Contacts of the helix formed by residues 80 - 95 (chain N) in PDB entry 6CM9
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 THR 80 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77N ARG* 5.3 12.8 + - + -
78N PRO* 2.9 27.9 + - + +
79N MET* 1.3 76.2 - - - +
81N TYR* 1.3 62.0 + - - +
82N LYS* 4.4 5.5 + - - +
83N ALA* 3.6 20.3 + - - +
84N ALA* 2.9 26.5 + - - +
120N TYR* 5.5 0.7 - - - -
139N PHE 4.9 2.2 - - - -
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Residues in contact with TYR 81 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80N THR* 1.3 78.7 - - - +
82N LYS* 1.3 65.3 + - + +
84N ALA* 2.9 19.5 + - - +
85N VAL* 2.9 34.9 + - + +
139N PHE* 3.6 42.4 + + + -
140N GLY* 4.2 2.7 - - - -
190N ALA* 3.5 36.3 - - + +
191N PHE* 3.2 38.1 - + - -
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Residues in contact with LYS 82 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80N THR* 4.7 6.5 - - - +
81N TYR* 1.3 90.1 - - + +
83N ALA* 1.3 59.1 + - + +
85N VAL* 3.8 7.3 - - - +
86N ASP* 2.9 49.4 + - - +
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Residues in contact with ALA 83 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77N ARG* 5.8 2.0 - - - +
79N MET* 3.4 24.8 - - + +
80N THR* 3.6 26.2 + - - +
81N TYR 3.2 0.4 - - - -
82N LYS* 1.3 84.3 - - + +
84N ALA* 1.3 55.1 + - - +
86N ASP* 3.8 7.6 - - - +
87N LEU* 2.9 29.6 + - - +
120N TYR* 4.7 13.2 - - + +
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Residues in contact with ALA 84 (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 MET* 4.5 11.4 - - + +
80N THR 2.9 18.0 + - - +
81N TYR 2.9 6.9 + - - +
83N ALA* 1.3 74.1 - - - +
85N VAL* 1.3 59.7 + - - +
87N LEU* 3.4 8.4 + - - +
88N SER* 2.9 32.4 + - - -
138N THR* 5.7 4.0 - - + -
139N PHE 4.7 1.1 - - - +
140N GLY* 3.3 32.3 - - - +
141N TRP* 4.5 8.8 - - + +
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Residues in contact with VAL 85 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81N TYR* 2.9 52.4 + - + +
82N LYS* 3.8 8.5 - - - +
84N ALA* 1.3 74.3 - - - +
86N ASP* 1.3 64.2 + - - +
88N SER* 3.2 6.7 + - - -
89N HIS* 2.8 57.9 + - + -
140N GLY 4.9 5.2 - - - +
142N CYS* 5.4 4.0 - - - -
190N ALA* 4.9 4.9 - - + -
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Residues in contact with ASP 86 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6N SER* 5.8 3.6 - - - -
82N LYS* 2.9 38.8 + - - +
83N ALA* 3.8 7.1 - - - +
85N VAL* 1.3 79.9 - - - +
87N LEU* 1.3 57.3 + - - +
89N HIS* 3.4 8.5 + - - +
90N PHE* 2.9 27.8 + - - +
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Residues in contact with LEU 87 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6N SER* 5.6 2.5 - - - +
9N SER* 6.1 1.8 - - - +
13N TRP* 5.9 0.9 - - + -
79N MET* 3.9 27.8 - - + -
83N ALA 2.9 18.9 + - - +
84N ALA* 3.7 5.6 - - - +
86N ASP* 1.3 73.2 - - - +
88N SER* 1.3 61.8 + - - +
90N PHE* 3.2 16.3 + - + +
91N LEU* 2.9 53.2 + - + +
114N ILE* 5.7 9.9 - - + -
124N TRP* 4.2 17.5 - - + -
141N TRP* 3.6 27.6 - - + -
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Residues in contact with SER 88 (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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84N ALA 2.9 22.1 + - - -
85N VAL* 3.2 9.1 + - - -
87N LEU* 1.3 77.1 - - - +
89N HIS* 1.3 60.1 + - - +
91N LEU* 3.4 1.6 + - - -
92N LYS* 2.9 28.3 + - - +
140N GLY 4.0 11.3 + - - -
141N TRP* 4.9 6.1 - - - -
142N CYS* 4.0 22.7 + - - +
143N TYR* 3.5 24.8 + - - -
185N PHE* 5.2 6.0 - - - -
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Residues in contact with HIS 89 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85N VAL* 2.8 48.8 + - + +
86N ASP* 3.9 8.9 + - - +
88N SER* 1.3 74.6 - - - +
90N PHE* 1.3 60.3 + - - +
92N LYS* 4.0 9.9 - - + -
93N GLU* 2.9 48.8 + - + +
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Residues in contact with PHE 90 (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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6N SER* 3.2 34.3 - - - +
9N SER* 3.4 23.8 - - - -
10N VAL* 4.0 20.4 - - + -
13N TRP* 3.5 40.7 - + - -
86N ASP 2.9 18.1 + - - +
87N LEU* 3.2 19.3 + - + +
89N HIS* 1.3 76.8 - - - +
91N LEU* 1.3 62.6 + - - +
93N GLU* 5.4 0.2 - - - -
94N LYS* 3.3 60.0 + - + +
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Residues in contact with LEU 91 (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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13N TRP* 3.9 26.2 - - + -
87N LEU* 2.9 44.9 + - + +
88N SER* 3.7 5.4 - - - +
90N PHE* 1.3 77.8 - - + +
92N LYS* 1.3 61.8 + - - +
95N GLY* 3.6 17.7 + - - -
97N LEU* 3.7 39.8 + - + +
98N GLU* 5.8 2.6 + - - +
141N TRP* 3.9 23.1 - - + -
143N TYR* 3.6 30.8 + - + +
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Residues in contact with LYS 92 (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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88N SER 2.9 17.6 + - - +
89N HIS* 3.7 13.5 - - + +
90N PHE 3.2 0.4 - - - -
91N LEU* 1.3 80.1 - - - +
93N GLU* 1.3 66.7 + - + +
95N GLY* 4.3 4.0 + - - -
98N GLU* 6.4 0.6 - - - +
143N TYR* 3.9 12.3 - - + +
185N PHE* 4.7 32.0 - - + +
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Residues in contact with GLU 93 (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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89N HIS* 2.9 31.5 + - + +
90N PHE* 5.4 0.2 - - - -
92N LYS* 1.3 84.1 - - + +
94N LYS* 1.3 75.1 + - + +
95N GLY* 3.5 0.9 + - - -
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Residues in contact with LYS 94 (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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10N VAL* 5.4 10.2 - - + +
13N TRP* 4.1 21.4 + - + +
90N PHE* 3.3 50.5 + - + +
93N GLU* 1.3 85.6 - - + +
95N GLY* 1.3 63.4 + - - +
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Residues in contact with GLY 95 (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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13N TRP* 2.9 30.6 + - - -
17N ARG* 4.5 1.0 + - - -
90N PHE 4.2 0.6 + - - -
91N LEU 3.6 18.5 + - - -
92N LYS 4.7 3.6 - - - -
93N GLU 3.4 3.3 - - - -
94N LYS* 1.3 79.3 - - - +
96N GLY* 1.3 59.4 + - - -
97N LEU 3.7 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