Contacts of the helix formed by residues 100 - 114 (chain E) in PDB entry 5TTE
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 LYS 100 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187B GLN* 6.1 0.2 - - - +
190B TYR* 3.8 22.0 - - - +
6E ARG* 3.9 7.2 - - - +
10E GLU* 4.0 7.6 - - + +
13E GLU* 2.5 42.2 + - - -
98E ALA 3.0 15.4 + - - +
99E THR* 1.3 78.4 - - - +
101E THR* 1.3 66.0 + - - +
102E ASP* 3.3 25.2 + - - +
103E GLN* 3.1 34.5 + - + +
104E VAL* 3.3 5.9 + - - +
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Residues in contact with THR 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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10E GLU* 2.8 27.5 + - - +
14E ILE* 5.0 3.8 - - + -
35E TRP* 4.3 22.3 - - + -
55E ILE* 4.5 9.2 - - + -
57E PHE* 3.6 22.7 - - + -
61E TYR* 3.3 12.5 + - - -
99E THR 3.8 0.8 + - - -
100E LYS* 1.3 67.6 - - - +
102E ASP* 1.3 58.8 + - - +
103E GLN 2.9 4.5 - - - -
104E VAL* 2.8 27.1 + - + +
105E ILE* 3.1 27.1 + - + +
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Residues in contact with ASP 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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13E GLU* 4.8 5.8 - - - +
14E ILE* 4.7 15.3 - - + +
19E MET* 3.7 31.0 - - + +
100E LYS* 3.3 36.2 + - - +
101E THR* 1.3 78.8 - - - +
103E GLN* 1.3 71.5 + - - +
105E ILE* 3.6 15.3 + - + +
106E GLN* 3.3 33.1 + - - +
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Residues in contact with GLN 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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234B HIS* 2.7 48.7 + - + +
89E VAL* 5.9 1.1 - - - +
98E ALA 5.3 0.5 - - - +
99E THR* 4.2 8.6 - - + +
100E LYS* 3.1 38.0 - - - +
101E THR 2.9 0.8 - - - -
102E ASP* 1.3 83.7 + - - +
104E VAL* 1.3 61.3 + - - +
106E GLN* 3.8 9.9 + - - +
107E SER* 3.4 19.2 + - - -
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Residues in contact with VAL 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E PRO* 5.7 7.2 - - + -
68E ILE* 4.1 23.1 - - + -
87E LEU* 4.4 4.3 - - + +
89E VAL* 4.2 9.6 - - + -
90E ILE* 3.6 35.7 - - + -
95E TRP* 4.4 7.4 - - + -
99E THR* 3.9 17.7 - - + -
100E LYS 3.3 11.4 + - - +
101E THR* 2.8 13.4 + - + +
103E GLN* 1.3 76.3 - - - +
105E ILE* 1.3 66.4 + - + +
107E SER* 3.0 10.4 + - - -
108E LEU* 2.9 19.1 + - - +
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Residues in contact with ILE 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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14E ILE* 5.0 8.1 - - + -
19E MET* 4.8 9.4 - - + -
21E ASN* 5.7 0.9 - - + +
22E PHE* 3.5 50.9 - - + -
35E TRP* 6.1 0.4 - - + -
39E ILE* 4.9 8.1 - - + -
53E ILE* 5.4 4.3 - - + -
55E ILE* 5.0 7.6 - - + -
68E ILE* 5.9 3.8 - - + -
101E THR* 3.1 29.8 + - + +
102E ASP* 3.8 17.5 - - + +
104E VAL* 1.3 79.5 - - + +
106E GLN* 1.3 57.8 + - + +
108E LEU* 2.8 25.2 + - + +
109E ILE* 2.9 30.2 + - + +
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Residues in contact with GLN 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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19E MET* 3.8 31.1 - - + +
21E ASN* 5.6 7.6 - - + +
102E ASP* 3.3 22.7 + - - +
103E GLN* 4.2 8.4 - - - +
105E ILE* 1.3 76.7 - - + +
107E SER* 1.3 59.1 + - - +
109E ILE* 3.7 12.2 + - + +
110E ALA* 3.6 18.0 + - - +
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Residues in contact with SER 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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87E LEU* 4.1 15.2 - - - +
89E VAL* 3.8 28.5 - - - +
103E GLN 3.4 13.5 + - - -
