Contacts of the helix formed by residues 98 - 111 (chain E) in PDB entry 3N2N
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 98 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96E THR* 3.0 14.9 + - - +
97E GLU* 1.3 79.3 - - + +
99E ARG* 1.3 62.0 + - - +
100E GLU* 3.5 13.1 - - - +
101E GLN* 3.2 41.5 + - + +
102E ILE* 2.9 29.4 + - - +
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Residues in contact with ARG 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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70E ALA 5.2 1.6 + - - -
73E PHE 2.8 24.9 + - - -
74E ILE* 3.1 35.3 + - + +
75E SER 3.1 22.1 + - - -
76E PRO* 3.7 5.5 - - - +
78E LEU* 2.8 28.3 + - - +
80E MET* 3.5 15.6 - - - +
97E GLU* 2.8 35.2 + - - +
98E ASP* 1.3 73.9 + - - +
100E GLU* 1.3 59.7 + - + +
102E ILE* 3.4 22.3 + - + +
103E ARG* 2.8 28.8 + - - +
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Residues in contact with GLU 100 (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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98E ASP* 3.3 12.8 + - - +
99E ARG* 1.3 76.1 - - + +
101E GLN* 1.3 63.7 + - - +
103E ARG* 2.8 46.8 + - - +
104E GLN* 3.0 37.5 + - - +
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Residues in contact with GLN 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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93E MET* 3.4 14.5 - - + +
94E LYS 5.1 1.9 - - - +
96E THR* 3.1 34.1 + - + +
98E ASP* 3.2 32.5 + - - +
100E GLU* 1.3 74.6 - - + +
102E ILE* 1.3 57.6 + - - +
104E GLN* 3.3 15.0 + - - +
105E GLY 2.9 24.1 + - - -
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Residues in contact with ILE 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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70E ALA* 4.4 6.7 - - + +
71E HIS* 6.3 0.2 - - + -
80E MET* 3.9 30.5 - - + -
82E PHE* 4.0 4.5 - - + -
93E MET* 3.6 23.3 - - + -
96E THR* 3.9 13.5 - - + +
98E ASP 2.9 16.8 + - - +
99E ARG* 3.5 51.1 - - + +
100E GLU 3.2 0.2 - - - -
101E GLN* 1.3 72.9 - - - +
103E ARG* 1.3 60.1 + - - +
105E GLY* 3.2 1.4 + - - -
106E LEU* 2.9 45.0 + - + +
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Residues in contact with ARG 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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99E ARG 2.8 20.5 + - - +
100E GLU* 2.8 40.0 + - - +
102E ILE* 1.3 73.2 - - - +
104E GLN* 1.3 87.2 + - - +
106E LEU* 3.3 11.1 + - - +
107E GLU* 3.0 58.3 + - + +
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Residues in contact with GLN 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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100E GLU* 3.0 31.8 + - - +
101E GLN* 3.6 13.5 - - - +
103E ARG* 1.3 99.6 - - - +
105E GLY* 1.3 62.0 + - - +
107E GLU* 3.3 11.9 + - - +
108E GLU* 3.1 37.0 + - - +
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Residues in contact with GLY 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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82E PHE* 3.8 18.6 - - - -
92E LEU* 3.5 18.0 - - - +
93E MET* 4.1 7.6 - - - -
101E GLN 2.9 15.3 + - - -
102E ILE 3.2 3.8 + - - -
104E GLN* 1.3 76.8 - - - +
106E LEU* 1.3 55.3 + - - +
108E GLU* 3.3 5.4 + - - -
109E LEU* 2.9 25.8 + - - +
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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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63E TYR* 3.2 29.9 + - + +
66E VAL* 3.9 17.7 - - + -
67E GLU* 4.0 17.9 - - + -
70E ALA* 3.8 13.5 - - + -
71E HIS* 3.6 35.7 - - + +
82E PHE* 3.7 23.3 - - + -
102E ILE* 2.9 25.0 + - + +
103E ARG* 3.7 7.9 - - - +
105E GLY* 1.3 75.5 - - - +
107E GLU* 1.3 58.2 + - + +
109E LEU* 3.3 3.3 + - + -
110E GLN* 3.0 24.9 + - - +
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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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63E TYR* 5.3 0.2 - - - -
103E ARG* 3.0 56.0 + - + +
104E GLN* 3.6 11.1 - - - +
105E GLY 3.3 0.2 - - - -
106E LEU* 1.3 76.1 - - + +
108E GLU* 1.3 61.6 + - + +
110E GLN* 3.6 12.3 + - - +
111E LYS* 3.6 27.0 + - - +
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Residues in contact with GLU 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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92E LEU* 4.0 33.3 - - + +
104E GLN* 3.1 23.9 + - - +
105E GLY* 3.6 9.4 - - - +
107E GLU* 1.3 77.0 - - + +
109E LEU* 1.3 63.2 - - - +
111E LYS* 3.3 26.9 + - - +
112E VAL* 3.6 11.6 + - - +
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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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49E LEU* 3.7 31.2 - - + -
59E TRP* 3.1 27.5 + - + -
63E TYR* 3.8 12.3 - - + -
66E VAL* 3.9 17.9 - - + -
82E PHE* 3.6 32.5 - - + -
84E VAL* 3.7 23.1 - - + -
92E LEU* 4.0 14.6 - - + +
105E GLY 2.9 16.2 + - - +
106E LEU* 3.3 9.2 + - + +
108E GLU* 1.3 73.7 - - - +
110E GLN* 1.3 64.1 + - - +
112E VAL* 3.1 16.6 + - + +
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Residues in contact with GLN 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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59E TRP* 4.2 8.6 + - - +
63E TYR* 3.7 33.4 - - + +
64E TYR* 5.8 2.7 - - + +
106E LEU 3.0 17.2 + - - +
107E GLU* 3.7 8.2 + - - +
108E GLU 3.3 0.2 - - - -
109E LEU* 1.3 76.7 - - - +
111E LYS* 1.3 74.0 + - - +
112E VAL 3.2 5.2 + - - +
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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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107E GLU* 3.6 20.6 + - - +
108E GLU* 3.3 19.9 + - - +
109E LEU 3.2 0.8 - - - -
110E GLN* 1.3 87.9 - - - +
112E VAL* 1.3 64.6 + - - +
113E LEU* 3.4 18.7 + - - +
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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