Contacts of the helix formed by residues 80 - 94 (chain Z) 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 ARG 80 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15981 G 2.5 60.4 + - - +
15991 U 3.0 26.8 + - - -
16001 G 6.2 0.8 - - - -
23S ARG* 5.2 2.8 - - - +
24S ARG* 5.0 1.8 - - - +
55S ARG* 4.4 3.8 - - - +
46Z ASN* 4.0 23.9 + - - +
47Z LEU 3.2 17.9 + - - +
48Z VAL* 3.3 38.8 - - + +
79Z ILE* 1.3 81.0 - - + +
81Z GLY* 1.3 66.0 + - - +
82Z SER* 3.3 23.1 - - - +
83Z LEU* 3.0 22.0 + - + +
84Z ALA* 3.1 8.1 + - - +
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Residues in contact with GLY 81 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15981 G 4.0 18.8 + - - -
166F ILE* 6.5 1.1 - - - -
74Z SER* 3.5 20.6 + - - -
79Z ILE 3.5 2.6 + - - -
80Z ARG* 1.3 76.7 - - - +
82Z SER* 1.3 59.9 + - - +
84Z ALA* 2.9 16.8 + - - +
85Z ARG* 2.9 16.1 + - - +
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Residues in contact with SER 82 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15971 C 3.2 37.2 - - - -
15981 G 3.7 18.8 + - - -
55S ARG* 2.2 31.0 + - - -
80Z ARG* 3.3 12.1 - - - +
81Z GLY* 1.3 76.5 - - - +
83Z LEU* 1.3 61.9 + - - +
85Z ARG* 3.7 14.6 + - - +
86Z ALA* 3.6 18.5 + - - +
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Residues in contact with LEU 83 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55S ARG* 4.1 19.3 - - + +
58S GLU* 6.0 0.7 - - - +
47Z LEU 4.9 0.2 - - - +
48Z VAL 3.2 26.9 - - - +
50Z PHE* 3.6 36.8 - - + +
79Z ILE* 3.7 23.1 - - + -
80Z ARG* 3.0 11.1 + - + +
82Z SER* 1.3 80.9 + - - +
84Z ALA* 1.3 53.9 + - - +
85Z ARG 3.3 0.2 - - - -
86Z ALA* 4.6 6.2 - - + +
87Z ALA* 2.7 40.6 + - - +
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Residues in contact with ALA 84 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70Z PRO* 4.9 5.4 - - + +
74Z SER* 3.5 33.7 - - - +
77Z LEU* 3.8 18.2 - - + -
79Z ILE* 5.2 0.6 - - - +
80Z ARG 3.1 6.1 + - - +
81Z GLY* 2.9 14.6 + - - +
83Z LEU* 1.3 75.8 - - - +
85Z ARG* 1.3 57.6 + - - +
87Z ALA* 4.0 4.7 - - - -
88Z LEU* 2.9 38.7 + - + +
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Residues in contact with ARG 85 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15951 U 6.0 0.9 - - - -
15961 U 2.8 70.0 + - - -
15971 C 2.2 44.4 + - - -
15981 G 5.1 7.4 + - - -
53S THR* 6.3 0.6 - - - +
81Z GLY 2.9 11.0 + - - +
82Z SER* 3.8 16.7 + - - +
83Z LEU 3.3 0.4 - - - -
84Z ALA* 1.3 77.0 - - - +
86Z ALA* 1.3 60.0 + - - +
88Z LEU* 4.1 1.1 - - - +
89Z GLN* 2.9 44.1 + - + +
107Z VAL* 5.9 7.9 - - + -
109Z TYR* 5.7 0.4 - - - -
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Residues in contact with ALA 86 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82Z SER 3.6 12.5 + - - +
83Z LEU* 4.6 6.5 - - + +
84Z ALA 3.5 0.2 - - - -
85Z ARG* 1.3 85.0 - - - +
87Z ALA* 1.3 56.1 + - - +
89Z GLN* 4.1 5.7 - - - +
90Z GLU* 2.9 30.9 + - - +
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Residues in contact with ALA 87 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55Z TYR* 4.7 19.7 - - + -
