Contacts of the helix formed by residues 140 - 149 (chain E) in PDB entry 1NVI
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 ARG 140 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138E GLU 4.3 7.5 + - - +
139E ALA* 1.3 80.5 - - - +
141E GLU* 1.3 64.5 + - - +
142E SER* 3.6 21.8 - - - +
143E ASP* 3.1 35.1 + - - +
144E GLN* 3.6 7.9 + - - +
151E SO4 3.9 25.5 + - - -
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Residues in contact with GLU 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E ALA 4.4 0.4 + - - -
140E ARG* 1.3 72.5 - - - +
142E SER* 1.3 57.5 + - - +
144E GLN* 2.9 40.4 + - - +
145E GLN* 3.0 32.5 + - - +
148E LYS* 4.9 5.0 + - - -
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Residues in contact with SER 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E ARG* 3.6 21.4 - - - +
141E GLU* 1.3 77.8 - - - +
143E ASP* 1.3 61.4 + - - +
145E GLN* 3.4 20.2 + - - +
146E ALA* 3.0 27.0 + - - +
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Residues in contact with ASP 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E ASP* 4.5 3.4 - - - +
119E LYS* 3.8 41.2 - - + +
120E THR* 3.4 21.2 - - + +
140E ARG* 3.1 34.5 + - - +
142E SER* 1.3 79.5 + - - +
144E GLN* 1.3 65.7 + - + +
146E ALA* 3.4 9.4 + - - +
147E ALA* 3.1 17.8 + - - +
151E SO4 4.8 7.4 + - - -
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Residues in contact with GLN 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D PRO* 6.1 2.8 - - - +
78D VAL* 6.2 0.6 - - - +
120E THR* 3.8 32.5 + - - +
140E ARG 4.3 7.7 + - - +
141E GLU* 2.9 36.0 + - - +
143E ASP* 1.3 76.8 - - - +
145E GLN* 1.3 61.9 + - - +
147E ALA* 3.3 2.1 + - - +
148E LYS* 3.1 60.2 + - + +
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Residues in contact with GLN 145 (chain E).
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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141E GLU* 3.0 33.5 + - - +
142E SER* 3.6 20.5 + - - +
143E ASP 3.3 0.2 - - - -
144E GLN* 1.3 73.3 - - - +
146E ALA* 1.3 64.5 + - - +
148E LYS* 3.4 5.1 + - - +
149E ARG* 3.3 26.2 + - - +
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Residues in contact with ALA 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E ASP* 3.3 23.7 - - + +
142E SER 3.0 17.6 + - - +
143E ASP* 3.6 12.1 - - - +
144E GLN 3.4 0.2 - - - -
145E GLN* 1.3 76.0 - - - +
147E ALA* 1.3 59.5 + - - +
149E ARG* 2.6 38.1 - - - +
150E TRP* 3.2 10.0 + - - -
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Residues in contact with ALA 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E ASP* 3.8 16.2 - - - +
117E TYR* 3.3 31.6 + - + -
120E THR* 3.6 26.5 - - + +
121E ARG* 6.0 0.9 - - - +
143E ASP 3.1 15.9 + - - +
144E GLN* 3.8 4.9 - - - +
145E GLN 3.2 0.2 - - - -
146E ALA* 1.3 77.8 - - - +
148E LYS* 1.3 65.4 + - + +
149E ARG 3.4 1.0 + - - -
150E TRP* 3.4 12.5 + - - +
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Residues in contact with LYS 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E TYR* 5.8 0.4 - - - -
141E GLU* 4.9 4.9 + - - -
144E GLN* 3.1 49.6 + - - +
145E GLN* 3.4 4.5 + - - +
147E ALA* 1.3 75.6 - - + +
149E ARG* 1.3 63.7 + - - +
150E TRP* 3.2 9.2 + - - +
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Residues in contact with ARG 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E GLN* 3.7 23.0 + - - +
116E ASP* 2.8 30.3 + - - -
145E GLN 3.3 10.3 + - - +
146E ALA* 2.6 41.5 + - - +
147E ALA 3.2 0.8 - - - -
148E LYS* 1.3 78.8 - - - +
150E TRP* 1.3 84.9 + - + +
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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