Contacts of the helix formed by residues 100 - 117 (chain N) in PDB entry 6CIM
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 SER 100 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25G T 5.5 4.3 - - - -
26G G 5.3 19.1 - - - -
27G A 5.6 12.1 - - - -
33J A 6.1 2.2 - - - -
98N PRO 3.8 1.8 + - - -
99N PRO* 1.3 77.7 - - - +
101N ALA* 1.3 59.6 + - - +
102N PHE* 4.1 9.0 - - - -
103N PHE* 2.7 36.2 + - - +
104N LEU* 3.0 9.9 + - - +
148N ALA* 4.8 1.8 - - - -
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Residues in contact with ALA 101 (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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100N SER* 1.3 72.0 - - - +
102N PHE* 1.3 64.4 + - - +
103N PHE 3.1 0.2 + - - -
104N LEU* 3.3 5.1 + - - +
105N PHE* 3.0 23.4 + - - +
133N TRP* 5.2 4.9 - - + -
141N LYS 5.4 0.4 - - - +
144N TYR* 3.4 45.2 - - + +
145N GLU* 3.6 13.9 - - + +
148N ALA* 3.6 12.8 - - + +
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Residues in contact with PHE 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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24G T 4.2 20.0 - - - -
25G T 3.3 48.9 - + - +
26G G 5.1 7.0 - - - -
100N SER* 3.2 6.8 - - - -
101N ALA* 1.3 78.3 - - - +
103N PHE* 1.3 72.6 + + - +
105N PHE* 3.4 8.7 - + - +
106N CYS* 2.9 46.3 + - - +
126N ALA* 5.3 2.2 - - + -
129N LEU* 4.5 4.5 - - + -
130N GLY* 4.0 27.1 - - - -
133N TRP* 3.8 45.1 - + + -
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Residues in contact with PHE 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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24G T 5.1 0.7 - - - -
25G T 4.9 0.4 - - - -
33J A 3.3 52.5 - + - -
34J A 3.1 66.9 - + - -
99N PRO* 3.6 18.2 - - + -
100N SER* 2.7 33.7 + - - +
102N PHE* 1.3 91.1 - + - +
104N LEU* 1.3 58.8 + - - +
106N CYS* 3.1 10.5 + - + +
107N SER* 3.0 26.7 + - - -
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Residues in contact with LEU 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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99N PRO* 4.1 17.5 - - + +
100N SER 3.0 10.2 + - - +
101N ALA* 4.0 7.0 - - - +
103N PHE* 1.3 72.5 - - - +
105N PHE* 1.3 65.9 + - - +
107N SER* 2.8 25.0 + - - +
108N GLU* 3.0 11.9 + - - +
144N TYR* 6.0 2.5 - - + +
147N LYS* 5.9 7.4 - - + -
151N LEU* 6.2 2.2 - - + -
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Residues in contact with PHE 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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101N ALA 3.0 17.3 + - - +
102N PHE* 3.4 11.0 - + - +
104N LEU* 1.3 77.4 - - - +
106N CYS* 1.3 61.5 + - + +
108N GLU* 3.2 5.7 + - - -
109N TYR* 2.9 84.2 + + + +
129N LEU* 4.4 14.8 - - + -
132N MET* 4.6 5.2 - - - -
133N TRP* 3.1 56.1 - + + +
141N LYS* 6.1 1.1 - - + -
144N TYR* 4.7 10.7 - - + +
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Residues in contact with CYS 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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24G T 5.9 1.1 - - - -
102N PHE* 2.9 37.6 + - + +
103N PHE* 3.1 13.9 + - + +
105N PHE* 1.3 81.0 - - - +
107N SER* 1.3 59.0 + - - +
109N TYR 3.7 0.6 - - - +
110N ARG* 2.9 30.7 + - - +
126N ALA* 5.5 4.7 - - - -
129N LEU* 3.6 42.0 - - - +
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Residues in contact with SER 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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34J A 6.6 0.4 - - - -
103N PHE 3.0 12.2 + - - -
104N LEU* 2.8 22.8 + - - +
106N CYS* 1.3 76.9 - - - +
108N GLU* 1.3 60.2 + - - +
109N TYR 3.6 0.2 + - - -
110N ARG* 3.7 11.8 + - - +
