Contacts of the helix formed by residues 64 - 74 (chain A) in PDB entry 2FC8
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 GLU 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A GLN* 3.9 12.3 - - - +
14A PRO* 2.9 50.5 - - + +
15A SER* 3.2 33.8 - - - +
16A LYS* 3.4 29.3 + - + +
63A SER* 1.3 72.5 - - - +
65A GLU* 1.3 63.8 + - + +
67A ALA* 3.1 4.1 + - - +
68A LYS* 2.9 24.0 + - - +
88A TRP* 4.0 1.9 - - - -
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Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A SER* 3.0 11.3 - - - -
64A GLU* 1.3 77.7 - - + +
66A ASP* 1.3 68.1 + - - +
68A LYS* 3.0 10.0 + - - +
69A ALA* 3.0 24.0 + - - +
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Residues in contact with ASP 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLY* 4.4 11.2 - - - +
61A PHE* 4.0 11.0 - - + -
62A ASN* 2.7 44.7 + - - +
63A SER* 3.0 6.6 + - - +
65A GLU* 1.3 81.9 - - - +
67A ALA* 1.3 63.2 + - - +
69A ALA* 3.5 6.9 + - - +
70A ALA* 3.1 22.3 + - - +
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Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A SER 4.0 1.6 - - - +
16A LYS 3.4 26.2 - - - +
18A LEU* 3.0 12.8 - - + +
61A PHE* 3.5 24.0 - - + -
63A SER 3.1 6.8 + - - +
64A GLU 3.3 8.5 - - - +
65A GLU 3.1 0.2 + - - -
66A ASP* 1.3 77.1 - - - +
68A LYS* 1.3 63.6 + - - +
70A ALA* 2.9 4.2 + - - +
71A LYS 2.8 17.7 + - - -
88A TRP* 3.7 16.4 - - + -
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Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A GLY 3.7 21.5 - - - +
8A PRO* 3.1 32.1 + - + +
9A ASN* 5.0 1.8 - - - +
14A PRO* 5.8 4.3 - - + -
64A GLU 2.9 15.2 + - - +
65A GLU* 3.5 10.3 - - - +
67A ALA* 1.3 71.9 - - - +
69A ALA* 1.3 57.2 + - - +
71A LYS* 2.6 40.9 + - - +
72A GLU* 3.1 30.4 + - + +
88A TRP* 3.3 28.7 - - + +
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Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A GLU 3.0 12.0 + - - +
66A ASP* 3.8 8.5 - - - +
68A LYS* 1.3 79.7 - - - +
70A ALA* 1.3 59.8 + - - +
72A GLU* 4.1 9.0 + - - +
73A ALA* 3.8 16.6 + - - +
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Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE* 4.0 18.4 - - + -
37A ASP 5.0 9.6 - - - +
38A GLY* 6.0 0.2 - - - -
61A PHE* 3.7 26.0 - - + -
66A ASP 3.1 12.4 + - - +
67A ALA 2.9 11.3 + - - +
68A LYS 2.9 0.8 - - - -
69A ALA* 1.3 75.2 - - - +
71A LYS* 1.3 63.6 + - - +
73A ALA* 3.4 7.2 + - - +
74A MET* 3.1 24.8 + - - +
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Residues in contact with LYS 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 3.5 30.9 - - + +
67A ALA 2.8 4.9 + - - +
68A LYS* 2.6 28.3 + - - +
70A ALA* 1.3 69.8 - - - +
72A GLU* 1.3 58.6 + - + +
75A GLU* 2.6 37.1 + - + -
86A LEU* 3.0 40.4 - - + +
87A ASP* 4.8 1.1 - - - +
88A TRP* 3.2 45.8 - - - +
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Residues in contact with GLU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LYS* 3.1 31.9 + - + +
69A ALA* 4.3 8.8 - - - +
71A LYS* 1.3 82.4 - - + +
73A ALA* 1.3 56.1 + - - +
75A GLU* 2.4 50.7 - - - +
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Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ALA 3.8 11.6 + - - +
70A ALA* 3.5 11.2 - - - +
71A LYS 3.2 0.6 - - - -
72A GLU* 1.3 82.3 - - - +
74A MET* 1.3 62.3 + - + +
75A GLU* 3.1 6.2 + - - +
76A ASP 4.5 1.4 + - - -
77A GLY* 4.8 2.1 + - - -
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Residues in contact with MET 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A SER* 3.2 36.6 - - - +
36A PHE* 3.9 14.4 - - + -
70A ALA 3.1 8.3 + - - +
73A ALA* 1.3 79.6 - - + +
75A GLU* 1.3 66.4 + - - +
76A ASP 3.1 2.9 - - - -
77A GLY* 2.8 37.4 + - - +
78A GLU 4.1 2.0 - - - +
79A ILE* 3.6 32.5 - - + -
84A VAL* 3.6 19.5 - - + +
86A LEU* 3.3 24.2 - - + +
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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