Contacts of the helix formed by residues 102 - 113 (chain E) in PDB entry 6Q2J
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 102 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42E VAL* 5.3 2.7 - - - -
43E ASP* 4.1 8.5 - - - +
100E SER* 3.9 4.2 + - - +
101E LEU* 1.3 75.2 - - - +
103E HIS* 1.3 67.1 + - - +
104E SER* 2.6 23.3 + - - +
105E SER* 2.4 37.3 + - - -
106E TRP* 3.5 16.1 - - - -
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Residues in contact with HIS 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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42E VAL* 3.9 27.2 - - + +
43E ASP* 4.7 6.6 + - - -
102E ASP* 1.3 76.7 - - - +
104E SER* 1.3 57.3 + - - +
106E TRP* 3.4 6.2 + - - +
107E GLU* 3.0 36.9 + - + +
151E ASN* 3.9 27.8 + - - -
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Residues in contact with SER 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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102E ASP* 2.6 28.1 + - - -
103E HIS* 1.3 79.0 - - - +
105E SER* 1.3 56.7 + - - +
107E GLU* 3.8 7.5 - - - +
108E LYS* 2.9 38.9 + - - +
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Residues in contact with SER 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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85E TRP* 3.2 38.2 + - - -
99E ARG* 5.8 1.0 + - - -
101E LEU* 4.9 0.7 - - - -
102E ASP* 2.4 31.5 + - - -
103E HIS 3.2 0.8 - - - -
104E SER* 1.3 80.7 + - - +
106E TRP* 1.3 66.8 + - - +
108E LYS* 3.2 11.7 + - - +
109E LEU* 2.9 32.9 + - - +
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Residues in contact with TRP 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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40E LEU* 4.6 8.1 - - + -
42E VAL* 5.6 0.4 - - + -
72E LEU* 6.5 0.7 - - + -
101E LEU* 3.4 37.9 - - + +
102E ASP 3.5 17.0 - - - -
103E HIS* 3.4 7.2 + - - +
105E SER* 1.3 77.5 - - - +
107E GLU* 1.3 63.2 + - - +
109E LEU* 3.8 21.4 - - + +
110E SER* 2.9 31.0 + - - -
118E LEU* 3.6 35.3 - - + +
121E VAL* 4.0 23.6 - - + -
149E PHE* 3.3 75.3 - + + -
151E ASN* 5.8 2.5 - - - +
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Residues in contact with GLU 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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103E HIS* 3.0 26.6 + - + +
104E SER* 3.9 7.0 - - - +
106E TRP* 1.3 77.9 - - - +
108E LYS* 1.3 60.8 + - - +
110E SER* 4.2 7.2 - - - -
111E VAL* 3.3 30.5 + - - +
151E ASN* 5.6 3.6 + - - -
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Residues in contact with LYS 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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81E HIS* 4.8 25.4 - - + +
85E TRP* 6.1 3.4 - - + -
104E SER* 2.9 32.8 + - - +
105E SER* 3.3 10.2 - - - +
107E GLU* 1.3 78.7 - - - +
109E LEU* 1.3 63.2 + - + +
111E VAL* 3.9 12.5 + - - +
112E ARG* 4.2 5.9 + - - +
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Residues in contact with LEU 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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72E LEU* 4.7 20.0 - - + -
80E LEU* 3.9 25.2 - - + +
81E HIS* 3.7 31.9 - - + +
85E TRP* 5.0 10.5 - - + -
101E LEU* 6.4 0.4 - - + -
105E SER 2.9 19.9 + - - +
106E TRP* 3.9 37.2 - - + +
108E LYS* 1.3 79.5 - - + +
110E SER* 1.3 64.2 + - - +
112E ARG* 3.3 17.0 + - - +
113E ASN* 3.5 9.5 + - - +
118E LEU* 3.7 18.0 - - + +
121E VAL* 5.0 4.5 - - + -
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Residues in contact with SER 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 TRP 2.9 20.5 + - - -
107E GLU* 3.6 9.8 + - - -
108E LYS 3.4 0.2 - - - -
109E LEU* 1.3 74.8 - - - +
111E VAL* 1.3 65.0 + - - +
113E ASN* 3.3 21.3 + - - +
115E GLY* 4.7 5.2 + - - -
116E PHE 3.9 14.0 + - - +
117E PRO* 4.8 2.3 - - - +
118E LEU* 4.5 16.0 + - - +
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Residues in contact with VAL 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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107E GLU* 3.3 19.9 + - - +
108E LYS* 4.1 7.2 - - - +
109E LEU 3.2 0.8 - - - -
110E SER* 1.3 78.1 - - - +
112E ARG* 1.3 61.1 + - - +
113E ASN 3.1 2.1 + - - -
114E HIS* 3.7 7.6 + - - -
115E GLY 4.5 4.0 + - - -
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Residues in contact with ARG 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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78E THR* 4.3 12.0 - - + +
79E ARG* 3.4 20.4 + - - +
80E LEU* 3.7 38.4 + - + +
108E LYS 4.2 5.8 + - - +
109E LEU* 3.3 12.5 + - - +
111E VAL* 1.3 74.8 - - - +
113E ASN* 1.3 55.7 + - - +
114E HIS* 2.9 36.8 + - - -
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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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75E THR* 4.7 17.3 + - - -
78E THR* 5.9 0.2 - - - -
80E LEU* 4.5 9.7 - - + +
109E LEU 3.5 6.3 + - - +
110E SER* 3.3 20.2 - - - +
111E VAL 3.1 1.8 - - - -
112E ARG* 1.3 73.8 - - - +
114E HIS* 1.3 71.2 + - - +
115E GLY 3.3 1.1 - - - -
116E PHE* 2.5 46.5 + - - +
117E PRO 3.4 2.6 + - - -
118E LEU* 3.4 40.9 - - + +
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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