Contacts of the helix formed by residues 101 - 117 (chain N) in PDB entry 4XLR
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 ASN 101 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60N ARG* 4.6 3.8 - - - +
99N ASP* 3.3 12.4 + - + +
100N GLY* 1.3 75.1 - - - +
102N PRO* 1.3 69.3 - - - +
103N TYR* 3.9 14.8 - - - +
104N ARG* 3.3 38.0 + - + +
105N ILE* 3.0 30.8 + - - +
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Residues in contact with PRO 102 (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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60N ARG* 3.9 16.8 - - - +
63N LEU* 3.6 30.7 - - + -
71N ILE* 3.6 4.6 - - + +
100N GLY 3.2 9.6 - - - +
101N ASN* 1.3 90.8 - - - +
103N TYR* 1.3 64.8 + - + +
105N ILE* 3.6 5.3 + - + -
106N ALA* 2.9 31.4 + - - +
136N LEU* 3.9 10.1 - - + +
139N GLU* 3.5 26.0 - - - +
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Residues in contact with TYR 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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63N LEU* 3.5 20.0 - - + +
67N GLU* 3.1 36.9 + - - +
70N VAL* 3.5 26.7 - - + +
71N ILE* 3.5 16.6 - - + -
74N LEU* 3.4 24.5 - - + +
101N ASN* 3.4 12.7 - - - +
102N PRO* 1.3 82.1 - - + +
104N ARG* 1.3 59.9 + - - +
106N ALA 3.4 0.3 + - - -
107N GLN* 2.9 30.9 + - - +
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Residues in contact with ARG 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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80N MET* 3.8 8.4 - - - +
92N LYS* 3.9 26.3 - - - +
95N GLU* 4.5 8.3 + - - -
96N ILE* 3.6 34.3 - - + +
99N ASP* 5.2 7.9 + - + +
101N ASN* 3.3 29.9 + - + +
103N TYR* 1.3 79.1 - - - +
105N ILE* 1.3 55.8 + - - +
107N GLN* 3.2 20.2 + - - +
108N MET* 2.9 29.8 + - - +
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Residues in contact with ILE 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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96N ILE* 3.3 36.1 - - + +
97N LEU* 4.2 4.3 - - + +
100N GLY* 3.9 21.8 - - - +
101N ASN 3.0 21.6 + - - +
102N PRO* 4.0 5.8 - - + +
104N ARG* 1.3 73.8 - - - +
106N ALA* 1.3 58.9 + - - +
108N MET* 3.5 6.8 + - + +
109N ALA* 2.9 28.8 + - - +
132N ALA* 3.7 35.7 - - + +
135N LEU* 4.4 23.8 - - + -
136N LEU* 4.4 7.2 - - + -
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Residues in contact with ALA 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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71N ILE* 3.7 31.6 - - + +
74N LEU* 3.0 21.9 - - + +
75N LEU* 3.4 7.0 - - + +
102N PRO 2.9 20.2 + - - +
103N TYR 3.6 4.3 - - - +
105N ILE* 1.3 77.4 - - - +
107N GLN* 1.3 58.5 + - - +
110N GLY 2.9 21.8 + - - -
136N LEU* 3.7 17.0 - - + +
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Residues in contact with GLN 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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74N LEU* 3.7 24.2 - - + +
78N GLY 4.1 1.9 - - - +
79N ARG* 3.1 32.7 + - - +
80N MET* 3.2 27.1 - - + +
81N PRO* 5.7 0.8 - - - +
103N TYR 2.9 17.9 + - - +
104N ARG* 3.2 19.0 + - - +
106N ALA* 1.3 73.1 - - - +
108N MET* 1.3 57.7 + - - +
110N GLY* 2.8 19.9 + - - -
111N GLN 3.0 11.8 + - - -
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Residues in contact with MET 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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80N MET* 3.5 24.1 - - + +
82N LEU* 5.1 4.7 - - + +
93N THR* 3.7 38.4 - - + +
96N ILE* 3.7 27.1 - - + -
97N LEU* 3.7 33.2 - - + -
104N ARG 2.9 14.9 + - - +
105N ILE* 3.9 7.0 - - + +
107N GLN* 1.3 74.6 - - - +
109N ALA* 1.3 62.6 + - - +
110N GLY 3.1 0.2 + - - -
111N GLN* 3.3 1.4 + - - +
112N LEU* 2.9 44.9 + - + +
128N ALA* 5.1 1.3 - - - +
132N ALA* 3.9 17.0 - - + -
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Residues in contact with ALA 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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75N LEU* 3.7 16.8 - - + +
