Contacts of the helix formed by residues 101 - 116 (chain Q) 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 ASP 101 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100Q VAL* 1.3 88.3 - - - +
102Q GLU* 1.3 61.7 - - - +
103Q ALA* 4.1 18.4 - - - +
104Q SER* 3.3 20.0 + - - -
105Q LYS* 3.7 6.2 + - - +
55g PRO 5.0 0.4 - - - +
56g GLN* 3.4 28.4 + - - +
57g ARG* 5.7 1.3 - - - -
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Residues in contact with GLU 102 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96Q TYR 4.4 2.4 - - - +
97Q GLN* 4.4 14.2 - - - +
100Q VAL 4.7 1.2 - - - +
101Q ASP* 1.3 72.5 - - - +
103Q ALA* 1.3 66.0 + - - +
104Q SER 3.2 0.2 - - - -
105Q LYS* 3.0 37.9 + - - +
106Q LYS* 2.9 40.3 + - - +
41g ILE* 5.3 1.1 - - + -
55g PRO* 3.8 17.0 - - + -
56g GLN 2.7 24.2 + - - +
57g ARG* 3.6 1.9 - - - +
58g ALA* 3.2 50.0 + - + +
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Residues in contact with ALA 103 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101Q ASP* 3.2 14.8 - - - +
102Q GLU* 1.3 79.1 - - - +
104Q SER* 1.3 60.3 + - - +
106Q LYS* 4.5 1.4 - - - +
107Q GLU* 3.3 25.5 + - - +
54g ILE* 5.1 12.1 - - + -
55g PRO* 3.6 32.5 + - + +
56g GLN* 5.5 0.2 - - - +
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Residues in contact with SER 104 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62Q ARG* 5.8 6.1 - - - -
96Q TYR* 4.6 8.0 - - - -
100Q VAL* 3.2 30.2 - - - +
101Q ASP* 3.3 6.5 + - - -
103Q ALA* 1.3 79.6 - - - +
105Q LYS* 1.3 63.6 + - - +
107Q GLU* 3.2 5.5 + - - +
108Q ILE* 2.9 31.7 + - - +
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Residues in contact with LYS 105 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93Q VAL* 3.1 47.1 - - + +
96Q TYR* 3.5 29.8 - - + +
97Q GLN* 3.6 19.8 - - - +
101Q ASP 4.1 7.2 - - - +
102Q GLU* 3.0 40.3 + - - +
104Q SER* 1.3 77.8 + - - +
106Q LYS* 1.3 64.8 + - - +
108Q ILE* 3.7 8.1 - - + -
109Q LYS* 2.9 48.5 + - - +
58g ALA* 5.6 1.7 - - - +
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Residues in contact with LYS 106 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102Q GLU* 2.9 27.5 + - - +
103Q ALA 4.5 2.5 - - - +
105Q LYS* 1.3 81.7 - - - +
107Q GLU* 1.3 61.5 + - - +
109Q LYS* 3.8 7.0 - - + +
110Q ASP* 2.9 39.9 + - - +
12g LYS 4.3 6.8 + - - +
13g GLY* 4.6 15.5 - - - -
41g ILE* 3.3 41.4 - - - +
43g TRP* 4.3 8.7 - - - -
55g PRO* 3.3 38.6 - - + +
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Residues in contact with GLU 107 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103Q ALA 3.3 17.7 + - - +
104Q SER* 3.2 8.2 + - - +
106Q LYS* 1.3 80.2 - - - +
108Q ILE* 1.3 57.7 + - - +
110Q ASP* 3.0 15.8 + - - +
111Q ILE* 2.9 35.1 + - + +
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Residues in contact with ILE 108 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57Q LEU* 5.6 2.5 - - + +
58Q LEU* 3.6 32.8 - - + -
62Q ARG* 3.8 33.4 - - - +
92Q LEU* 6.1 1.1 - - + -
93Q VAL* 5.5 3.4 - - + -
96Q TYR* 3.9 20.6 - - + -
104Q SER 2.9 19.9 + - - +
105Q LYS* 3.5 15.5 - - + +
107Q GLU* 1.3 77.1 - - - +
109Q LYS* 1.3 61.5 + - - +
111Q ILE* 3.3 16.4 + - + +
112Q LEU* 2.9 39.9 + - + +
