Contacts of the helix formed by residues 131 - 142 (chain N) in PDB entry 6MZL
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 PRO 131 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C LEU* 4.9 25.4 - - + +
37C LEU* 6.2 0.4 - - + -
40C SER* 5.7 1.8 - - - -
129N THR 3.6 6.7 - - - +
130N ILE* 1.3 88.7 - - + +
132N ASP* 1.3 64.8 + - - +
133N ALA* 3.2 3.8 - - + +
134N VAL* 3.1 35.1 + - + +
135N THR* 3.2 13.7 + - - -
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Residues in contact with ASP 132 (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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128N PRO* 3.3 39.4 - - - +
130N ILE 3.3 5.5 + - - +
131N PRO* 1.3 68.7 - - - +
133N ALA* 1.3 59.3 + - - +
135N THR* 4.4 1.3 - - - -
136N GLY* 2.9 25.2 + - - -
149N PRO* 5.3 8.6 - - + +
152N ILE* 3.7 29.6 - - + +
153N ARG* 4.7 6.1 + - - +
156N SER* 4.1 5.9 + - - -
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Residues in contact with ALA 133 (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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131N PRO* 3.2 3.3 - - + -
132N ASP* 1.3 78.6 - - - +
134N VAL* 1.3 62.0 + - + +
136N GLY* 3.4 1.6 + - - -
137N TYR* 2.9 28.9 + - - +
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Residues in contact with VAL 134 (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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33C SER* 3.8 23.3 - - - +
36C LEU* 3.8 28.9 - - + -
37C LEU* 4.4 13.7 - - + -
130N ILE* 5.3 0.4 - - + -
131N PRO* 3.1 25.6 + - + +
133N ALA* 1.3 76.8 - - + +
135N THR* 1.3 60.3 + - - +
137N TYR* 3.2 5.9 + - - +
138N TYR* 2.9 59.1 + - + -
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Residues in contact with THR 135 (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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37C LEU* 5.4 2.5 - - - +
69C LEU* 5.2 15.0 - - + +
130N ILE* 3.3 21.7 - - - +
131N PRO 3.2 8.8 + - - -
132N ASP* 4.1 0.4 - - - -
134N VAL* 1.3 75.6 - - - +
136N GLY* 1.3 57.4 + - - +
138N TYR* 3.5 6.1 + - - +
139N LEU* 2.9 43.1 + - + +
152N ILE* 3.8 20.6 - - + +
155N ILE* 4.8 6.1 - - + -
156N SER* 3.1 33.8 + - - +
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Residues in contact with GLY 136 (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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132N ASP 2.9 19.6 + - - -
133N ALA* 3.7 2.2 - - - -
134N VAL 3.2 0.2 - - - -
135N THR* 1.3 78.1 - - - +
137N TYR* 1.3 55.1 + - - +
139N LEU* 3.3 7.6 + - - +
140N ASN* 2.8 36.3 + - - +
144N PHE 4.4 1.3 - - - +
152N ILE* 4.6 12.0 - - - +
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Residues in contact with TYR 137 (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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30C GLU* 3.7 31.3 + - + +
33C SER* 4.8 13.7 - - - -
471F GLN* 4.1 12.0 + - - -
488F GLY 5.2 3.2 + - - -
133N ALA 2.9 16.9 + - - +
134N VAL* 3.2 6.5 + - - +
136N GLY* 1.3 76.7 - - - +
138N TYR* 1.3 74.3 + + - +
140N ASN* 2.9 33.5 + - + +
141N ARG* 2.9 37.8 + - + +
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Residues in contact with TYR 138 (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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30C GLU* 3.9 1.7 + - - +
33C SER* 2.6 39.0 + - - -
34C ARG* 3.3 14.3 + - - +
37C LEU* 3.7 19.3 - - + -
66C GLN* 3.1 46.2 + - + +
69C LEU* 4.6 20.7 - - + +
70C GLN* 4.5 12.5 + - + +
134N VAL* 2.9 33.0 + - + +
135N THR* 4.1 3.6 - - - +
137N TYR* 1.3 84.7 - + - +
139N LEU* 1.3 59.6 + - - +
141N ARG* 3.8 35.3 + - - +
142N ALA* 3.2 21.0 + - - +
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Residues in contact with LEU 139 (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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69C LEU* 4.0 28.3 - - + +
72C LEU* 5.8 0.4 - - + -
73C GLY* 4.5 7.6 - - - +
135N THR* 2.9 32.4 + - + +
136N GLY* 3.5 5.8 - - - +
138N TYR* 1.3 77.7 - - - +
140N ASN* 1.3 50.5 + - - +
141N ARG 3.4 0.7 - - - -
142N ALA* 3.1 9.2 - - + -
143N GLY 2.6 11.1 + - - -
144N PHE* 2.4 72.5 + - + +
152N ILE* 3.7 17.5 - - + -
155N ILE* 3.9 24.7 - - + -
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Residues in contact with ASN 140 (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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490F ALA* 3.3 23.0 - - - +
538F ILE* 5.7 3.8 - - - +
540F TYR* 2.6 41.8 + - + -
136N GLY 2.8 26.9 + - - +
137N TYR* 2.9 28.1 + - + +
139N LEU* 1.3 75.4 - - - +
141N ARG* 1.3 60.4 + - - +
143N GLY* 3.1 14.1 + - - +
144N PHE 3.4 6.4 - - - +
145N GLU* 4.7 0.5 - - - -
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Residues in contact with ARG 141 (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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30C GLU* 4.5 17.1 + - - +
34C ARG* 4.5 16.4 - - - +
66C GLN* 5.4 2.2 + - - +
70C GLN* 3.8 28.0 + - - +
488F GLY 4.9 10.3 - - - +
489F PHE* 4.9 14.4 - - + +
490F ALA* 3.4 21.0 - - - +
543F SER* 3.7 14.2 + - - +
69H SER* 4.4 20.6 - - - -
73H TYR* 4.3 22.8 + - - +
137N TYR* 2.9 42.9 + - + +
138N TYR* 3.9 33.4 - - - +
140N ASN* 1.3 76.3 - - - +
142N ALA* 1.3 58.1 + - - +
143N GLY 3.2 0.2 - - - -
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Residues in contact with ALA 142 (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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70C GLN* 4.0 31.2 - - + +
73C GLY* 4.3 9.1 - - - -
77C HIS* 2.6 34.3 + - - -
542F HIS 4.1 2.7 - - - -
543F SER* 4.0 12.3 - - - +
138N TYR 3.2 19.2 + - - +
139N LEU* 3.1 20.4 + - + +
140N ASN 3.2 0.6 - - - -
141N ARG* 1.3 74.5 - - - +
143N GLY* 1.3 49.2 + - - +
144N PHE 3.4 0.4 - - - -
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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