Contacts of the helix formed by residues 49 - 66 (chain P) 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 LEU 49 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30P TYR* 4.5 21.8 - - + +
45P LEU* 3.8 32.8 - - + +
48P GLY* 1.3 81.4 - - - +
50P ARG* 1.3 82.9 + - - +
51P ARG 3.6 0.3 + - - -
52P LYS* 3.9 12.5 + - - +
53P GLN* 3.6 42.8 + - + +
54P HIS* 6.1 0.4 - - + +
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Residues in contact with ARG 50 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16181 C 3.0 36.6 + - - +
16191 A 5.2 2.4 + - - -
48P GLY* 5.5 5.3 - - - -
49P LEU* 1.3 89.6 - - - +
51P ARG* 1.3 87.1 + - + +
52P LYS* 4.8 21.5 - - + +
54P HIS* 2.5 43.1 + - - +
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Residues in contact with ARG 51 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12981 G 4.7 10.9 + - - +
12991 A 3.7 33.9 + - - -
13001 U 3.7 31.0 - - + +
13011 A 5.0 2.0 - - - -
15141 G 5.8 7.3 - - - -
50P ARG* 1.3 99.3 - - + +
52P LYS* 1.3 70.7 + - - +
54P HIS* 4.2 3.8 - - - -
55P SER* 2.9 43.7 + - - -
80P LEU* 5.8 7.5 - - - +
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Residues in contact with LYS 52 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16191 A 5.8 6.3 - - - -
44P ARG* 3.0 42.3 - - - +
48P GLY 5.8 2.7 + - - -
49P LEU* 3.9 14.5 + - - +
50P ARG* 4.8 20.7 - - + +
51P ARG* 1.3 89.1 - - - +
53P GLN* 1.3 74.1 + - - +
55P SER* 5.0 0.4 - - - -
56P LEU* 2.9 36.3 + - - +
80P LEU* 3.8 29.6 - - + -
83P MET* 3.7 21.7 - - + +
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Residues in contact with GLN 53 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30P TYR* 5.3 11.1 - - - -
45P LEU* 4.8 9.0 - - - +
49P LEU* 3.6 37.7 - - + +
50P ARG 3.9 1.2 + - - -
52P LYS* 1.3 85.5 + - + +
54P HIS* 1.3 59.1 + - - +
55P SER 3.2 6.1 + - - -
57P LEU* 3.5 37.0 + - + +
58P LYS* 4.6 3.1 + - - +
61P ARG* 5.2 1.0 + - - -
83P MET* 4.1 17.0 - - + +
86P LEU* 3.5 31.4 - - - +
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Residues in contact with HIS 54 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13001 U 3.1 30.6 + + - +
49P LEU* 5.2 0.9 - - + -
50P ARG* 2.5 28.9 + - - +
51P ARG* 3.3 3.3 + - - +
53P GLN* 1.3 76.4 - - - +
55P SER* 1.3 57.3 + - - +
58P LYS* 3.1 47.6 + - - +
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Residues in contact with SER 55 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12991 A 4.3 14.0 + - - -
13001 U 4.3 29.7 + - - -
51P ARG* 2.9 25.3 + - - -
52P LYS* 5.0 0.4 - - - -
53P GLN 3.2 0.6 - - - -
54P HIS* 1.3 81.1 - - - +
56P LEU* 1.3 68.4 + - - +
57P LEU 3.2 1.3 - - - -
58P LYS* 3.0 7.6 + - - +
59P ARG* 2.9 22.3 + - - +
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Residues in contact with LEU 56 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12981 G 5.4 11.0 - - - +
12991 A 6.5 0.4 - - - -
52P LYS* 2.9 19.6 + - - +
55P SER* 1.3 75.5 - - - +
57P LEU* 1.3 58.0 + - - +
59P ARG* 3.3 9.6 + - + +
60P LEU* 2.9 26.7 + - + +
76P VAL* 4.1 21.8 - - + -
77P LYS 5.1 0.9 - - - +
78P THR* 3.5 43.5 - - + +
80P LEU* 3.8 22.0 - - + -
83P MET* 4.6 17.0 - - + -
94P VAL* 6.0 3.6 - - + -
116P LEU* 5.9 2.5 - - + -
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Residues in contact with LEU 57 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52P LYS 3.9 2.6 + - - -
53P GLN* 3.5 36.3 + - + +
55P SER 3.2 0.8 - - - -
56P LEU* 1.3 76.9 - - - +
58P LYS* 1.3 60.4 + - - +
60P LEU* 3.3 8.4 + - + +
61P ARG* 2.9 65.5 + - + +
83P MET* 5.7 5.4 - - + +
86P LEU* 3.6 31.4 - - + -
88P GLU* 4.4 11.9 - - + +
89P MET* 3.9 27.6 - - + -
