Contacts of the helix formed by residues 133 - 142 (chain Q) in PDB entry 1NJI
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 SER 133 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1793A C 3.4 27.4 + - - -
1794A G 3.4 16.8 - - - -
97Q ARG* 5.3 0.2 - - - +
101Q GLN* 3.6 14.0 + - - +
131Q PHE* 3.3 2.2 - - - +
132Q ASP* 1.3 81.7 - - - +
134Q VAL* 1.3 65.7 + - - +
135Q ALA* 3.6 8.1 + - - +
136Q ASP* 3.2 20.5 + - - +
137Q LEU* 3.0 20.3 + - - +
139Q ARG* 4.5 2.1 + - - -
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Residues in contact with VAL 134 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1794A G 3.0 21.8 + - - +
1795A G 4.7 4.7 - - - +
100Q ALA* 3.9 36.8 - - + +
101Q GLN* 4.0 7.9 - - + +
104Q LYS* 4.0 23.3 - - + -
133Q SER* 1.3 72.7 - - - +
135Q ALA* 1.3 51.4 + - - +
137Q LEU* 2.7 28.4 + - - +
138Q GLU* 2.7 38.3 + - - +
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Residues in contact with ALA 135 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1793A C 3.6 22.4 + - - +
1794A G 5.0 1.0 + - - -
133Q SER* 3.3 1.7 - - - +
134Q VAL* 1.3 78.7 - - - +
136Q ASP* 1.3 58.7 + - - +
138Q GLU* 3.2 11.7 + - - +
139Q ARG* 2.8 59.2 + - - +
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Residues in contact with ASP 136 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130Q GLU 4.4 3.8 - - - +
131Q PHE* 4.0 9.1 - - - -
132Q ASP* 3.4 30.8 + - + +
133Q SER* 3.2 27.1 + - - +
134Q VAL 3.2 0.4 - - - -
135Q ALA* 1.3 79.6 - - - +
137Q LEU* 1.3 62.6 + - - +
139Q ARG* 3.5 24.9 + - - +
140Q TYR* 3.1 21.3 + - - +
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Residues in contact with LEU 137 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101Q GLN* 4.0 22.0 - - + +
104Q LYS* 4.3 15.9 - - + -
105Q LEU* 3.3 39.5 - - + -
122Q LEU* 4.4 10.1 - - + -
131Q PHE* 3.4 47.8 - - + +
133Q SER 3.0 12.0 + - - +
134Q VAL* 2.7 16.1 + - - +
136Q ASP* 1.3 69.7 - - - +
138Q GLU* 1.3 67.0 + - - +
140Q TYR* 3.0 5.5 + - - +
141Q ILE* 2.9 30.9 + - + +
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Residues in contact with GLU 138 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104Q LYS* 3.5 34.5 + - + -
108Q LEU* 5.9 0.9 - - + -
134Q VAL* 2.7 35.9 + - + +
135Q ALA* 3.6 11.8 + - - +
137Q LEU* 1.3 71.2 - - - +
139Q ARG* 1.3 65.5 + - + +
141Q ILE* 2.9 29.3 + - + +
142Q ASP* 3.2 16.4 + - - +
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Residues in contact with ARG 139 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1793A C 5.1 1.6 + - - -
133Q SER* 4.5 2.4 + - - -
135Q ALA* 2.8 39.8 + - - +
136Q ASP* 3.5 39.2 + - - +
138Q GLU* 1.3 72.7 - - + +
140Q TYR* 1.3 63.4 + - - +
142Q ASP* 3.2 19.6 + - - +
143Q ALA 3.4 10.7 - - - +
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Residues in contact with TYR 140 (chain Q).
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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121Q ASP* 4.9 1.1 + - - -
122Q LEU* 3.4 33.0 - - + -
125Q LYS* 2.7 34.6 + - + -
131Q PHE* 3.8 23.8 - + + -
136Q ASP 3.1 10.8 + - - +
137Q LEU 3.0 9.1 + - - +
139Q ARG* 1.3 79.3 - - - +
141Q ILE* 1.3 67.1 + - - +
143Q ALA* 3.0 22.1 + - - +
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Residues in contact with ILE 141 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105Q LEU* 4.5 2.7 - - + -
108Q LEU* 3.6 31.2 - - + -
113Q THR* 5.8 4.7 - - + -
114Q LEU* 4.6 11.9 - - + -
122Q LEU* 3.9 31.0 - - + -
137Q LEU* 2.9 32.7 + - + +
138Q GLU* 2.9 16.3 + - + +
140Q TYR* 1.3 80.2 - - - +
142Q ASP* 1.3 61.8 + - - +
143Q ALA* 2.7 12.0 + - - -
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Residues in contact with ASP 142 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138Q GLU* 3.4 18.2 - - - +
139Q ARG* 3.2 9.1 + - - +
140Q TYR 3.2 1.4 - - - -
141Q ILE* 1.3 81.9 - - - +
143Q ALA* 1.3 73.3 + - - +
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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