Contacts of the helix formed by residues 98 - 116 (chain E) in PDB entry 4QOZ
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 VAL 98 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81E LYS* 3.6 8.3 - - - +
97E GLY* 1.3 77.6 - - - +
99E LYS* 1.3 67.4 - - - +
100E ASP* 4.3 7.2 - - - +
101E VAL* 3.1 24.9 + - + +
102E LEU* 3.1 7.8 + - - +
270E VAL* 4.3 17.3 - - + -
282E GLU 5.3 0.9 - - - +
283E LYS* 3.0 59.4 + - + +
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Residues in contact with LYS 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E ASN 5.3 5.6 + - - -
79E MET 3.5 25.3 + - - -
80E SER* 4.3 6.9 - - - +
81E LYS* 3.5 36.5 - - + +
84E LEU* 3.9 13.7 - - + -
98E VAL* 1.3 75.3 - - - +
100E ASP* 1.3 63.0 + - - +
102E LEU* 3.2 6.5 + - - +
103E LYS* 2.9 45.5 + - + +
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Residues in contact with ASP 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E VAL* 3.3 3.2 - - + +
99E LYS* 1.3 80.0 + - - +
101E VAL* 1.3 57.0 + - - +
103E LYS* 3.7 25.1 + - - +
104E LYS* 3.0 28.6 + - - +
268E TYR 3.3 25.4 - - - +
269E LYS* 4.6 7.6 - - + +
270E VAL* 3.2 27.5 - - + +
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Residues in contact with VAL 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E ARG 4.3 7.0 - - - +
97E GLY* 4.4 1.3 - - - -
98E VAL* 3.1 21.0 + - + +
100E ASP* 1.3 75.6 - - - +
102E LEU* 1.3 65.6 + - - +
104E LYS* 3.3 1.7 + - - +
105E ARG* 2.9 55.1 + - - +
264E TYR* 5.0 0.4 - - - +
268E TYR* 3.7 36.6 - - + -
270E VAL* 4.5 3.6 - - + -
283E LYS* 3.9 19.1 - - + +
284E LEU* 3.7 18.2 - - + -
312E ASP* 4.6 0.2 - - - +
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Residues in contact with LEU 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E LYS* 3.7 36.3 - - - +
84E LEU* 4.1 15.5 - - + -
85E ARG* 3.8 23.1 - - + +
88E LEU* 3.8 24.0 - - + +
95E THR 3.3 22.4 - - - +
96E ARG 3.6 16.2 - - - +
97E GLY 3.7 7.6 - - - +
98E VAL 3.1 10.5 + - - +
99E LYS* 3.4 6.1 - - - +
101E VAL* 1.3 76.3 - - - +
103E LYS* 1.3 62.1 + - - +
105E ARG* 3.2 6.4 + - - +
106E LEU* 2.9 26.3 + - - +
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Residues in contact with LYS 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E ILE* 4.2 16.2 - - + +
77E ASN* 3.1 37.1 + - - +
84E LEU* 3.7 20.2 - - + -
99E LYS* 2.9 43.6 + - + +
100E ASP* 3.7 22.3 + - - +
102E LEU* 1.3 78.2 - - - +
104E LYS* 1.3 57.1 + - - +
106E LEU* 3.3 1.7 + - - +
107E LYS* 2.9 46.0 + - - +
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Residues in contact with LYS 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D G 6.2 0.2 - - - -
18D A 3.3 34.9 + - - -
100E ASP 3.0 19.7 + - - +
101E VAL 3.3 3.3 + - - +
103E LYS* 1.3 75.9 - - - +
105E ARG* 1.3 63.9 + - - +
107E LYS* 3.4 14.6 + - + +
108E ASN* 2.9 25.9 + - - +
267E PHE* 3.4 66.3 + - + +
268E TYR* 4.3 9.2 - - + -
269E LYS* 4.1 7.7 - - - +
312E ASP* 5.4 0.7 - - + -
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Residues in contact with ARG 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E LEU* 3.8 15.0 - - + -
93E LEU* 4.5 14.4 - - + +
94E GLU* 2.9 45.7 + - - +
96E ARG 3.0 24.6 + - - +
101E VAL* 2.9 35.5 + - - +
102E LEU* 3.6 11.8 - - - +
104E LYS* 1.3 76.3 - - - +
106E LEU* 1.3 63.3 + - - +
108E ASN* 3.2 9.7 + - - +
109E TYR* 3.1 20.6 + - - +
284E LEU* 4.4 3.8 + - - +
308E ARG* 3.3 27.5 - - - +
312E ASP* 2.8 49.0 + - - +
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Residues in contact with LEU 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E ILE* 4.0 11.0 - - + -
79E MET* 4.0 14.6 - - + -
84E LEU* 3.8 26.9 - - + +
87E LYS* 3.9 28.9 - - + -
88E LEU* 3.9 21.7 - - + +
91E PHE* 4.0 20.6 - - + -
102E LEU 2.9 16.8 + - - +
103E LYS 3.8 3.1 - - - +
105E ARG* 1.3 77.2 - - - +
107E LYS* 1.3 64.0 + - - +