77Z LEU* 5.7 2.2 - - + -
83Z LEU 2.7 23.6 + - - +
84Z ALA* 3.6 6.7 - - - +
85Z ARG 3.1 0.2 - - - -
86Z ALA* 1.3 74.9 - - - +
88Z LEU* 1.3 65.6 + - + +
90Z GLU* 2.9 12.9 + - - +
91Z LEU* 2.9 34.4 + - + +
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Residues in contact with LEU 88 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68Z ILE* 3.7 19.3 - - + -
70Z PRO* 4.6 16.4 - - + -
73Z VAL* 4.3 14.6 - - + -
74Z SER 5.9 0.2 - - - +
77Z LEU* 4.3 22.4 - - + -
84Z ALA* 2.9 28.8 + - + +
85Z ARG* 4.3 0.7 - - - +
87Z ALA* 1.3 76.9 - - + +
89Z GLN* 1.3 57.8 + - - +
91Z LEU* 3.1 19.6 + - + +
92Z LEU 2.9 22.3 + - - -
97Z ILE* 5.8 2.8 - - + +
109Z TYR* 3.4 48.2 + - + +
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Residues in contact with GLN 89 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85Z ARG* 2.9 32.7 + - + +
86Z ALA* 4.1 6.1 - - - +
88Z LEU* 1.3 74.9 - - - +
90Z GLU* 1.3 57.5 + - - +
92Z LEU* 3.1 26.6 + - - +
93Z SER* 2.9 28.0 + - - -
99Z LEU* 3.7 13.8 - - - +
102Z LYS* 4.4 11.2 - - - +
107Z VAL* 4.1 12.3 - - - +
109Z TYR* 2.5 27.4 + - - +
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Residues in contact with GLU 90 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4S VAL* 3.7 26.1 - - - +
55Z TYR* 4.5 12.9 + - - -
86Z ALA 2.9 20.8 + - - +
87Z ALA* 2.9 11.8 + - - +
89Z GLN* 1.3 75.7 - - - +
91Z LEU* 1.3 56.5 + - + +
93Z SER* 2.9 13.0 + - - -
94Z LYS* 2.8 41.7 + - + +
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Residues in contact with LEU 91 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55Z TYR* 3.8 26.7 - - + +
59Z CYS* 6.0 2.0 - - - -
62Z VAL* 3.9 26.0 - - + -
87Z ALA* 2.9 27.6 + - + +
88Z LEU* 3.1 19.5 + - + +
90Z GLU* 1.3 75.8 - - + +
92Z LEU* 1.3 65.0 + - - +
94Z LYS* 3.3 33.3 + - + +
95Z GLY 3.5 4.0 + - - -
96Z LEU* 3.6 13.7 + - + +
97Z ILE* 3.7 39.8 + - + -
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Residues in contact with LEU 92 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88Z LEU 2.9 11.9 + - - +
89Z GLN* 3.1 22.9 + - - +
91Z LEU* 1.3 76.4 - - - +
93Z SER* 1.3 58.7 + - - +
95Z GLY* 2.9 21.2 + - - -
96Z LEU 4.5 0.2 + - - -
97Z ILE 3.5 22.3 + - - +
98Z LYS* 4.2 12.1 - - - -
99Z LEU* 3.5 35.0 - - + +
109Z TYR* 4.6 1.3 - - + -
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Residues in contact with SER 93 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89Z GLN 2.9 13.8 + - - -
90Z GLU* 2.9 15.9 + - - -
92Z LEU* 1.3 78.2 - - - +
94Z LYS* 1.3 60.4 + - - +
95Z GLY 3.3 0.7 + - - -
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Residues in contact with LYS 94 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55Z TYR* 5.6 2.0 - - - +
59Z CYS* 6.4 2.0 - - - -
90Z GLU* 2.8 24.9 + - + +
91Z LEU* 3.5 34.8 - - + +
92Z LEU 3.1 0.8 - - - -
93Z SER* 1.3 78.0 - - - +
95Z GLY* 1.3 61.8 + - - +
96Z LEU* 4.6 17.7 - - + +
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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