Contacts of the helix formed by residues 105 - 120 (chain N) in PDB entry 3L73
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 105 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82N MET* 3.4 47.9 - - + +
101N ALA* 4.2 2.7 - - + +
102N LEU* 2.9 25.9 + - - +
104N LYS* 1.3 98.0 - - - +
106N MET* 1.3 64.6 + - - +
107N PRO* 3.1 4.9 - - - -
108N LYS* 2.9 10.4 + - + +
109N VAL* 2.8 30.7 + - + +
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Residues in contact with MET 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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35N CYS* 5.0 2.7 - - - -
37N VAL* 4.8 3.7 - - + +
102N LEU 3.6 4.7 + - - -
103N SER* 3.2 19.6 + - - +
104N LYS 3.1 0.2 - - - -
105N ASP* 1.3 75.6 - - - +
107N PRO* 1.3 74.6 - - + +
109N VAL* 3.4 9.2 - - - +
110N VAL* 2.9 51.8 + - + +
203N ILE* 3.2 50.3 - - + -
207N GLU* 4.1 13.7 - - - +
208N LEU* 3.5 31.9 - - + -
211N ALA* 3.9 8.3 - - + -
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Residues in contact with PRO 107 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103N SER 4.6 0.4 - - - +
104N LYS 3.4 13.9 - - - +
105N ASP* 3.3 2.7 - - - +
106N MET* 1.3 109.3 - - + +
108N LYS* 1.3 67.7 + - + +
109N VAL 3.1 2.2 + - - -
110N VAL* 3.2 5.7 + - + +
111N GLU* 3.2 19.6 + - - +
207N GLU* 5.5 7.9 - - + +
211N ALA* 4.3 12.5 - - + +
215N HIS* 4.7 5.9 - - + -
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Residues in contact with LYS 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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70N ARG* 4.6 3.9 - - - +
78N GLU* 3.6 25.6 + - - +
82N MET* 4.2 22.9 - - + -
105N ASP* 2.9 18.0 + - + +
107N PRO* 1.3 78.8 - - + +
109N VAL* 1.3 62.7 + - - +
111N GLU* 3.1 34.9 + - - -
112N LEU* 3.3 19.3 + - + +
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Residues in contact with VAL 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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35N CYS* 6.0 2.2 - - - -
37N VAL* 3.3 27.4 - - + -
82N MET* 4.7 4.7 - - + -
99N ILE* 3.7 34.8 - - + +
101N ALA* 4.1 17.0 - - + -
105N ASP* 2.8 42.9 + - + +
106N MET* 3.4 9.2 - - - +
108N LYS* 1.3 74.4 - - - +
110N VAL* 1.3 57.0 + - - +
112N LEU* 2.6 35.7 + - + +
113N LEU* 2.9 13.4 + - + +
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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
----------------------------------------------------------
37N VAL* 4.8 8.3 - - + -
106N MET* 2.9 41.3 - - + +
107N PRO* 3.4 6.5 - - + +
109N VAL* 1.3 76.0 - - - +
111N GLU* 1.3 61.2 + - - +
113N LEU* 3.4 10.8 + - + +
114N ALA* 3.0 23.4 + - - +
197N LEU* 4.3 11.9 - - + -
208N LEU* 4.1 11.2 - - + -
211N ALA* 4.0 25.8 - - + +
212N ALA* 4.4 0.4 - - - -
215N HIS* 4.6 2.7 - - + +
216N PHE* 4.0 20.8 - - + -
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Residues in contact with GLU 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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69N LYS* 3.3 14.9 + - - +
70N ARG* 2.7 31.0 + - - +
107N PRO 3.2 6.0 + - - +
108N LYS* 3.1 36.3 + - - +
109N VAL 3.0 0.8 - - - -
110N VAL* 1.3 80.3 - - - +
112N LEU* 1.3 58.1 + - - +
114N ALA* 3.5 2.3 + - - +
115N ASP* 2.9 30.0 + - - +
215N HIS* 3.1 44.9 + - + +
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Residues in contact with LEU 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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70N ARG* 3.5 29.4 - - - +
75N PHE* 3.9 25.1 - - + -
78N GLU* 4.2 16.8 - - + +
79N VAL* 4.3 20.6 - - + -
82N MET* 4.4 20.2 - - - -
86N PHE* 5.3 0.4 - - - -
99N ILE* 4.5 16.2 - - + -
108N LYS* 3.3 15.7 + - + +
109N VAL* 2.6 18.6 + - - +
111N GLU* 1.3 70.8 - - + +
113N LEU* 1.3 69.1 + - - +
115N ASP* 3.1 7.0 + - + +
116N VAL* 2.8 25.1 + - + +
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Residues in contact with LEU 113 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37N VAL* 3.8 24.9 - - + +
