Contacts of the helix formed by residues 102 - 115 (chain N) in PDB entry 2ZJR
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 GLU 102 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97N ASP* 5.0 3.5 - - - +
98N ILE* 2.8 30.6 + - + +
99N ALA 5.2 0.2 - - - -
101N ARG* 1.3 98.5 + - - +
103N PRO* 1.3 61.9 - - - +
104N GLU* 3.2 12.3 - - + +
105N ALA* 3.6 22.0 - - + +
106N PHE* 2.8 18.9 + - - +
40O VAL* 6.0 7.2 - - + -
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Residues in contact with PRO 103 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72N HIS* 5.1 4.0 + - + +
99N ALA 5.3 4.5 - - - +
100N ALA 5.0 6.1 - - - +
101N ARG 2.7 21.5 - - - +
102N GLU* 1.3 74.3 - - - +
104N GLU* 1.3 75.7 + - + +
106N PHE* 4.0 7.1 - - + +
107N LYS* 2.9 26.3 + - - +
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Residues in contact with GLU 104 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102N GLU* 4.9 11.6 - - + +
103N PRO* 1.3 87.1 - - + +
105N ALA* 1.3 67.4 + - - +
107N LYS* 3.7 5.2 - - - +
108N ALA* 3.6 10.7 + - - +
43O GLU* 3.5 23.6 - - - +
45O THR* 4.8 9.1 - - + +
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Residues in contact with ALA 105 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98N ILE* 3.8 12.8 - - + -
102N GLU* 3.3 24.3 + - + +
103N PRO 3.2 0.2 - - - -
104N GLU* 1.3 76.6 - - - +
106N PHE* 1.3 55.1 + - - +
108N ALA* 2.4 42.7 + - - +
109N LEU* 3.6 7.1 + - + -
38O LEU* 5.7 8.1 - - + -
40O VAL* 5.6 3.4 - - + -
45O THR* 4.0 23.7 - - + +
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Residues in contact with PHE 106 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65N ILE* 3.5 14.4 - - + -
68N GLY* 3.1 34.5 - - - -
69N ALA* 3.4 18.4 - - - -
71N LEU* 6.4 0.2 - - + -
72N HIS* 4.0 9.0 - - - -
79N PHE* 3.7 30.5 - + - -
95N LEU* 4.7 6.5 - - + -
98N ILE* 3.8 4.6 - - + +
99N ALA* 3.2 41.7 - - + -
102N GLU 2.8 20.1 + - - +
103N PRO* 4.0 6.1 - - + +
105N ALA* 1.3 71.6 - - - +
107N LYS* 1.3 66.1 + - - +
109N LEU* 3.3 12.6 + - + +
110N VAL* 2.9 35.4 + - + +
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Residues in contact with LYS 107 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72N HIS* 3.8 34.4 + - + +
103N PRO 2.9 18.1 + - - +
104N GLU* 3.7 6.5 - - - +
105N ALA 2.6 4.0 + - - -
106N PHE* 1.3 72.8 - - - +
108N ALA* 1.3 58.6 + - - +
110N VAL* 2.6 34.5 + - + +
111N ASP* 3.0 14.9 + - + -
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Residues in contact with ALA 108 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104N GLU 3.6 5.2 + - - +
105N ALA* 2.4 30.0 + - - +
107N LYS* 1.3 73.3 - - - +
109N LEU* 1.3 54.6 + - + +
111N ASP* 3.2 5.1 + - - +
112N ALA* 2.7 33.3 + - - +
45O THR* 4.6 11.2 - - + +
47O PHE* 3.2 30.7 - - + -
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Residues in contact with LEU 109 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79N PHE* 4.3 17.7 - - + -
83N LEU* 4.2 13.3 - - + +
89N ASP* 3.0 29.8 - - - +
91N ASN* 4.1 15.3 - - - +
95N LEU* 4.6 9.0 - - + -
98N ILE* 4.2 19.5 - - + -
105N ALA* 4.2 6.1 - - + +
106N PHE* 3.3 22.7 + - + +
108N ALA* 1.3 76.1 - - + +
110N VAL* 1.3 72.3 + - - +
112N ALA* 3.3 9.2 - - - +
113N SER* 3.1 17.3 + - - -
38O LEU* 4.6 16.2 - - + -
47O PHE* 3.6 15.7 - - + -
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Residues in contact with VAL 110 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68N GLY 4.9 0.4 - - - +
69N ALA* 5.0 1.8 - - - -
72N HIS* 3.2 41.7 - - + -
74N MET* 3.3 33.0 - - + +
79N PHE* 4.1 6.9 - - + -
106N PHE* 2.9 42.8 + - + +
107N LYS* 2.6 15.2 + - + +
109N LEU* 1.3 78.8 - - - +
111N ASP* 1.3 58.6 + - + +
113N SER* 2.7 26.9 + - - -
114N ARG* 3.5 2.8 + - + -
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Residues in contact with ASP 111 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107N LYS* 3.0 16.5 + - + +
108N ALA* 3.8 6.7 - - - +
110N VAL* 1.3 81.0 - - + +
112N ALA* 1.3 62.1 + - - +
113N SER 3.1 0.4 - - - -
114N ARG* 3.1 33.1 + - - +
115N ASN* 2.9 48.4 + - - -
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Residues in contact with ALA 112 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83N LEU* 6.4 0.2 - - + -
89N ASP* 4.6 14.6 - - - +
108N ALA 2.7 22.6 + - - +
109N LEU* 3.3 14.4 - - - +
110N VAL 2.8 0.2 + - - -
111N ASP* 1.3 73.0 - - - +
113N SER* 1.3 61.3 + - - +
115N ASN* 3.3 25.3 + - - +
116N ALA* 3.6 5.5 + - - +
47O PHE* 4.5 13.7 - - + -
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Residues in contact with SER 113 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74N MET* 3.6 17.3 - - - +
78N THR* 5.3 0.7 - - - +
79N PHE 3.5 6.5 + - - -
82N GLY* 2.6 36.7 - - - -
83N LEU* 4.0 10.8 - - - +
86N ALA* 6.5 0.7 - - - -
109N LEU 3.1 8.2 + - - -
110N VAL 2.7 16.8 + - - -
112N ALA* 1.3 68.6 - - - +
114N ARG* 1.3 68.0 + - - -
115N ASN 2.8 1.6 - - - -
116N ALA* 2.7 19.7 + - - +
117N ARG* 2.7 14.7 + - - +
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Residues in contact with ARG 114 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74N MET* 4.3 11.0 - - + +
110N VAL* 3.5 3.2 + - + +
111N ASP* 3.1 33.0 + - - +
113N SER* 1.3 77.5 - - - +
115N ASN* 1.3 94.4 + - - +
116N ALA 3.0 5.0 + - - -
117N ARG* 3.0 28.7 + - + +
118N GLN* 3.4 24.2 + - + +
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Residues in contact with ASN 115 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111N ASP* 2.9 42.7 + - - +
112N ALA* 3.3 10.0 - - - +
113N SER 2.8 1.2 - - - -
114N ARG* 1.3 97.9 + - - +
116N ALA* 1.3 59.4 + - - +
118N GLN* 5.6 1.3 - - - -
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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