Contacts of the helix formed by residues 30 - 42 (chain e) 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 GLY 30 (chain e).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5241 U 3.4 24.6 + - - -
6421 U 5.8 3.8 + - - -
6431 A 5.2 1.8 - - - -
38J ARG* 3.6 19.0 - - - +
39J ASN* 6.1 0.9 - - - -
29e THR* 1.3 72.8 - - - +
31e ARG* 1.3 66.2 + - - -
32e ALA 3.1 1.6 + - - -
33e LYS* 3.3 12.8 + - - +
34e ARG* 3.6 9.2 + - - +
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Residues in contact with ARG 31 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5231 A 4.5 10.5 + - - +
5241 U 4.7 16.4 + - - +
5261 A 2.4 40.8 + - - -
5271 C 4.4 0.8 + - - -
36J GLY 5.3 1.3 - - - +
37J LEU 3.5 18.8 - - - +
38J ARG* 3.5 26.9 + - + +
124J HIS* 3.5 48.2 + - + +
127J ARG* 3.2 45.0 - - - +
128J VAL* 3.6 9.7 - - - +
29e THR 3.8 0.2 + - - -
30e GLY* 1.3 71.0 - - - -
32e ALA* 1.3 64.0 + - + +
34e ARG* 3.3 3.5 + - - +
35e ARG* 2.9 28.5 + - - +
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Residues in contact with ALA 32 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5241 U 5.5 2.9 - - - +
5251 A 4.7 1.3 - - - +
5261 A 3.2 36.8 - - - +
28e LYS* 3.1 20.9 - - + +
29e THR 3.4 14.6 + - - +
30e GLY 3.1 0.8 - - - -
31e ARG* 1.3 82.9 - - + +
33e LYS* 1.3 60.5 + - - +
35e ARG* 3.1 9.1 + - - +
36e MET 2.9 24.3 + - - -
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Residues in contact with LYS 33 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5941 A 5.7 1.4 + - - -
5951 U 4.6 5.9 + - - -
6411 A 4.2 10.3 - - - +
6421 U 2.5 36.0 + - - +
27e LYS* 5.4 11.4 - - - +
28e LYS* 3.2 30.9 + - - +
29e THR* 4.0 16.5 + - - +
30e GLY 3.3 10.9 + - - +
32e ALA* 1.3 78.0 - - - +
34e ARG* 1.3 65.9 + - + +
36e MET* 3.3 13.7 + - + +
37e GLN* 2.9 47.6 + - + +
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Residues in contact with ARG 34 (chain e).
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 5.3 4.2 + - - -
6411 A 3.3 25.3 + - - -
6421 U 2.9 42.5 + - - -
29J LEU* 4.3 12.6 - - + +
32J ILE* 3.9 30.3 - - + +
33J GLY* 6.2 0.2 - - - -
37J LEU 4.5 1.1 - - - +
38J ARG 3.1 24.0 - - - +
39J ASN* 4.3 11.8 - - - +
40J LYS* 2.9 32.5 - - - +
30e GLY 3.6 5.7 + - - +
31e ARG 3.3 7.3 + - - +
32e ALA 3.2 0.4 - - - -
33e LYS* 1.3 81.0 - - + +
35e ARG* 1.3 60.9 + - - +
37e GLN* 3.4 12.2 + - - +
38e TYR* 2.9 31.2 + - - +
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Residues in contact with ARG 35 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5271 C 2.2 39.4 + - - -
5281 A 3.7 23.0 + - - -
5501 C 5.2 7.3 + - - -
5511 U 4.3 9.6 + - - -
33J GLY* 6.2 1.3 - - - -
124J HIS* 3.2 52.7 + - + +
28e LYS* 5.1 9.6 - - - +
31e ARG* 2.9 14.8 + - - +
32e ALA* 3.4 11.4 - - - +
34e ARG* 1.3 76.8 - - - +
36e MET* 1.3 56.6 + - - +
38e TYR* 3.4 5.8 + - + +
39e ASN* 2.9 57.7 + - - +
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Residues in contact with MET 36 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5511 U 5.7 2.9 - - - +
5521 G 5.1 12.3 - - - +
27e LYS* 6.3 2.5 - - + -
28e LYS* 3.6 41.0 - - + +
32e ALA 2.9 12.9 + - - +
33e LYS* 3.6 15.9 - - + +
35e ARG* 1.3 73.2 - - - +
37e GLN* 1.3 81.5 + - - +
39e ASN* 4.1 5.2 - - - +
40e ARG* 2.9 36.1 + - + +
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Residues in contact with GLN 37 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6391 C 3.5 32.5 + - - -
6401 A 4.9 10.0 + - - +
29J LEU* 4.8 16.8 - - + +
33e LYS* 2.9 31.3 + - + +
34e ARG* 3.4 15.5 + - - +
36e MET* 1.3 100.3 - - - +
38e TYR* 1.3 61.5 + - - +
40e ARG* 3.7 18.6 + - - +
41e ARG* 3.9 17.2 + - - +
42e PHE* 3.3 17.8 - - - -
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Residues in contact with TYR 38 (chain e).
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* 3.4 22.4 - - + +
30J LYS* 3.6 26.3 + - + +
32J ILE* 6.2 0.2 - - + -
33J GLY* 3.4 37.5 - - - -
34J GLU* 4.6 2.9 + - - +
34e ARG 2.9 17.9 + - - +
35e ARG* 3.9 4.5 - - + +
37e GLN* 1.3 76.8 - - - +
39e ASN* 1.3 78.5 + - - +
42e PHE* 3.1 61.6 + + + +
43e VAL* 5.6 6.6 - - + +
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Residues in contact with ASN 39 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5501 C 2.8 39.0 + - - +
5511 U 2.4 40.1 + - - +
124J HIS* 5.9 0.2 + - - -
35e ARG* 2.9 47.9 + - - +
36e MET* 4.1 4.6 - - - +
38e TYR* 1.3 92.6 - - - +
40e ARG* 1.3 68.4 + - - +
43e VAL* 3.2 12.2 - - - +
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Residues in contact with ARG 40 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5511 U 5.3 5.4 - - - -
6381 C 4.1 28.8 + - - -
6391 C 5.0 2.7 + - - -
36e MET* 2.9 22.9 + - + +
37e GLN* 3.8 18.4 - - - +
38e TYR 3.2 0.6 - - - -
39e ASN* 1.3 81.4 - - - +
41e ARG* 1.3 87.1 + - + +
44e ASN* 3.5 5.2 - - - +
45e VAL* 3.2 17.9 - - - +
55e PRO 4.9 10.3 + - - -
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Residues in contact with ARG 41 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6381 C 4.8 0.6 + - - -
6391 C 3.0 27.5 + - - -
29J LEU* 5.2 6.1 - - - +
37e GLN* 3.9 19.8 + - - +
40e ARG* 1.3 99.4 - - + +
42e PHE* 1.3 95.6 + - + +
43e VAL 3.5 2.0 - - - -
45e VAL* 3.4 34.6 - - + +
46e VAL* 4.8 2.4 + - - +
53e LYS* 5.3 10.5 - - - +
55e PRO* 4.5 26.3 + - - +
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Residues in contact with PHE 42 (chain e).
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* 4.4 26.0 - - + -
29J LEU* 3.6 42.6 - - + -
30J LYS* 5.0 7.6 - - + -
37e GLN 3.3 27.6 - - - -
38e TYR* 3.1 48.7 + + + +
40e ARG 3.6 0.2 - - - -
41e ARG* 1.3 105.5 - - + +
43e VAL* 1.3 60.6 + - - +
46e VAL* 4.8 10.5 - - - +
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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