Contacts of the helix formed by residues 141 - 147 (chain N) in PDB entry 2D2C
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 141 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83N ARG* 5.2 0.9 + - - -
136N TYR 4.0 3.1 - - - +
139N PRO* 2.8 39.3 + - - +
140N TRP* 1.3 81.5 - - - +
142N GLN* 1.3 57.0 + - - +
143N VAL* 3.7 3.6 - - - +
144N GLY* 3.3 22.4 - - - +
145N TYR* 2.3 35.8 + - - +
301N HEM 4.3 3.6 - - - +
61O MET* 4.2 15.3 - - - +
62O VAL 4.1 13.3 - - - +
63O GLY* 3.7 13.5 - - - +
64O GLU* 3.5 8.1 - - - -
1309O BNT 4.0 13.7 - - + -
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Residues in contact with GLN 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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141N ASP* 1.3 73.7 - - - +
143N VAL* 1.3 62.5 + - + +
145N TYR* 3.9 13.5 - - - -
146N TRP* 3.3 34.1 + - - +
63O GLY 3.8 0.6 + - - -
64O GLU* 2.6 53.6 + - + +
66O ALA* 6.2 1.1 - - + -
67O ASN 2.8 29.0 + - - -
70O ALA* 3.1 26.0 - - - +
71O THR 3.7 4.5 + - - -
72O PRO* 3.6 26.8 - - + +
1309O BNT 5.1 4.9 - - + +
16P PRO 4.6 7.3 - - - +
17P THR 5.4 1.1 - - - +
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Residues in contact with VAL 143 (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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136N TYR* 3.3 25.4 - - + +
141N ASP* 4.2 5.2 - - + -
142N GLN* 1.3 78.0 - - + +
144N GLY* 1.3 66.3 + - - +
147N ALA* 3.2 32.4 + - - +
72O PRO* 4.4 8.1 - - + -
74O GLU* 3.2 39.9 - - + +
75O ILE* 4.2 18.4 - - - +
76O LEU 4.2 2.5 - - - +
1309O BNT 3.8 23.3 - - + -
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Residues in contact with GLY 144 (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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136N TYR* 3.5 22.4 - - - -
137N SER* 2.7 30.9 - - - -
141N ASP* 3.0 26.8 + - - +
143N VAL* 1.3 77.0 - - - +
145N TYR* 1.3 69.4 + - - +
148N VAL* 4.1 2.6 - - - +
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Residues in contact with TYR 145 (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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137N SER* 4.8 1.8 - - - -
140N TRP* 3.8 42.9 - + + +
141N ASP 2.3 32.1 + - - +
142N GLN* 3.7 15.3 - - - +
143N VAL 3.1 0.6 - - - -
144N GLY* 1.3 76.6 - - - +
146N TRP* 1.3 82.9 + + - +
148N VAL* 3.0 12.8 + - - +
149N LYS* 3.6 30.3 + - + -
175N VAL* 3.6 36.1 + - + +
64O GLU* 4.8 1.3 - - - -
67O ASN 4.4 0.4 - - - -
68O PRO* 3.0 44.4 + - + +
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Residues in contact with TRP 146 (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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112D GLY 4.2 17.3 - - - -
113D CYS* 4.2 8.1 - - - -
114D VAL* 3.8 24.2 - - + -
142N GLN* 3.3 37.0 + - - +
145N TYR* 1.3 97.8 - + - +
147N ALA* 1.3 53.0 + - - +
148N VAL 2.6 1.9 + - - -
149N LYS* 2.5 61.0 + - + +
150N ILE* 2.8 26.6 + - + +
68O PRO 3.0 29.2 + - - -
69O PHE* 3.3 3.4 - - + -
70O ALA 3.1 18.6 - - - +
71O THR* 3.9 22.7 - - - -
72O PRO* 4.1 15.7 - - + -
75O ILE* 5.4 6.5 - - + -
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Residues in contact with ALA 147 (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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136N TYR* 4.2 10.4 - - + -
143N VAL 3.2 18.7 + - - +
145N TYR 3.0 3.2 + - - -
146N TRP* 1.3 72.0 - - - +
148N VAL* 1.3 62.6 + - + +
149N LYS 3.5 0.4 - - - -
150N ILE* 4.1 11.2 - - - +
151N VAL* 3.3 23.3 - - - +
75O ILE* 4.5 7.1 - - + +
76O LEU 3.1 37.0 - - - +
77O PRO* 5.1 3.5 - - + +
85O PHE* 6.5 0.7 - - + -
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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