38N GLY* 3.7 24.2 - - - -
39N VAL* 4.6 7.6 - - + +
86N PHE* 4.1 8.7 - - + -
97N PHE* 3.9 21.1 - - + +
99N ILE* 4.1 20.6 - - + -
109N VAL* 2.9 14.8 + - + +
110N VAL* 3.6 13.7 - - + +
112N LEU* 1.3 74.2 - - - +
114N ALA* 1.3 56.2 + - - +
116N VAL* 2.5 34.0 + - - +
117N VAL* 3.2 14.3 + - - +
197N LEU* 3.9 20.4 - - + -
216N PHE* 4.5 7.2 - - + -
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Residues in contact with ALA 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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110N VAL 3.0 14.6 + - - +
111N GLU 3.7 4.0 - - - +
113N LEU* 1.3 78.4 - - - +
115N ASP* 1.3 62.2 + - - +
117N VAL* 4.0 0.7 - - - -
118N GLN* 3.0 34.5 + - - +
215N HIS* 3.8 30.7 - - + +
216N PHE* 3.5 30.4 - - + -
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Residues in contact with ASP 115 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67N THR* 2.4 39.4 + - + +
69N LYS* 3.8 19.7 + - - +
70N ARG* 3.5 26.6 + - - +
75N PHE* 5.2 1.6 - - - -
111N GLU 2.9 19.5 + - - +
112N LEU* 3.2 12.6 - - + +
113N LEU 2.8 0.2 + - - -
114N ALA* 1.3 76.9 - - - +
116N VAL* 1.3 57.3 + - - +
119N ASN* 2.9 53.1 + - - +
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Residues in contact with VAL 116 (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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63N ALA* 2.8 43.0 - - + +
64N PHE* 4.9 1.3 - - + -
67N THR* 4.0 8.5 - - + -
75N PHE* 4.1 13.7 - - + -
86N PHE* 3.8 32.5 - - + -
97N PHE* 5.2 6.3 - - + -
112N LEU 2.8 24.7 - - - +
113N LEU* 2.5 15.2 + - - +
115N ASP* 1.3 71.4 - - - +
117N VAL* 1.3 69.4 + - + +
120N CYS* 3.4 24.7 + - + +
190N PHE* 5.8 0.2 - - - -
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Residues in contact with VAL 117 (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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39N VAL* 3.4 33.7 - - + -
41N ILE* 4.7 5.4 - - + -
97N PHE* 4.6 16.4 - - + -
113N LEU* 3.2 8.3 + - - +
114N ALA 3.5 9.9 - - - +
116N VAL* 1.3 80.0 - - + +
118N GLN* 1.3 73.3 + - + +
120N CYS 5.0 0.3 + - - -
186N ILE* 3.8 22.9 - - - +
190N PHE* 3.9 21.2 - - + +
195N MET* 4.4 18.6 - - + -
216N PHE* 3.9 20.2 - - + -
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Residues in contact with GLN 118 (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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114N ALA* 3.0 21.8 + - - +
117N VAL* 1.3 91.8 - - + +
119N ASN* 1.3 73.2 + - - +
120N CYS 3.7 1.8 + - - -
186N ILE* 5.6 2.4 - - - +
195N MET* 5.6 6.3 - - + +
215N HIS 3.2 23.9 + - - +
216N PHE* 3.6 26.3 - - + -
217N SER* 4.4 3.2 + - - -
218N GLY* 5.0 5.0 + - - -
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Residues in contact with ASN 119 (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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67N THR* 3.2 5.7 - - - -
68N LYS* 3.2 34.7 + - + +
69N LYS* 5.2 7.5 - - - +
115N ASP* 2.9 45.5 + - - +
118N GLN* 1.3 90.4 - - - +
120N CYS* 1.3 67.3 + - - +
121N ALA 3.1 3.1 + - - -
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Residues in contact with CYS 120 (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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59N VAL* 5.4 3.8 - - + -
62N LEU* 4.1 28.3 - - - -
63N ALA* 4.4 7.9 - - - +
66N GLY 4.4 4.5 - - - -
67N THR* 4.5 2.9 - - - +
68N LYS* 4.9 5.4 - - - -
116N VAL* 3.4 18.7 + - - +
117N VAL 5.0 0.4 + - - -
118N GLN 3.7 2.8 + - - -
119N ASN* 1.3 75.5 - - - +
121N ALA* 1.3 69.3 + - - +
122N LEU* 3.4 43.0 + - + +
179N ARG* 4.8 1.7 + - - -
186N ILE* 4.3 17.7 - - + +
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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
------------------------------------------------------------
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