Contacts of the helix formed by residues 63 - 73 (chain A) in PDB entry 2FC9
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 PHE 63 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A THR* 6.2 4.0 - - + -
11A TRP* 4.8 1.6 - + - -
13A GLY 4.1 11.9 - - - -
14A GLU* 3.4 45.3 - - + +
15A SER 3.7 23.3 - - - +
16A LYS* 3.9 3.2 - - - +
62A SER* 1.3 77.5 + - - +
64A GLU* 1.3 75.1 + - + +
66A ALA* 4.3 0.2 - - - -
67A LYS* 3.2 51.3 + - + +
87A LEU* 4.1 11.7 - - + -
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Residues in contact with GLU 64 (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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14A GLU* 5.3 1.6 - - - +
62A SER* 2.8 18.7 + - - +
63A PHE* 1.3 99.8 + - + +
65A ASP* 1.3 70.2 + - - +
67A LYS* 3.7 3.0 - - - +
68A GLU* 3.0 20.5 + - - +
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Residues in contact with ASP 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LYS* 3.3 38.2 + - + +
60A PHE* 3.8 26.9 - - + -
61A ALA* 4.1 20.1 - - - +
62A SER 3.3 3.7 + - - +
64A GLU* 1.3 78.1 - - - +
66A ALA* 1.3 61.1 + - - +
68A GLU* 2.7 43.5 + - - +
69A ALA* 3.1 6.2 + - - +
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Residues in contact with ALA 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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15A SER 3.5 13.2 - - - +
16A LYS 3.2 26.2 - - - +
18A LEU* 3.0 29.0 - - + +
60A PHE* 3.4 16.6 - - + -
62A SER 3.1 14.7 + - - +
63A PHE* 4.3 0.4 - - - -
65A ASP* 1.3 77.9 - - - +
67A LYS* 1.3 57.8 + - - +
70A LEU* 3.0 24.1 + - - +
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Residues in contact with LYS 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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8A ASN* 5.6 3.2 + - - +
9A SER 4.1 18.6 + - - -
10A THR* 5.1 4.6 - - - +
11A TRP* 4.8 5.7 - - - -
63A PHE* 3.2 49.5 + - + +
64A GLU* 3.7 2.7 - - - +
65A ASP 3.1 0.8 - - - -
66A ALA* 1.3 77.5 - - - +
68A GLU* 1.3 60.2 + - - +
70A LEU* 4.0 20.7 - - + +
71A ASN* 2.9 70.4 + - - +
87A LEU* 4.0 15.1 - - - +
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Residues in contact with GLU 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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38A LYS* 3.3 30.7 + - + -
64A GLU 3.0 13.2 + - - +
65A ASP* 2.7 29.9 + - - +
67A LYS* 1.3 73.5 - - - +
69A ALA* 1.3 56.7 + - + +
71A ASN* 4.0 7.0 - - - +
72A SER* 3.9 15.8 + - - -
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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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35A VAL 5.6 0.2 - - - +
36A PHE* 3.5 31.6 - - + -
38A LYS* 6.1 3.8 - - + -
60A PHE* 3.8 20.4 - - + -
65A ASP 3.1 5.0 + - - +
68A GLU* 1.3 75.0 - - + +
70A LEU* 1.3 61.1 + - - +
71A ASN 3.1 2.0 - - - -
72A SER* 4.6 1.3 - - - +
73A CYS* 2.6 45.7 + - - +
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Residues in contact with LEU 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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8A ASN* 4.2 7.7 - - - +
18A LEU* 3.8 10.2 - - + +
66A ALA 3.0 18.2 + - - +
67A LYS* 3.3 26.0 + - + +
69A ALA* 1.3 76.8 - - - +
71A ASN* 1.3 57.8 + - - +
74A ASN* 3.2 25.6 + - - +
85A LEU* 2.9 52.3 - - + +
86A GLU* 3.9 2.5 - - - +
87A LEU* 3.4 39.3 - - + +
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Residues in contact with ASN 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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8A ASN* 3.4 38.7 + - - +
67A LYS* 2.9 52.7 + - - +
68A GLU* 4.0 7.6 - - - +
70A LEU* 1.3 80.6 - - - +
72A SER* 1.3 59.3 + - - +
74A ASN* 3.9 2.9 - - - +
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Residues in contact with SER 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 GLU 3.9 9.4 + - - -
69A ALA* 3.2 4.9 + - - -
71A ASN* 1.3 79.5 - - - +
73A CYS* 1.3 57.8 + - - +
74A ASN* 2.6 26.5 + - - +
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Residues in contact with CYS 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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35A VAL* 3.5 24.9 - - + -
36A PHE* 3.0 34.5 - - + -
69A ALA* 2.6 32.2 + - - +
72A SER* 1.3 73.9 - - - +
74A ASN* 1.3 62.7 + - - +
75A LYS 3.1 0.3 + - - -
76A ARG* 2.8 36.8 + - + +
83A ILE 4.1 0.5 - - - +
85A LEU* 3.1 21.5 - - + +
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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