - -
47J LYS* 5.4 5.4 - - - -
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Residues in contact with LEU 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6401 A 4.7 14.4 - - - +
25J LEU* 2.9 29.8 + - + +
26J ASP* 3.7 7.4 - - - +
28J GLU* 1.3 77.5 - - - +
30J LYS* 1.3 56.8 + - - +
32J ILE* 3.9 5.9 - - + +
33J GLY 2.9 23.7 + - - -
40J LYS* 3.4 27.6 - - - +
34e ARG* 4.3 15.9 - - + +
37e GLN* 4.8 17.9 - - + -
38e TYR* 3.4 13.5 - - + +
41e ARG* 5.2 6.5 - - - +
42e PHE* 3.6 34.1 - - + -
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Residues in contact with LYS 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J ASP* 2.9 16.8 + - + +
27J GLN* 3.2 41.3 + - - +
29J LEU* 1.3 77.4 - - - +
31J LEU* 1.3 57.7 + - - +
34J GLU* 2.9 29.6 + - - +
103J GLU* 5.6 3.2 + - - -
38e TYR* 3.6 22.1 + - + +
42e PHE* 5.0 8.9 - - + -
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Residues in contact with LEU 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J GLN* 2.9 23.1 + - + +
28J GLU* 3.6 6.7 - - + +
29J LEU 3.2 0.2 - - - -
30J LYS* 1.3 77.1 - - + +
32J ILE* 1.3 66.4 + - - +
34J GLU* 3.1 10.6 + - - +
35J TYR* 2.9 39.9 + - + +
43J VAL* 3.8 29.2 - - + -
102J ILE* 4.5 14.6 - - + -
103J GLU* 4.0 20.6 - - + +
106J LEU* 3.7 31.4 - - + -
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Residues in contact with ILE 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28J GLU 2.9 21.7 + - - +
29J LEU* 3.9 6.7 - - + +
31J LEU* 1.3 74.5 - - - +
33J GLY* 1.3 58.4 + - - +
34J GLU 3.1 0.2 + - - -
35J TYR 5.2 0.2 - - - -
36J GLY* 2.4 40.9 + - - +
37J LEU* 3.9 32.3 - - + +
39J ASN 4.3 9.9 - - - +
40J LYS* 3.5 35.7 - - + -
43J VAL* 3.6 26.2 - - + -
34e ARG* 3.9 30.7 - - + +
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Residues in contact with GLY 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J LEU 2.9 11.3 + - - -
30J LYS 3.8 0.7 - - - -
32J ILE* 1.3 78.2 - - - +
34J GLU* 1.3 61.7 + - - +
36J GLY* 4.2 3.8 + - - -
124J HIS* 5.4 6.6 + - - -
34e ARG 5.6 0.4 - - - -
35e ARG* 6.2 1.8 - - - -
38e TYR* 3.4 49.9 - - - +
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Residues in contact with GLU 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J LYS 2.9 20.3 + - - +
31J LEU* 3.3 14.9 - - - +
32J ILE 3.1 0.2 - - - -
33J GLY* 1.3 80.8 - - - +
35J TYR* 1.3 93.6 + - + +
36J GLY 3.8 0.2 + - - -
103J GLU* 4.4 8.3 - - - +
123J ILE* 5.6 4.2 - - - +
38e TYR* 4.4 4.2 - - - +
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Residues in contact with TYR 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J LEU* 2.9 35.0 + - + +
32J ILE 3.4 0.2 - - - -
34J GLU* 1.3 108.3 + - + +
36J GLY* 1.3 54.7 + - - +
37J LEU* 3.6 18.6 - - + -
103J GLU* 3.1 35.7 + - + +
106J LEU* 3.4 42.0 - - + +
107J GLU* 3.7 15.1 + - + +
111J GLN* 2.3 36.9 + - - +
112J THR* 3.7 16.9 + - + -
123J ILE* 4.2 8.2 - - - +
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Residues in contact with GLY 36 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32J ILE* 2.4 25.3 + - - -
33J GLY* 4.2 3.0 - - - -
34J GLU 3.5 2.0 - - - -
35J TYR* 1.3 72.1 - - - +
37J LEU* 1.3 61.6 + - - -
111J GLN* 3.5 15.3 + - - +
123J ILE* 4.7 6.2 - - - +
124J HIS* 4.2 25.2 - - - -
127J ARG* 3.9 13.9 + - - +
31e ARG* 5.3 1.5 - - - +
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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