Contacts of the helix formed by residues 84 - 99 (chain C) in PDB entry 2FPO
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 ASP 84 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82C GLU* 3.0 17.7 + - - +
83C MSE 1.3 81.3 - - + +
85C ARG* 1.3 53.1 + - - +
86C ALA* 3.0 13.3 + - - +
87C VAL* 2.9 33.5 + - + +
88C SER* 2.8 35.9 + - - -
107C ASN* 3.9 0.4 - - - -
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Residues in contact with ARG 85 (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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83C MSE 3.3 4.8 + - - +
84C ASP* 1.3 72.4 + - - +
86C ALA* 1.3 69.7 + - - +
88C SER* 3.1 7.6 + - - -
89C GLN* 3.0 68.5 + - + +
107C ASN* 3.7 21.8 - - - +
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Residues in contact with ALA 86 (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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27C PRO* 3.9 14.7 - - + +
84C ASP* 3.0 8.4 + - - +
85C ARG* 1.3 86.7 - - - +
87C VAL* 1.3 66.4 + - + +
89C GLN* 3.4 12.2 + - - +
90C GLN* 3.2 22.9 + - - +
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Residues in contact with VAL 87 (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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27C PRO* 4.1 23.1 - - + +
28C ASP 6.0 2.7 - - - +
62C GLY* 3.0 39.5 - - - +
63C SER* 4.1 2.9 - - - +
82C GLU* 3.8 11.2 - - + +
84C ASP* 2.9 37.2 + - + +
86C ALA* 1.3 76.1 - - + +
88C SER* 1.3 56.9 + - - +
90C GLN* 3.3 3.6 + - - +
91C LEU* 3.0 25.8 + - - +
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Residues in contact with SER 88 (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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82C GLU* 4.0 21.8 - - - -
84C ASP 2.8 16.2 + - - -
85C ARG 3.1 12.0 + - - -
87C VAL* 1.3 76.8 - - - +
89C GLN* 1.3 62.6 + - - +
91C LEU* 3.4 8.2 + - - +
92C ILE* 3.1 30.6 + - - +
105C VAL* 3.8 20.0 - - - +
107C ASN* 3.4 21.7 + - - +
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Residues in contact with GLN 89 (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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85C ARG* 3.0 59.0 + - + +
86C ALA* 3.8 7.6 - - - +
87C VAL 3.3 0.4 - - - -
88C SER* 1.3 77.8 - - - +
90C GLN* 1.3 62.0 + - - +
92C ILE* 3.2 16.2 + - + +
93C LYS* 3.2 38.6 + - - +
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Residues in contact with GLN 90 (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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25C PRO* 3.3 34.3 - - - +
26C VAL* 4.1 1.8 - - + -
27C PRO* 3.8 27.8 - - + +
86C ALA 3.2 14.0 + - - +
87C VAL 3.8 2.5 - - - +
89C GLN* 1.3 75.7 - - - +
91C LEU* 1.3 60.2 + - - +
93C LYS* 3.2 29.5 + - - +
94C ASN* 2.9 50.6 + - - +
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Residues in contact with LEU 91 (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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61C ALA* 3.8 23.8 - - + -
62C GLY 3.8 18.6 - - - +
63C SER 4.2 6.7 - - - +
64C GLY* 4.1 20.6 - - - -
68C LEU* 4.2 18.2 - - + -
80C LEU* 3.9 22.4 - - + -
82C GLU* 5.1 4.7 - - + -
87C VAL 3.0 14.6 + - - +
88C SER* 3.5 10.8 - - - +
89C GLN 3.3 0.2 - - - -
90C GLN* 1.3 76.3 - - - +
92C ILE* 1.3 56.8 + - - +
94C ASN* 3.2 6.0 + - + +
95C LEU* 3.0 28.0 + - + +
105C VAL* 3.8 20.9 - - + -
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Residues in contact with ILE 92 (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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112B SER* 6.2 0.7 - - - +
88C SER* 3.1 21.2 + - - +
89C GLN* 3.2 14.1 + - + +
91C LEU* 1.3 74.2 - - - +
93C LYS* 1.3 66.5 + - + +
95C LEU* 3.5 8.1 + - + +
96C ALA* 3.1 21.7 + - + +
105C VAL* 3.7 34.8 - - + +
107C ASN* 6.6 0.2 - - + -
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Residues in contact with LYS 93 (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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89C GLN* 3.2 28.4 + - - +
90C GLN* 3.2 32.7 + - - +
92C ILE* 1.3 78.0 - - + +
94C ASN* 1.3 62.2 + - - +
96C ALA* 3.2 8.5 + - - +
97C THR* 2.9 32.1 + - - +
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Residues in contact with ASN 94 (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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24C LEU* 3.9 25.7 - - + +
25C PRO* 2.9 35.4 + - - +
26C VAL* 4.4 8.3 - - - +
63C SER 4.8 6.5 + - - -
68C LEU* 4.5 15.4 - - + +
90C GLN* 2.9 36.6 + - - +
91C LEU* 3.2 8.4 + - - +
93C LYS* 1.3 76.6 - - - +
95C LEU* 1.3 56.6 + - - +
97C THR* 3.3 8.7 + - - -
98C LEU* 3.0 36.0 + - - +
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Residues in contact with LEU 95 (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 LEU* 3.7 25.3 - - + +
71C LEU* 3.8 22.0 - - + -
80C LEU* 4.3 7.2 - - + -
91C LEU* 3.0 15.2 + - + +
92C ILE* 3.6 9.6 - - + +
94C ASN* 1.3 74.3 - - - +
96C ALA* 1.3 57.4 + - - +
98C LEU* 3.3 4.5 + - + -
99C LYS 2.9 22.5 + - - -
100C ALA* 2.9 31.7 + - + +
103C ALA* 3.9 26.2 - - + +
104C ARG* 5.0 0.4 - - - -
105C VAL* 3.6 30.7 - - + -
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Residues in contact with ALA 96 (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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92C ILE* 3.1 15.2 + - + +
93C LYS* 3.2 12.1 + - - +
95C LEU* 1.3 74.7 - - - +
97C THR* 1.3 64.8 + - - +
99C LYS* 3.0 20.4 + - - +
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Residues in contact with THR 97 (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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22C ARG* 3.8 26.6 + - - +
24C LEU* 3.9 17.5 - - + -
25C PRO* 6.0 2.0 - - + +
93C LYS* 2.9 17.9 + - - +
94C ASN* 3.4 12.4 + - - -
96C ALA* 1.3 75.9 - - - +
98C LEU* 1.3 62.8 + - - +
99C LYS* 3.3 12.0 + - - +
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Residues in contact with LEU 98 (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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14C ILE* 4.2 1.8 - - + -
19C TRP* 3.8 67.6 + - + -
22C ARG* 3.9 25.7 + - + +
24C LEU* 3.6 37.0 - - + -
68C LEU* 3.9 23.1 - - + -
94C ASN 3.0 20.7 + - - +
95C LEU* 3.7 5.8 - - + +
96C ALA 3.3 0.2 - - - -
97C THR* 1.3 74.2 - - - +
99C LYS* 1.3 67.6 + - - +
100C ALA* 3.3 2.2 + - + +
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Residues in contact with LYS 99 (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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19C TRP* 5.4 0.5 - - - -
95C LEU 2.9 4.4 + - - -
96C ALA* 3.0 19.8 + - - +
97C THR 3.9 7.8 + - - +
98C LEU* 1.3 80.9 - - - +
100C ALA* 1.3 60.7 + - - +
101C GLY 3.5 3.9 + - - -
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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