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Residues in contact with LYS 58 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13001 U 4.7 1.6 + - - +
53P GLN 4.6 1.3 + - - +
54P HIS* 3.1 58.8 + - - +
55P SER* 3.0 8.6 + - - +
57P LEU* 1.3 76.2 - - - +
59P ARG* 1.3 59.0 + - - +
60P LEU 3.1 0.2 - - - -
61P ARG* 3.0 33.1 + - - +
62P LYS* 2.9 25.6 + - - +
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Residues in contact with ARG 59 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12961 U 4.6 13.9 + - - -
12971 U 3.7 41.8 + - - -
12981 G 5.2 0.7 - - - -
12991 A 3.6 20.7 + - - -
55P SER* 2.9 12.4 + - - +
56P LEU* 3.6 14.8 - - - +
58P LYS* 1.3 75.6 - - - +
60P LEU* 1.3 56.6 + - - +
62P LYS* 3.2 37.8 + - - +
63P ALA* 2.9 25.1 + - - +
76P VAL* 3.7 36.1 - - + +
77P LYS 5.7 0.4 + - - -
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Residues in contact with LEU 60 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56P LEU* 2.9 15.0 + - + +
57P LEU* 3.4 13.0 - - + +
58P LYS 3.1 0.4 - - - -
59P ARG* 1.3 75.6 - - - +
61P ARG* 1.3 58.7 + - - +
63P ALA* 3.1 11.5 + - + +
64P LYS* 2.9 29.1 + - + +
76P VAL* 5.0 8.0 - - + +
88P GLU 4.8 4.0 - - - +
89P MET* 3.6 57.0 - - + +
92P SER* 3.7 26.0 - - - +
93P MET 4.6 2.7 - - - +
94P VAL* 3.7 24.2 - - + -
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Residues in contact with ARG 61 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53P GLN 5.2 1.6 + - - -
57P LEU* 2.9 44.1 + - + +
58P LYS* 3.2 43.3 - - - +
60P LEU* 1.3 76.6 - - - +
62P LYS* 1.3 54.6 + - - +
64P LYS* 3.4 6.9 + - - +
65P LYS* 2.9 33.3 + - - +
88P GLU* 3.4 32.7 + - + +
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Residues in contact with LYS 62 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12951 A 5.4 8.3 - - - +
12961 U 5.5 4.5 + - - -
58P LYS 2.9 11.6 + - - +
59P ARG* 3.5 45.8 + - - +
60P LEU 3.2 0.2 - - - -
61P ARG* 1.3 74.1 - - - +
63P ALA* 1.3 66.5 + - - +
65P LYS* 3.1 26.7 + - + +
66P GLU* 3.1 29.5 + - - +
74P GLU* 5.1 8.3 + - - -
76P VAL* 5.8 3.0 - - - +
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Residues in contact with ALA 63 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59P ARG 2.9 13.8 + - - +
60P LEU* 3.1 18.6 + - + +
62P LYS* 1.3 82.4 - - - +
64P LYS* 1.3 59.5 + - - +
65P LYS 3.4 0.5 + - - -
66P GLU 4.2 11.6 - - - +
67P ALA* 5.3 0.5 - - - +
73P PRO* 3.9 16.4 - - + +
74P GLU* 3.6 31.8 + - + +
76P VAL* 3.7 16.2 - - + -
92P SER* 5.2 3.1 - - - +
93P MET 5.3 0.7 - - - +
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Residues in contact with LYS 64 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60P LEU* 2.9 15.3 + - - +
61P ARG* 4.0 5.8 - - - +
63P ALA* 1.3 75.7 - - - +
65P LYS* 1.3 65.7 + - - +
66P GLU* 3.5 0.8 - - - -
67P ALA* 4.6 6.3 + - - +
73P PRO* 5.0 3.6 - - - -
88P GLU* 3.7 22.0 - - - +
89P MET 4.8 0.2 - - - -
90P VAL 2.4 32.8 + - - +
91P GLY* 3.2 13.8 + - - +
92P SER* 3.0 31.1 + - - +
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Residues in contact with LYS 65 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61P ARG* 2.9 21.6 + - - +
62P LYS* 3.1 23.5 + - + +
64P LYS* 1.3 80.9 - - - +
66P GLU* 1.3 84.6 + - + +
67P ALA 3.7 2.1 + - - -
68P PRO* 5.7 1.2 - - - +
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Residues in contact with GLU 66 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62P LYS* 3.1 25.5 + - - +
63P ALA 4.2 8.2 + - - +
65P LYS* 1.3 103.2 - - + +
67P ALA* 1.3 60.6 + - - +
68P PRO* 3.9 13.7 - - + -
74P GLU* 5.1 15.6 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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