111N PRO* 3.7 8.7 - - - +
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Residues in contact with GLU 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 LEU 3.0 12.1 + - - +
105N PHE* 3.2 6.0 + - - +
107N SER* 1.3 82.6 + - - +
109N TYR* 1.3 67.7 + - + +
110N ARG 3.4 0.2 - - - -
111N PRO* 3.3 19.1 - - - +
112N LYS* 5.0 0.7 + - - +
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Residues in contact with TYR 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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105N PHE* 2.9 59.3 + + + +
106N CYS 3.7 0.4 - - - -
108N GLU* 1.3 84.4 - - + +
110N ARG* 1.3 66.2 + - - +
111N PRO* 3.4 1.6 - - - -
112N LYS* 3.2 44.1 + - + +
113N ILE* 3.3 22.5 + - - +
129N LEU* 3.7 17.7 - - + +
132N MET* 4.6 18.2 - - + -
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Residues in contact with ARG 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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35J G 6.3 2.9 - - - -
106N CYS 2.9 17.4 + - - +
107N SER* 3.8 8.5 - - - +
108N GLU 3.4 0.2 - - - -
109N TYR* 1.3 76.1 - - - +
111N PRO* 1.3 64.5 - - + +
113N ILE* 3.9 3.3 - - - +
114N LYS* 2.9 31.6 + - - +
129N LEU* 5.2 7.4 - - + -
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Residues in contact with PRO 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 SER 3.7 7.0 - - - +
108N GLU 3.3 19.3 - - - +
109N TYR 3.6 0.2 - - - -
110N ARG* 1.3 94.1 - - + +
112N LYS* 1.3 56.6 + - - +
114N LYS* 3.7 6.2 - - + +
115N GLY* 2.8 27.5 + - - -
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Residues in contact with LYS 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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108N GLU 5.6 0.4 - - - +
109N TYR* 3.2 54.2 + - + +
110N ARG 3.3 1.0 - - - -
111N PRO* 1.3 79.8 - - + +
113N ILE* 1.3 62.8 + - - +
115N GLY* 3.2 2.3 + - - -
116N GLU* 3.1 35.8 + - + +
132N MET* 5.9 4.9 - - + -
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Residues in contact with ILE 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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109N TYR 3.3 13.6 + - - +
110N ARG* 4.2 2.7 - - - +
112N LYS* 1.3 79.4 - - - +
114N LYS* 1.3 60.5 + - - +
116N GLU* 4.2 5.1 - - - +
117N HIS* 3.2 27.5 + - - +
120N LEU* 5.2 6.1 - - + +
125N VAL* 5.6 8.7 - - + +
128N LYS* 6.0 4.0 - - + -
129N LEU* 4.8 18.4 - - + -
132N MET* 4.8 11.2 - - + -
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Residues in contact with LYS 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 ARG 2.9 20.2 + - - +
111N PRO* 3.7 7.6 - - + +
112N LYS 3.1 0.2 - - - -
113N ILE* 1.3 76.6 - - - +
115N GLY* 1.3 63.0 + - - +
117N HIS 2.9 23.9 - - - +
118N PRO* 3.4 12.0 - - + +
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Residues in contact with GLY 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 PRO 2.8 17.5 + - - -
112N LYS 3.8 1.3 - - - -
114N LYS* 1.3 77.2 - - - +
116N GLU* 1.3 71.6 + - - +
118N PRO* 4.8 4.3 - - - +
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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 LYS* 3.1 24.1 + - + +
113N ILE* 4.2 4.3 - - - +
115N GLY* 1.3 85.0 - - - +
117N HIS* 1.3 81.6 + - + +
118N PRO* 4.1 4.8 - - - +
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Residues in contact with HIS 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 ILE* 3.2 14.3 + - - +
114N LYS* 2.9 13.9 - - - +
116N GLU* 1.3 93.5 - - + +
118N PRO* 1.4 66.5 - - - +
119N GLY 3.6 1.3 + - - -
120N LEU* 3.8 44.1 + - + +
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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