Contacts of the helix formed by residues 137 - 150 (chain O) in PDB entry 6NCA
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 137 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85O TYR* 3.4 33.4 + - - -
123O TYR* 4.7 0.5 - - - -
135O ALA* 4.2 0.3 - - - +
136O ALA* 1.3 84.4 - - + +
138O MET* 1.3 68.4 + - - +
139O ALA* 4.1 5.2 - - - +
140O ALA* 3.1 26.5 + - - +
141O GLN* 3.0 22.6 + - - +
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Residues in contact with MET 138 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55E GLU 5.5 2.9 - - - +
56E GLY* 5.2 3.6 - - - -
57E PRO* 3.5 41.3 - - + -
137O ASP* 1.3 75.7 - - - +
139O ALA* 1.3 63.7 + - - +
141O GLN* 2.9 42.1 + - + +
142O THR* 3.4 9.0 + - - -
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Residues in contact with ALA 139 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84O TYR* 4.1 27.2 - - + +
85O TYR* 3.6 38.4 - - + +
123O TYR* 3.3 13.4 + - + -
137O ASP* 3.3 3.1 + - - +
138O MET* 1.3 78.8 - - - +
140O ALA* 1.3 62.4 + - - +
142O THR* 3.4 20.9 + - - -
143O THR* 3.7 1.0 + - - -
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Residues in contact with ALA 140 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123O TYR* 3.2 46.3 - - + +
124O ILE* 4.4 4.1 - - + +
135O ALA* 3.7 6.2 - - + +
136O ALA 3.5 9.4 - - - +
137O ASP* 3.1 23.5 + - - +
139O ALA* 1.3 77.6 - - - +
141O GLN* 1.3 64.1 + - - +
143O THR* 3.3 5.7 + - - -
144O LYS* 3.0 20.6 + - - +
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Residues in contact with GLN 141 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135O ALA* 3.7 21.0 + - - +
137O ASP* 3.0 17.5 + - - +
138O MET* 2.9 35.1 + - + +
140O ALA* 1.3 78.3 - - - +
142O THR* 1.3 56.9 + - - +
144O LYS* 3.1 20.0 + - - +
145O HIS* 2.4 48.3 + - + -
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Residues in contact with THR 142 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84O TYR* 3.7 30.7 - - + +
138O MET 3.4 9.2 + - - -
139O ALA* 3.6 11.8 + - - -
140O ALA 3.2 0.6 - - - -
141O GLN* 1.3 79.4 - - - +
143O THR* 1.3 60.9 + - - +
145O HIS* 3.5 6.8 + - - +
146O LYS* 3.4 33.8 + - - +
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Residues in contact with THR 143 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93 VAL* 3.2 31.9 + - + +
84O TYR* 3.7 3.3 - - - -
123O TYR* 2.5 33.8 + - + -
124O ILE* 4.2 7.2 - - + -
139O ALA 3.7 0.4 + - - -
140O ALA 3.3 6.7 + - - -
142O THR* 1.3 74.1 - - - +
144O LYS* 1.3 66.8 + - - +
146O LYS* 3.4 4.9 + - - +
147O TRP* 3.0 61.1 + - + +
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Residues in contact with LYS 144 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124O ILE* 3.9 12.3 - - + +
133O TRP* 3.6 43.2 + - + +
135O ALA* 4.5 9.2 - - + +
140O ALA 3.0 14.3 + - - +
141O GLN* 3.1 28.5 + - - +
143O THR* 1.3 76.6 - - - +
145O HIS* 1.3 57.7 + - + +
147O TRP* 3.2 2.9 + - - +
148O GLU* 2.7 69.3 + - - +
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Residues in contact with HIS 145 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141O GLN* 2.4 50.9 + - + +
142O THR* 3.9 6.5 - - - +
143O THR 3.3 0.4 - - - -
144O LYS* 1.3 85.0 - - + +
146O LYS* 1.3 60.0 + - + +
148O GLU* 3.3 14.1 + - - +
149O ALA* 2.9 30.3 + - - +
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Residues in contact with LYS 146 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83 VAL 5.7 2.5 - - - +
93 VAL* 4.5 14.5 + - - +
80O THR* 5.5 2.2 - - - +
84O TYR* 3.6 22.4 + - - -
142O THR* 3.4 24.8 + - - +
143O THR* 3.4 6.0 + - - +
144O LYS 3.3 0.4 - - - -
145O HIS* 1.3 77.6 - - + +
147O TRP* 1.3 65.7 + - + +
149O ALA* 3.3 5.3 + - - +
150O ALA* 2.8 32.3 + - - +
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Residues in contact with TRP 147 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73 ILE* 3.5 28.5 - - + +
83 VAL 3.0 23.4 + - - -
93 VAL* 4.1 14.4 - - + -
97O ARG* 5.0 1.1 - - - -
114O HIS* 4.7 6.5 - + - -
116O TYR* 3.6 33.7 - + - -
124O ILE* 3.6 26.7 - - + -
133O TRP* 3.4 49.6 + + + -
143O THR* 3.0 37.3 + - + +
144O LYS* 3.7 4.7 - - - +
146O LYS* 1.3 80.8 - - + +
148O GLU* 1.3 65.6 + - - +
150O ALA* 5.9 0.4 - - + -
151O HIS* 3.4 1.6 + - - -
152O VAL* 3.1 43.4 + - + +
153O ALA 4.5 0.3 + - - -
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Residues in contact with GLU 148 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131O ARG 5.7 0.3 - - - +
132O SER* 5.6 2.3 - - - -
133O TRP* 3.9 22.4 + - + +
144O LYS* 2.7 57.3 + - - +
145O HIS* 3.7 18.9 + - - +
147O TRP* 1.3 73.7 - - - +
149O ALA* 1.3 60.1 + - - +
151O HIS* 3.4 21.0 + - - +
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Residues in contact with ALA 149 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145O HIS 2.9 17.4 + - - +
146O LYS* 3.8 5.4 - - - +
148O GLU* 1.3 77.2 - - - +
150O ALA* 1.3 58.6 + - - +
151O HIS* 3.2 15.3 + - - -
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Residues in contact with ALA 150 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146O LYS 2.8 18.0 + - - +
147O TRP* 5.9 0.2 - - + -
148O GLU 3.3 0.2 - - - -
149O ALA* 1.3 74.4 - - - +
151O HIS* 1.3 70.3 + - - +
152O VAL* 3.2 17.3 + - + +
155O GLN* 5.6 1.9 - - - +
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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