Contacts of the helix formed by residues 61 - 72 (chain M) 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 TYR 61 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35M ILE* 3.2 33.8 - - + +
56M CYS* 3.5 26.9 - - + -
58M GLU* 4.3 21.5 + - + +
59M PRO 4.7 1.1 - - - +
60M MET* 1.3 77.0 - - - +
62M VAL* 1.3 79.3 + - + +
63M LYS* 3.2 3.9 - - - +
64M LEU* 3.0 31.9 + - + +
65M VAL* 3.8 6.8 + - + +
107M SER* 3.3 36.2 - - - -
108M CYS* 2.7 30.8 - - - -
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Residues in contact with VAL 62 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52M LEU* 3.5 36.1 - - + +
53M ALA 3.1 28.3 - - - +
54M SER* 4.3 12.1 - - - +
56M CYS* 4.5 1.6 - - - -
61M TYR* 1.3 88.9 - - + +
63M LYS* 1.3 72.8 + - + +
65M VAL* 2.9 22.4 + - - +
66M GLU* 3.0 16.5 + - - +
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Residues in contact with LYS 63 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60M MET* 4.7 14.9 - - - +
61M TYR 3.2 2.3 - - - +
62M VAL* 1.3 85.1 - - + +
64M LEU* 1.3 56.7 + - - +
66M GLU* 3.3 22.7 - - - +
67M ALA* 2.8 29.5 + - - +
108f VAL* 3.6 24.9 - - + -
111f ASN* 2.8 37.2 + - - +
112f GLY* 3.5 31.0 - - - +
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Residues in contact with LEU 64 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60M MET 3.5 16.4 - - - +
61M TYR* 3.1 23.8 - - + +
63M LYS* 1.3 77.7 - - - +
65M VAL* 1.3 57.7 + - + +
67M ALA* 3.2 5.2 + - - +
68M LEU* 2.9 36.2 + - + +
104f LYS* 5.7 2.2 - - + -
106f TYR* 3.4 50.9 - - + +
107f LYS 3.6 12.3 - - - +
108f VAL* 3.6 22.7 - - + -
114f ILE* 3.7 18.6 - - + +
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Residues in contact with VAL 65 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38M ALA* 6.4 0.9 - - + -
42M LEU* 4.6 6.5 - - + -
50M CYS* 3.5 31.2 - - - -
51M VAL 4.6 1.3 - - - +
52M LEU* 3.9 20.0 - - + -
61M TYR* 4.4 11.4 - - + +
62M VAL* 2.9 11.4 + - - +
64M LEU* 1.3 73.8 - - + +
66M GLU* 1.3 57.2 + - - +
67M ALA 3.0 4.4 + - - -
68M LEU* 3.2 8.2 + - + +
69M CYS* 2.9 28.1 + - - -
76M LEU* 3.6 13.2 - - + -
108M CYS* 4.1 26.5 - - + -
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Residues in contact with GLU 66 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52M LEU* 4.4 6.2 - - + +
62M VAL* 3.0 13.3 + - - +
63M LYS* 3.3 41.1 - - + +
65M VAL* 1.3 76.2 - - - +
67M ALA* 1.3 59.8 + - - +
69M CYS* 4.1 2.4 - - - +
70M ALA* 2.9 30.9 + - - +
76M LEU* 3.6 24.1 - - + +
111f ASN 5.0 1.4 - - - +
112f GLY* 4.4 8.5 - - - -
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Residues in contact with ALA 67 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63M LYS 2.8 21.8 + - - +
64M LEU 3.3 6.3 - - - +
65M VAL 3.0 0.4 - - - -
66M GLU* 1.3 76.9 - - - +
68M LEU* 1.3 60.5 + - - +
70M ALA* 3.7 3.9 - - - +
71M GLU* 2.9 38.0 + - + +
112f GLY 3.0 21.3 - - - +
113f LYS* 4.5 0.9 - - + -
114f ILE* 3.4 27.4 - - + +
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Residues in contact with LEU 68 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39M ALA* 4.0 23.1 - - + +
42M LEU* 3.6 41.3 - - + -
43M ASP* 3.3 22.7 - - - +
64M LEU* 2.9 20.2 + - + +
65M VAL* 3.2 4.2 + - + +
67M ALA* 1.3 76.5 - - - +
69M CYS* 1.3 57.9 + - - +
71M GLU* 4.9 0.4 - - + -
72M HIS* 2.7 50.6 + - + +
106f TYR* 5.6 6.3 - - + -
114f ILE* 3.6 20.0 - - + -
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Residues in contact with CYS 69 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42M LEU* 4.2 6.7 - - - -
50M CYS* 3.6 29.4 - - - -
65M VAL 2.9 20.5 + - - +
66M GLU* 4.1 2.2 - - - +
68M LEU* 1.3 76.8 - - - +
70M ALA* 1.3 62.3 + - - +
73M GLN* 3.3 1.4 + - - -
74M ILE* 2.6 62.4 + - - +
76M LEU* 3.5 30.5 - - + -
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Residues in contact with ALA 70 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66M GLU 2.9 20.5 + - - +
67M ALA* 3.2 6.7 + - - +
69M CYS* 1.3 76.7 - - - +
71M GLU* 1.3 70.0 + - - +
73M GLN* 3.6 21.7 + - - -
112f GLY 5.7 1.1 - - - +
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Residues in contact with GLU 71 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45M ARG* 5.3 5.4 + - - -
67M ALA* 2.9 22.4 + - + +
68M LEU* 4.9 0.4 - - + -
70M ALA* 1.3 83.6 - - + +
72M HIS* 1.3 71.0 + - + +
73M GLN* 3.3 8.5 + - - +
113f LYS* 4.4 27.3 - - + +
114f ILE* 6.1 2.9 - - + -
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Residues in contact with HIS 72 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42M LEU 3.0 24.9 + - - -
43M ASP* 3.6 18.2 + - - +
45M ARG* 3.5 44.1 + - + +
68M LEU* 2.7 54.3 + - + +
71M GLU* 1.3 84.0 - - + +
73M GLN* 1.3 70.7 + - - +
74M ILE* 3.4 20.4 + - + +
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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