Contacts of the helix formed by residues 64 - 75 (chain C) in PDB entry 2F8X
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 SER 64 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C ARG 4.5 2.6 + - - -
30C GLY* 3.5 18.9 - - - -
31C ASP 4.1 1.0 + - - -
63C GLY* 1.3 71.9 - - - -
65C GLY* 1.3 64.2 + - - +
67C LYS* 3.3 19.3 + - - +
68C LYS* 3.4 16.4 + - - +
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Residues in contact with GLY 65 (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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30C GLY* 2.8 27.8 + - - -
31C ASP 3.3 8.7 + - - -
32C GLN* 3.9 8.9 - - - +
63C GLY 3.0 2.2 - - - -
64C SER* 1.3 80.1 + - - +
66C TRP* 1.3 58.7 + - - +
68C LYS* 3.1 8.7 + - - +
69C LYS* 2.8 30.3 + - - +
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Residues in contact with TRP 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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31C ASP 4.5 0.2 + - - -
32C GLN* 2.9 30.0 - - + +
33C THR 3.3 19.1 + - - +
34C VAL* 4.2 12.6 - - + -
61C LEU* 3.1 38.7 - - + +
62C MET 2.8 31.4 + - - -
63C GLY 3.3 8.4 + - - +
64C SER 3.3 0.8 - - - -
65C GLY* 1.3 76.7 - - - +
67C LYS* 1.3 57.3 + - - +
69C LYS* 3.4 4.0 + - - +
70C LYS* 3.0 24.3 + - - +
85C PRO* 3.9 22.3 - - + +
107C ASN* 6.1 0.4 - - - +
131C MET* 2.9 31.9 - - + -
133C TYR* 3.8 6.7 - + - -
139C ILE* 3.7 21.1 - - + -
326C PHE* 4.6 8.5 - + - -
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Residues in contact with LYS 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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63C GLY 4.5 0.8 + - - +
64C SER* 3.3 12.5 + - - +
66C TRP* 1.3 76.1 - - - +
68C LYS* 1.3 60.2 + - + +
69C LYS 3.1 1.8 - - - -
70C LYS* 2.8 25.8 + - + +
71C GLU* 2.8 40.9 + - + +
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Residues in contact with LYS 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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28C GLU* 4.3 27.1 + - + +
30C GLY* 4.6 19.2 - - - +
64C SER* 3.4 13.4 + - - +
65C GLY* 3.1 9.5 + - - +
67C LYS* 1.3 79.3 - - + +
69C LYS* 1.3 58.4 + - - +
71C GLU* 3.5 14.2 + - - +
72C GLN* 2.9 29.5 + - - +
75C ARG* 4.4 4.2 + - - +
327C TYR* 3.7 23.6 + - + -
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Residues in contact with LYS 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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32C GLN* 3.5 19.5 - - - +
65C GLY 2.8 15.3 + - - +
66C TRP 3.5 6.7 - - - +
68C LYS* 1.3 75.6 - - - +
70C LYS* 1.3 65.2 + - - +
72C GLN* 3.1 26.8 + - - +
73C MET* 3.0 38.1 + - + +
133C TYR* 3.2 48.7 - - + +
137C ASP* 5.6 1.6 - - - -
328C GLU* 3.3 29.0 + - + +
332C PRO* 4.3 8.9 - - - +
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Residues in contact with LYS 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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66C TRP 3.0 13.2 + - - +
67C LYS* 2.8 15.6 + - + +
69C LYS* 1.3 76.6 - - - +
71C GLU* 1.3 68.4 + - + +
73C MET* 3.3 2.4 + - - +
74C GLU* 3.1 45.7 + - - +
80C GLU* 3.9 25.6 + - - +
83C SER* 3.2 43.3 + - - +
84C GLN* 4.0 15.0 + - - -
85C PRO* 5.8 1.1 - - - +
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Residues in contact with GLU 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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67C LYS* 2.8 46.1 + - + +
68C LYS* 3.8 11.6 - - - +
70C LYS* 1.3 82.2 - - + +
72C GLN* 1.3 63.6 + - - +
74C GLU* 3.1 9.2 + - - +
75C ARG* 2.9 43.8 + - + +
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Residues in contact with GLN 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 LYS 2.9 18.7 + - - +
69C LYS* 3.1 32.0 + - - +
70C LYS 3.3 0.2 - - - -
71C GLU* 1.3 78.2 - - - +
73C MET* 1.3 74.2 + - - +
75C ARG* 3.3 28.9 + - - +
76C ASP* 2.9 38.8 + - - +
332C PRO* 4.2 21.4 - - + +
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Residues in contact with MET 73 (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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69C LYS* 3.0 41.4 + - + +
70C LYS* 3.7 4.0 - - - +
72C GLN* 1.3 92.0 - - - +
74C GLU* 1.3 63.0 + - - +
76C ASP* 3.1 18.2 + - - +
78C CYS* 3.4 25.9 - - - +
82C GLU 4.4 0.7 - - - +
83C SER* 3.9 24.2 - - - -
133C TYR* 4.0 15.5 - - + -
135C ASN* 3.5 28.7 - - - +
137C ASP* 3.4 28.7 - - + +
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Residues in contact with GLU 74 (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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70C LYS* 3.1 31.1 + - - +
71C GLU* 3.7 8.9 - - - +
73C MET* 1.3 71.5 - - - +
75C ARG* 1.3 53.3 + - + +
76C ASP 2.3 20.1 + - - -
77C GLY* 2.6 15.2 + - - -
78C CYS 3.6 22.1 + - - +
80C GLU* 3.9 30.4 + - - +
83C SER* 3.8 16.0 + - - +
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Residues in contact with ARG 75 (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 LYS* 4.4 4.8 + - - +
71C GLU* 2.9 31.5 + - + +
72C GLN* 3.3 36.2 - - - +
73C MET 3.4 0.4 - - - -
74C GLU* 1.3 72.2 - - + +
76C ASP* 1.3 66.1 - - - +
77C GLY 3.7 0.4 - - - -
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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