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Residues in contact with LYS 109 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14731 G 5.9 1.0 + - - -
93Q VAL* 4.9 8.8 - - + +
105Q LYS* 2.9 40.5 + - + +
106Q LYS* 3.8 7.2 - - + +
108Q ILE* 1.3 77.2 - - + +
110Q ASP* 1.3 61.6 + - - +
112Q LEU* 3.3 10.2 + - - +
113Q ILE* 2.9 50.2 + - + +
120Q LEU* 3.6 38.6 - - + +
15g ASN* 5.8 3.8 - - - +
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Residues in contact with ASP 110 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106Q LYS* 2.9 26.3 + - - +
107Q GLU* 3.0 20.4 + - - +
109Q LYS* 1.3 79.2 - - - +
111Q ILE* 1.3 59.5 + - + +
113Q ILE* 3.4 12.0 + - - +
114Q GLN* 2.9 40.3 + - + +
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Residues in contact with ILE 111 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57Q LEU* 3.7 31.2 - - + -
58Q LEU* 5.9 1.1 - - + -
107Q GLU* 2.9 23.9 + - + +
108Q ILE* 3.5 21.1 - - + +
109Q LYS 3.2 0.2 - - - -
110Q ASP* 1.3 80.4 - - + +
112Q LEU* 1.3 67.0 + - + +
114Q GLN* 3.1 9.0 + - + +
115Q TYR* 2.9 24.8 + - + +
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Residues in contact with LEU 112 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54Q PRO* 6.0 1.3 - - + -
58Q LEU* 3.8 39.0 - - + -
89Q SER* 3.7 32.1 - - - +
92Q LEU* 5.7 2.7 - - + -
93Q VAL* 4.0 17.0 - - + -
108Q ILE* 2.9 26.4 + - + +
109Q LYS* 3.8 5.4 - - - +
111Q ILE* 1.3 78.1 - - + +
113Q ILE* 1.3 61.8 + - + +
115Q TYR* 4.7 1.8 - - + +
116Q ASP 2.8 21.1 + - - +
119Q LEU* 3.3 34.8 - - + +
120Q LEU* 5.3 9.1 + - + -
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Residues in contact with ILE 113 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14721 C 5.6 5.8 - - - +
14731 G 6.1 0.7 - - - +
109Q LYS* 2.9 48.6 + - + +
110Q ASP* 3.8 10.8 - - - +
112Q LEU* 1.3 77.9 - - - +
114Q GLN* 1.3 73.0 + - - +
115Q TYR 3.4 0.2 + - - -
116Q ASP* 3.4 18.4 + - - +
117Q ARG* 4.2 9.4 + - + +
120Q LEU* 4.6 18.6 - - + -
121Q VAL* 6.4 1.3 - - + -
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Residues in contact with GLN 114 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110Q ASP* 2.9 30.4 + - + +
111Q ILE* 3.1 9.8 + - + +
113Q ILE* 1.3 85.4 - - - +
115Q TYR* 1.3 65.8 + - - +
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Residues in contact with TYR 115 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F PRO* 3.4 36.8 - - + -
18F LYS* 5.2 10.3 - - - -
46F ALA 4.9 12.4 + - - -
47F LYS* 5.0 5.4 - - - +
48F TYR* 4.5 7.7 - + - -
50Q LYS* 4.6 3.2 + - - -
53Q GLU* 3.0 45.5 + - + +
57Q LEU* 5.7 2.9 - - + -
85Q ARG* 3.4 9.6 - - - -
111Q ILE* 2.9 18.1 + - + +
112Q LEU* 4.1 4.9 - - + +
113Q ILE 3.3 0.2 - - - -
114Q GLN* 1.3 79.9 - - - +
116Q ASP* 1.3 69.4 + - + +
119Q LEU* 3.7 18.6 - - + -
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Residues in contact with ASP 116 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F SER* 5.0 5.4 + - - -
50Q LYS* 4.6 11.8 + - - -
85Q ARG* 4.7 1.1 + - - +
112Q LEU 2.8 18.7 + - - +
113Q ILE* 3.4 9.1 - - - +
114Q GLN 3.5 0.4 - - - -
115Q TYR* 1.3 98.8 - - + +
117Q ARG* 1.3 79.9 + - - +
118Q THR* 2.5 37.1 + - - +
119Q LEU* 3.9 12.2 + - + +
120Q LEU 4.8 0.7 + - - -
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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