Contacts of the helix formed by residues 65 - 72 (chain C) 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 LYS 65 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A ASN* 5.8 1.6 - - - +
73A ASP* 4.5 14.1 + - - -
118A GLU* 3.5 46.6 + - + +
120A ARG* 5.1 4.0 - - - -
63C VAL 2.9 5.9 + - - -
64C THR* 1.3 76.5 - - - +
66C LEU* 1.3 59.2 + - - +
67C GLY 3.6 0.7 - - - -
68C ARG* 3.2 35.2 - - - +
69C LEU* 3.6 23.6 + - - +
266C TYR* 3.5 45.7 + - + +
273C LEU* 3.2 32.3 - - + +
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Residues in contact with LEU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C THR* 2.6 20.8 + - + +
65C LYS* 1.3 73.9 - - - +
67C GLY* 1.3 60.3 + - - +
68C ARG 3.3 0.2 - - - -
69C LEU* 3.2 8.1 + - - +
70C VAL* 2.9 33.9 + - + +
75C ILE* 4.1 15.3 - - + -
81C ILE* 3.8 31.0 - - + -
86C LEU* 4.8 7.9 - - + -
87C PRO 4.1 19.1 - - - +
88C ILE* 4.2 12.6 - - + -
93C ILE* 3.7 27.1 - - + -
266C TYR* 4.3 18.8 + - + +
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Residues in contact with GLY 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C TRP* 3.4 36.1 - - - -
62C PRO* 5.2 0.4 - - - -
63C VAL 3.7 6.7 + - - -
64C THR* 4.8 0.2 - - - +
66C LEU* 1.3 78.2 - - - +
68C ARG* 1.3 60.1 + - - +
70C VAL* 3.4 14.1 - - - +
71C LYS* 2.9 34.1 + - - +
93C ILE* 5.5 0.4 - - - -
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Residues in contact with ARG 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A GLU* 5.3 2.2 + - - -
62C PRO* 3.8 26.9 - - + -
63C VAL* 4.2 11.9 + - - +
64C THR 5.1 0.2 - - - +
65C LYS* 3.2 45.3 - - - +
66C LEU 3.3 0.2 - - - -
67C GLY* 1.3 78.3 - - - +
69C LEU* 1.3 55.8 + - - +
71C LYS* 3.4 5.7 + - - +
72C ASP* 2.9 38.3 + - - +
272C HIS 4.0 0.4 + - - -
273C LEU* 3.3 31.0 + - + +
276C THR* 2.2 57.9 + - + +
277C HIS* 5.3 1.7 - - - +
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Residues in contact with LEU 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C LYS 3.6 10.3 - - - +
66C LEU* 3.2 9.6 + - - +
68C ARG* 1.3 75.2 - - - +
70C VAL* 1.3 65.3 + - - +
72C ASP* 3.5 13.2 + - - +
73C MET 3.4 1.9 + - - -
74C LYS* 3.3 30.4 + - + -
75C ILE* 3.8 21.9 + - + -
265C PRO* 4.4 19.1 - - + +
266C TYR* 3.6 37.7 - - + -
269C PHE* 3.8 27.4 - - + +
272C HIS* 4.9 1.6 - - + -
273C LEU* 3.7 21.5 - - + -
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Residues in contact with VAL 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C TRP* 6.3 0.7 - - + -
66C LEU* 2.9 31.8 + - + +
67C GLY* 3.4 15.3 - - - +
68C ARG 3.2 0.2 - - - -
69C LEU* 1.3 78.3 - - - +
71C LYS* 1.3 62.3 + - - +
73C MET* 3.2 14.2 + - - +
75C ILE* 5.2 7.4 - - + +
93C ILE* 4.5 8.1 - - + +
96C PHE* 3.8 34.5 - - + -
97C PHE* 3.6 39.0 - - + -
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Residues in contact with LYS 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C GLU* 3.6 25.2 + - - +
60C TRP* 3.5 33.5 - - + +
62C PRO* 3.2 41.0 - - + +
67C GLY 2.9 18.4 + - - +
68C ARG* 3.9 4.5 - - - +
70C VAL* 1.3 71.8 - - + +
72C ASP* 1.3 64.8 + - - +
73C MET* 3.0 9.8 + - - +
96C PHE* 5.1 11.0 - - + -
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Residues in contact with ASP 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C ARG* 2.9 29.5 + - - +
69C LEU* 3.9 7.9 - - - +
70C VAL 3.3 0.6 - - - -
71C LYS* 1.3 77.5 - - - +
73C MET* 1.3 67.9 + - - +
74C LYS* 3.2 35.2 + - + -
272C HIS* 3.4 33.1 - - - +
273C LEU* 6.0 0.2 - - - +
276C THR* 5.0 7.4 - - - +
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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