Contacts of the helix formed by residues 60 - 73 (chain S) in PDB entry 5FLX
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 THR 60 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54S LYS* 5.3 4.2 + - - +
58S GLU 3.9 2.5 + - - -
59S LEU* 1.3 80.2 - - - +
61S GLU* 1.3 57.5 + - + +
62S ASP* 3.5 22.7 - - + +
63S GLU* 2.9 14.0 + - - +
64S VAL* 2.7 30.9 + - - -
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Residues in contact with GLU 61 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13S LEU* 5.9 6.7 - - + -
59S LEU 3.6 2.6 + - - -
60S THR* 1.3 75.3 - - + +
62S ASP* 1.3 68.1 + - - +
64S VAL* 3.0 17.8 + - + +
65S GLU* 2.8 52.9 + - - +
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Residues in contact with ASP 62 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60S THR* 3.2 13.8 - - + +
61S GLU* 1.3 86.1 + - - +
63S GLU* 1.3 56.6 + - - +
65S GLU* 3.2 13.1 + - - +
66S ARG* 2.9 28.6 + - - +
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Residues in contact with GLU 63 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48S ALA* 3.1 27.2 - - - +
50S ILE* 3.2 25.2 - - + +
54S LYS* 5.9 2.7 - - - +
59S LEU* 3.6 17.3 - - + -
60S THR* 2.9 22.5 + - - +
62S ASP* 1.3 76.2 - - - +
64S VAL* 1.3 60.5 + - - +
66S ARG* 3.5 28.4 + - - -
67S VAL* 2.9 36.8 + - - +
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Residues in contact with VAL 64 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10S GLN* 4.8 1.6 - - - +
13S LEU* 3.8 35.7 - - + -
15S VAL* 4.8 6.5 - - + -
59S LEU* 3.5 19.7 - - + +
60S THR 2.7 22.8 + - - +
61S GLU* 3.0 19.9 + - + +
63S GLU* 1.3 73.2 - - - +
65S GLU* 1.3 60.6 + - + +
67S VAL* 3.3 5.5 + - - +
68S ILE* 2.9 49.7 + - + +
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Residues in contact with GLU 65 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61S GLU* 2.8 39.7 + - - +
62S ASP* 3.7 14.6 - - - +
64S VAL* 1.3 77.3 - - + +
66S ARG* 1.3 58.1 + - - +
68S ILE* 3.2 14.4 + - + +
69S THR* 2.9 30.6 + - - -
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Residues in contact with ARG 66 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47S LYS 4.7 5.1 + - - -
48S ALA* 3.3 46.5 + - - +
49S ASP* 5.4 4.2 + - - -
62S ASP* 2.9 20.5 + - - +
63S GLU* 3.5 20.8 + - - +
65S GLU* 1.3 74.8 - - - +
67S VAL* 1.3 65.3 + - - +
69S THR* 3.0 13.4 + - + -
70S ILE* 3.0 37.5 + - + +
77S TYR* 6.0 4.0 - - - -
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Residues in contact with VAL 67 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26S ILE* 6.2 2.7 - - + -
30S ILE* 4.8 15.3 - - + -
44S VAL* 4.0 19.3 - - + -
45S LEU* 5.8 2.0 - - + -
48S ALA* 4.0 6.1 - - + -
50S ILE* 3.6 30.7 - - + -
59S LEU* 5.1 5.2 - - + -
63S GLU* 2.9 33.1 + - + +
64S VAL* 3.7 6.3 - - - +
66S ARG* 1.3 74.9 - - - +
68S ILE* 1.3 60.3 + - + +
70S ILE* 3.0 10.9 + - - +
71S MET* 2.8 37.8 + - + +
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Residues in contact with ILE 68 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14S ARG 5.6 1.1 - - - +
15S VAL* 3.8 33.9 - - + -
16S LEU* 4.3 25.4 - - + +
64S VAL* 2.9 36.9 + - + +
65S GLU* 3.5 14.4 - - + +
67S VAL* 1.3 76.4 - - + +
69S THR* 1.3 59.2 + - - +
71S MET* 2.8 29.1 + - + +
72S GLN* 3.0 20.4 + - + +
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Residues in contact with THR 69 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65S GLU* 2.9 15.5 + - - +
66S ARG* 3.0 14.7 + - + -
68S ILE* 1.3 76.2 - - - +
70S ILE* 1.3 63.3 + - + +
71S MET 3.4 0.3 + - - -
72S GLN* 3.5 32.8 + - - +
73S ASN* 3.9 8.8 - - - +
76S GLN* 6.1 0.9 - - - +
77S TYR* 4.7 19.2 - - + +
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Residues in contact with ILE 70 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40S TYR* 4.0 4.7 + - - -
44S VAL* 3.8 24.4 - - + +
47S LYS* 4.5 20.9 - - + +
48S ALA* 4.6 13.9 - - + +
66S ARG* 3.0 30.5 + - + +
67S VAL* 3.0 10.5 + - - +
69S THR* 1.3 78.2 - - + +
71S MET* 1.3 63.5 + - - +
73S ASN 4.7 2.5 - - - -
74S PRO* 3.9 21.4 - - + +
77S TYR* 3.7 41.5 - - + -
79S ILE* 5.0 8.0 - - + +
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Residues in contact with MET 71 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15S VAL* 6.0 4.5 - - + -
16S LEU* 5.6 12.8 - - + -
30S ILE* 4.1 17.7 - - + -
33S ILE* 5.3 6.1 - - + -
36S VAL* 3.5 19.7 - - + -
40S TYR* 3.1 47.7 + - + +
44S VAL* 4.0 18.6 - - - -
67S VAL* 2.8 28.9 + - + +
68S ILE* 2.8 26.3 + - + +
70S ILE* 1.3 77.1 - - - +
72S GLN* 1.3 64.7 + - - +
74S PRO* 4.3 3.1 - - - +
97S GLN* 4.5 9.0 - - - +
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Residues in contact with GLN 72 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16S LEU* 6.1 4.7 - - + +
68S ILE* 3.0 17.6 + - + +
69S THR* 3.5 30.0 + - - +
71S MET* 1.3 80.6 - - - +
73S ASN* 1.3 72.7 + - + +
74S PRO* 3.7 5.4 - - - +
96S SER* 5.3 1.6 + - - -
97S GLN* 3.9 18.2 + - - +
99S LEU* 5.4 14.6 - - + -
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Residues in contact with ASN 73 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69S THR 3.9 10.5 + - - +
70S ILE 3.9 3.7 - - - +
72S GLN* 1.3 89.1 - - + +
74S PRO* 1.3 62.9 - - - +
75S ARG* 3.4 25.5 + - - +
76S GLN* 3.2 47.2 + - - +
77S TYR* 4.5 9.0 - - - -
95S TYR 5.1 2.9 - - - +
96S SER* 5.9 1.4 - - - -
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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