105N ILE 2.9 19.6 + - - +
106N ALA 3.6 4.7 - - - +
108N MET* 1.3 77.7 - - - +
110N GLY* 1.3 57.1 + - - +
112N LEU* 4.4 0.4 - - - -
113N ARG* 2.9 33.3 + - - +
129N LEU* 3.4 11.4 - - + +
132N ALA* 3.8 20.6 - - + -
133N ILE* 3.9 13.2 - - + -
136N LEU* 4.4 3.1 - - + -
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Residues in contact with GLY 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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74N LEU 3.7 1.3 - - - -
75N LEU* 3.7 20.1 - - - +
76N LYS 5.6 0.5 - - - +
78N GLY 3.0 18.6 - - - +
106N ALA 2.9 11.7 + - - -
107N GLN 2.8 10.6 + - - -
109N ALA* 1.3 74.7 - - - +
111N GLN* 1.3 59.0 - - - -
113N ARG* 3.9 2.2 - - - +
114N ALA* 2.9 28.2 + - - +
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Residues in contact with GLN 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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78N GLY 3.3 2.6 + - - -
79N ARG* 3.1 46.5 - - - +
80N MET* 3.1 44.5 + - + +
82N LEU* 4.3 7.4 - - + -
107N GLN 3.0 8.0 + - - +
108N MET 4.2 3.8 - - - +
110N GLY* 1.3 74.7 - - - +
112N LEU* 1.3 58.6 + - - +
114N ALA* 3.1 6.0 + - - +
115N TRP* 2.9 68.9 + - + +
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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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82N LEU* 3.6 25.1 - - + -
93N THR* 3.8 17.0 - - + -
108N MET* 2.9 41.4 + - + +
109N ALA 4.9 0.2 - - - +
111N GLN* 1.3 78.4 - - - +
113N ARG* 1.3 57.2 + - - +
115N TRP* 3.0 19.5 + - + +
116N GLU 2.9 22.5 + - - -
121N LEU* 3.8 11.4 - - + +
125N ASP* 3.8 39.3 - - + +
128N ALA 5.3 0.7 - - - -
129N LEU* 3.7 25.6 - - + +
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Residues in contact with ARG 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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75N LEU 5.5 0.2 - - - +
109N ALA 2.9 21.1 + - - +
110N GLY 3.9 2.7 - - - +
112N LEU* 1.3 73.6 - - - +
114N ALA* 1.3 66.7 + - - +
116N GLU* 3.0 35.9 + - - +
117N VAL* 3.2 35.4 + - + +
129N LEU* 3.7 16.2 - - + +
133N ILE* 5.9 0.4 - - - -
159N TRP* 3.4 73.2 - - + +
160N GLY 4.9 7.5 + - - -
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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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76N LYS 6.1 0.7 - - - +
79N ARG* 3.4 35.7 - - + +
110N GLY 2.9 17.1 + - - +
111N GLN* 3.2 15.9 - - - +
113N ARG* 1.3 77.2 - - - +
115N TRP* 1.3 60.2 + - + +
117N VAL* 4.1 4.9 + - - +
118N GLU* 3.6 21.7 + - - +
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Residues in contact with TRP 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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80N MET 5.5 0.2 - - - -
82N LEU* 3.6 38.4 - - + -
83N PRO 5.3 0.7 - - - -
89N ARG* 3.3 34.1 - - - -
111N GLN* 2.9 45.3 + - + +
112N LEU* 3.0 22.2 + - + +
114N ALA* 1.3 80.1 - - + +
116N GLU* 1.3 62.8 + - - +
117N VAL 3.2 0.7 - - - -
118N GLU* 3.3 6.9 + - + -
119N ARG* 3.3 58.4 + - + +
120N GLY 3.2 24.8 + - - +
121N LEU* 4.1 13.2 - - + -
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Residues in contact with GLU 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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112N LEU 2.9 8.1 + - - +
113N ARG* 3.0 35.3 + - - +
115N TRP* 1.3 76.5 - - - +
117N VAL* 1.3 60.6 + - + +
118N GLU 3.7 0.3 + - - -
120N GLY* 4.5 9.0 + - - -
121N LEU* 3.8 33.6 + - + +
126N ARG* 3.4 23.3 - - - +
129N LEU* 3.6 19.8 - - + +
130N ARG* 5.5 3.3 + - - +
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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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113N ARG* 3.2 49.9 + - + +
114N ALA* 4.6 4.9 - - - +
115N TRP 3.2 0.4 - - - -
116N GLU* 1.3 77.4 - - + +
118N GLU* 1.3 62.7 + - + +
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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