109E TYR* 3.1 7.7 + - + +
110E TYR* 3.0 48.1 + - + -
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Residues in contact with LYS 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D G 2.8 28.0 + - - +
73E ASN* 3.4 32.7 - - - +
76E ILE* 3.7 31.4 - - + -
77E ASN* 2.8 33.4 + - - +
103E LYS* 2.9 32.5 + - - +
104E LYS* 3.8 15.1 - - + +
106E LEU* 1.3 77.2 - - - +
108E ASN* 1.3 56.9 + - - +
110E TYR* 3.5 2.5 + - - +
111E LYS* 2.9 30.7 + - - +
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Residues in contact with ASN 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E LYS* 2.9 19.2 + - + +
105E ARG* 3.5 5.3 + - - +
107E LYS* 1.3 73.4 - - - +
109E TYR* 1.3 64.0 + - - +
111E LYS* 3.8 10.2 - - - +
112E LYS* 2.9 50.4 + - - +
267E PHE* 5.9 0.4 - - + -
311E GLN 4.2 6.5 + - - -
312E ASP* 3.1 37.4 + - - +
313E GLY* 3.5 14.6 - - - +
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Residues in contact with TYR 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E PHE* 3.5 62.8 + + + +
93E LEU* 4.0 28.5 - - + -
105E ARG 3.1 11.6 + - - +
106E LEU* 3.3 9.9 - - + +
108E ASN* 1.3 82.8 - - - +
110E TYR* 1.3 74.8 + + - +
112E LYS* 3.7 9.8 - - + +
113E GLN* 3.0 62.1 + - + +
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Residues in contact with TYR 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E ILE* 6.0 0.2 - - - -
72E THR* 3.8 26.7 - - + -
73E ASN* 6.1 0.2 - - - +
76E ILE* 3.6 17.7 - - + -
87E LYS* 3.2 35.8 + - + +
91E PHE* 3.5 19.9 - + - -
106E LEU* 3.0 54.1 + - + +
107E LYS 4.0 3.8 - - - +
109E TYR* 1.3 83.2 - + - +
111E LYS* 1.3 63.7 + - - +
113E GLN* 3.3 5.7 + - + +
114E LYS* 2.9 42.3 + - + +
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Residues in contact with LYS 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D U 3.2 30.9 + - - +
17D G 5.4 0.2 + - - -
18D A 5.1 6.5 + - - -
61E PHE* 6.2 0.4 - - - -
66E TYR* 5.4 3.4 - - - -
69E ILE* 4.4 23.3 - - + -
73E ASN* 6.1 0.4 - - - +
107E LYS 2.9 18.6 + - - +
108E ASN* 3.8 9.6 - - - +
110E TYR* 1.3 76.1 - - - +
112E LYS* 1.3 63.1 + - - +
114E LYS* 3.3 5.3 + - - +
115E LEU* 3.2 53.2 + - + +
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Residues in contact with LYS 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E ASN* 2.9 41.3 + - - +
109E TYR* 3.7 9.6 - - + +
111E LYS* 1.3 77.2 - - - +
113E GLN* 1.3 65.9 + - - +
115E LEU* 4.2 7.2 - - - +
116E MET* 3.0 30.4 + - - +
311E GLN 5.2 5.1 + - - -
313E GLY* 6.3 1.1 - - - -
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Residues in contact with GLN 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E TYR* 3.0 61.6 + - + +
110E TYR* 3.7 7.2 - - + +
112E LYS* 1.3 89.3 - - - +
114E LYS* 1.3 64.1 + - + +
115E LEU 3.5 0.2 + - - -
116E MET* 3.6 15.2 + - - +
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Residues in contact with LYS 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E VAL* 4.2 22.8 - - + +
68E GLU* 4.3 26.2 + - + +
69E ILE* 4.4 14.3 - - + +
72E THR* 2.6 40.0 + - - +
110E TYR* 2.9 32.4 + - + +
111E LYS 3.3 2.7 + - - +
113E GLN* 1.3 80.3 - - + +
115E LEU* 1.3 59.5 + - - +
116E MET* 4.7 6.2 - - - +
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Residues in contact with LEU 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E VAL* 5.0 11.9 - - + -
66E TYR* 4.5 19.7 - - + +
69E ILE* 4.0 21.8 - - + -
111E LYS* 3.2 39.4 + - + +
112E LYS* 4.2 6.7 - - - +
114E LYS* 1.3 74.7 - - - +
116E MET* 1.3 81.2 + - - +
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Residues in contact with MET 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E LYS* 3.0 20.3 + - - +
113E GLN* 4.0 11.9 - - - +
114E LYS 3.6 4.9 - - - +
115E LEU* 1.3 91.0 - - - +
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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