Contacts of the helix formed by residues 63 - 78 (chain A) in PDB entry 1FR2
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 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ASP* 2.5 30.6 + - - -
62A ASP* 1.3 77.6 + - - +
64A PRO* 1.3 75.7 - - - +
65A SER* 3.4 9.9 + - - -
66A GLY 3.0 12.1 + - - -
67A ILE* 2.9 21.4 + - - +
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Residues in contact with PRO 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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16A LEU* 3.9 9.0 - - + -
19A VAL* 3.8 12.5 - - + +
20A THR* 3.4 36.1 - - + +
23A CYS* 4.0 25.8 - - + -
24A ASN* 5.9 1.8 - - - +
62A ASP 4.6 0.2 - - - +
63A SER* 1.3 88.4 - - - +
65A SER* 1.3 61.8 + - - +
67A ILE* 3.3 2.4 + - - +
68A VAL* 3.0 27.0 + - - +
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Residues in contact with SER 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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16A LEU* 4.0 16.2 - - - +
61A ASP* 5.2 1.0 + - - -
63A SER* 3.4 9.2 + - - -
64A PRO* 1.3 79.4 - - - +
66A GLY* 1.3 59.2 + - - +
68A VAL* 3.8 3.7 - - - +
69A ASN* 2.9 30.7 + - - +
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Residues in contact with GLY 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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61A ASP* 3.3 37.6 - - - +
63A SER* 3.0 7.5 + - - -
65A SER* 1.3 83.0 + - - +
67A ILE* 1.3 55.2 + - - +
69A ASN* 3.4 6.7 + - - +
70A THR* 3.0 31.0 + - - -
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Residues in contact with ILE 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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19A VAL* 4.0 10.8 - - + -
23A CYS* 3.7 30.1 - - - -
40A PHE* 3.8 30.5 - - + -
52A LEU* 3.7 29.2 - - + +
53A ILE* 3.7 17.5 - - + +
61A ASP 4.0 8.7 - - - +
62A ASP* 3.8 13.7 - - - +
63A SER 2.9 11.9 + - - +
64A PRO 3.6 5.8 - - - +
66A GLY* 1.3 73.9 - - - +
68A VAL* 1.3 65.9 + - - +
70A THR* 3.1 7.2 + - - -
71A VAL* 2.9 25.0 + - + +
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Residues in contact with VAL 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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12A GLU* 4.0 34.1 - - + +
15A PHE* 4.0 5.4 - - + -
16A LEU* 3.8 33.9 - - + -
19A VAL* 4.0 16.6 - - + -
64A PRO 3.0 20.4 + - - +
65A SER* 3.8 6.5 - - - +
67A ILE* 1.3 76.1 - - - +
69A ASN* 1.3 59.2 + - - +
71A VAL* 3.3 8.2 + - - +
72A LYS* 2.9 27.0 + - + +
83A PHE* 4.4 14.5 - - + -
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Residues in contact with ASN 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 SER 2.9 18.1 + - - +
66A GLY* 3.6 7.4 - - - +
67A ILE 3.2 0.2 - - - -
68A VAL* 1.3 78.1 - - - +
70A THR* 1.3 59.8 + - - +
72A LYS* 3.2 9.2 + - - +
73A GLN* 2.9 52.0 + - - +
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Residues in contact with THR 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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46A HIS* 4.6 9.9 - - + -
52A LEU* 4.1 26.2 - - + -
57A LYS* 6.4 0.2 - - - +
60A ASP* 4.7 22.2 + - + +
61A ASP 4.8 4.9 + - - -
66A GLY 3.0 17.5 + - - -
67A ILE* 3.6 10.3 - - - -
69A ASN* 1.3 80.1 + - - +
71A VAL* 1.3 64.0 + - - +
73A GLN* 4.1 4.7 - - - +
74A TRP* 3.0 23.4 + - + +
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Residues in contact with VAL 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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7A ILE* 5.7 1.1 - - + -
15A PHE* 4.2 17.7 - - + -
40A PHE* 4.2 8.1 - - + -
44A THR* 3.7 37.0 - - + -
46A HIS* 5.3 2.2 - - + +
52A LEU* 3.8 21.8 - - + -
67A ILE 2.9 17.4 + - - +
68A VAL 3.6 7.6 - - - +
70A THR* 1.3 74.8 - - - +
72A LYS* 1.3 66.6 + - - +
74A TRP* 3.3 5.1 + - + +
75A ARG* 2.9 43.4 + - + +
83A PHE* 4.7 7.0 - - + -
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Residues in contact with LYS 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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12A GLU* 2.7 37.1 + - - +
68A VAL 2.9 17.0 + - - +
69A ASN* 3.2 12.1 + - - +
71A VAL* 1.3 77.3 - - - +
73A GLN* 1.3 72.0 + - - +
75A ARG* 3.6 4.6 + - - +
76A ALA* 3.0 30.6 + - + +
83A PHE* 4.1 21.3 - - + -
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Residues in contact with GLN 73 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A ASN* 2.9 42.1 + - - +
70A THR* 4.1 4.3 - - - +
72A LYS* 1.3 89.9 + - - +
74A TRP* 1.3 60.7 + - - +
76A ALA* 3.3 11.1 + - - +
77A ALA* 2.9 30.9 + - - +
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Residues in contact with TRP 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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44A THR 3.7 14.6 - - - -
45A GLU 3.4 19.7 - - - -
46A HIS* 3.4 33.7 - + + +
47A PRO* 3.5 27.4 - - + +
70A THR* 3.0 19.7 + - + +
71A VAL* 3.8 3.1 - - + +
73A GLN* 1.3 75.4 - - - +
75A ARG* 1.3 85.3 + - + +
77A ALA* 3.1 2.4 + - - -
78A ASN* 2.8 64.5 + - + +
80A LYS* 3.5 38.8 - - + -
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Residues in contact with ARG 75 (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 ILE* 3.2 32.9 - - - +
43A MET 3.6 6.5 + - - -
44A THR 3.0 23.3 + - - +
45A GLU* 3.0 28.5 + - - -
71A VAL* 2.9 34.6 + - + +
72A LYS* 4.0 4.5 - - - +
74A TRP* 1.3 93.2 - - + +
76A ALA* 1.3 63.5 + - - +
78A ASN* 3.3 5.5 + - - +
80A LYS* 3.1 51.1 + - + +
81A SER* 2.8 42.9 + - - +
82A GLY* 5.4 4.0 - - - -
83A PHE* 6.0 2.5 - - - -
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Residues in contact with ALA 76 (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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72A LYS* 3.0 20.4 + - + +
73A GLN* 3.6 14.6 - - - +
74A TRP 3.2 0.2 - - - -
75A ARG* 1.3 78.7 - - - +
77A ALA* 1.3 59.4 + - - +
78A ASN 3.5 0.3 + - - -
79A GLY* 4.1 5.4 + - - -
80A LYS 4.7 4.5 - - - -
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Residues in contact with ALA 77 (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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73A GLN 2.9 17.4 + - - +
74A TRP* 3.1 5.6 + - - +
76A ALA* 1.3 75.6 - - - +
78A ASN* 1.3 69.0 + - - +
79A GLY 3.6 1.2 + - - -
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Residues in contact with ASN 78 (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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74A TRP* 2.8 73.2 + - + +
75A ARG* 3.3 1.5 + - - +
77A ALA* 1.3 89.9 - - - +
79A GLY* 1.3 61.7 + - - +
80A LYS* 3.3 13.3 + - - +
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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