104E VAL 3.0 11.9 + - - -
106E GLN* 1.3 76.9 - - - +
108E LEU* 1.3 59.8 - - - +
110E ALA* 3.7 8.3 + - - +
111E LEU* 3.7 13.0 + - - +
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Residues in contact with LEU 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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39E ILE* 3.6 28.9 - - + -
53E ILE* 4.5 11.0 - - + -
68E ILE* 4.5 14.8 - - + -
70E PHE* 4.1 22.9 - - + -
79E ILE* 6.2 0.7 - - + -
85E VAL* 3.8 32.1 - - + -
87E LEU* 3.8 17.9 - - + +
104E VAL 2.9 9.8 + - - +
105E ILE* 2.8 13.4 + - - +
107E SER* 1.3 76.1 - - - +
109E ILE* 1.3 64.9 + - - +
110E ALA 3.2 0.2 - - - -
111E LEU* 3.2 13.9 + - + +
112E VAL* 3.1 23.2 + - + +
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Residues in contact with ILE 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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21E ASN* 3.3 45.1 - - + +
39E ILE* 3.6 39.9 - - + -
40E VAL 5.3 1.6 - - - +
41E PRO* 5.4 5.4 - - + -
42E ASP* 5.0 0.9 - - - +
105E ILE* 2.9 25.5 + - + +
106E GLN* 3.8 15.0 - - + +
107E SER 3.4 0.2 - - - -
108E LEU* 1.3 77.3 - - - +
110E ALA* 1.3 57.3 + - - +
112E VAL* 3.0 8.1 + - + +
113E ASN* 2.8 48.7 + - - +
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Residues in contact with ALA 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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106E GLN 3.6 10.7 + - - +
107E SER* 3.9 11.2 - - - +
108E LEU 3.2 0.2 - - - -
109E ILE* 1.3 79.9 - - - +
111E LEU* 1.3 56.1 + - - +
113E ASN* 4.5 4.9 - - - +
114E ASP* 3.0 35.0 + - - +
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Residues in contact with LEU 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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76E HIS* 2.8 27.3 + - + -
78E ASN* 3.4 38.4 - - + +
79E ILE* 5.4 3.4 - - + -
85E VAL* 4.0 18.8 - - + -
86E LYS 3.8 21.8 - - - +
87E LEU* 4.6 9.6 - - + -
107E SER 3.7 9.7 + - - +
108E LEU* 3.2 17.5 + - + +
110E ALA* 1.3 78.3 - - - +
112E VAL* 1.3 60.5 - - + +
114E ASP 4.2 2.7 - - - +
115E PRO* 3.4 9.8 - - + +
116E GLN* 4.0 26.0 - - + +
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Residues in contact with VAL 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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39E ILE* 5.5 10.3 - - + -
41E PRO* 3.9 29.6 - - + -
46E TYR* 3.7 32.9 - - + -
51E PHE* 5.6 4.5 - - + -
70E PHE* 4.6 22.0 - - + -
74E ILE* 6.2 2.7 - - + -
76E HIS* 3.9 7.5 + - + -
79E ILE* 4.9 9.2 - - + -
108E LEU* 3.1 17.8 + - + +
109E ILE* 3.0 11.9 + - + +
111E LEU* 1.3 79.5 - - + +
113E ASN* 1.3 68.4 + - - +
115E PRO* 3.8 4.5 - - - +
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Residues in contact with ASN 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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41E PRO* 3.9 22.0 - - - +
42E ASP* 4.0 17.9 + - - +
43E ASN* 3.7 33.3 + - - +
44E PRO 5.1 6.9 - - - +
46E TYR* 5.5 2.3 - - - -
109E ILE* 2.8 36.9 + - - +
110E ALA* 4.1 6.0 - - - +
112E VAL* 1.3 76.0 - - - +
114E ASP* 1.3 72.8 + - - +
115E PRO* 3.4 6.6 - - - +
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Residues in contact with ASP 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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43E ASN* 4.6 6.8 + - - -
110E ALA 3.0 19.2 + - - +
111E LEU* 3.8 4.6 - - - +
113E ASN* 1.3 89.3 - - - +
115E PRO* 1.3 70.3 - - - +
116E GLN* 4.9 2.3 - - - +
129E TYR* 5.1 4.0 - - - +
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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