Contacts of the helix formed by residues 126 - 136 (chain M) 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 126 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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697A G 3.5 34.8 - - - -
698A A 3.3 22.7 + - - -
107M LYS* 4.8 0.2 - - - -
108M VAL 3.4 7.9 + - - -
109M LEU* 4.4 6.5 - - - -
110M GLY 3.3 6.4 + - - -
125M PHE* 1.3 77.4 - - - +
127M GLU* 1.3 68.1 + - - +
128M GLY 4.3 0.4 - - - -
129M ALA* 2.9 24.7 + - - +
130M ARG* 3.1 14.0 + - - +
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Residues in contact with GLU 127 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697A G 3.3 16.5 + - - +
126M SER* 1.3 73.7 - - - +
128M GLY* 1.3 65.0 + - - +
130M ARG* 3.0 8.5 + - - +
131M GLU* 2.9 47.2 + - + +
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Residues in contact with GLY 128 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697A G 5.1 0.8 + - - -
698A A 3.5 19.4 + - - -
110M GLY* 4.1 7.6 - - - -
126M SER* 3.2 1.0 - - - -
127M GLU* 1.3 78.5 - - - +
129M ALA* 1.3 59.2 + - - +
131M GLU* 4.1 7.5 + - - +
132M LYS* 3.0 37.8 + - - +
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Residues in contact with ALA 129 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66M VAL* 4.3 4.3 - - + -
108M VAL* 3.6 30.3 - - + +
109M LEU 3.8 9.6 - - - +
110M GLY* 3.8 8.6 - - - -
125M PHE* 4.3 5.6 - - + -
126M SER* 2.9 26.2 + - - +
128M GLY* 1.3 74.6 - - - +
130M ARG* 1.3 61.3 + - - +
132M LYS* 3.9 1.0 - - - +
133M VAL* 3.0 35.9 + - - +
140M VAL* 5.2 1.3 - - - -
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Residues in contact with ARG 130 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125M PHE* 3.8 28.8 - - + +
126M SER 3.1 10.1 + - - +
127M GLU* 3.0 10.6 + - - +
129M ALA* 1.3 74.7 - - - +
131M GLU* 1.3 69.3 + - + +
133M VAL* 3.2 1.4 + - - -
134M GLU* 2.9 42.5 + - - +
140M VAL* 4.0 28.3 - - + +
142M LEU* 3.8 35.4 - - - +
149M ARG* 3.6 30.6 - - - +
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Residues in contact with GLU 131 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127M GLU* 2.9 43.6 + - + +
128M GLY* 4.1 7.0 + - - +
130M ARG* 1.3 78.4 - - + +
132M LYS* 1.3 59.3 + - + +
134M GLU* 3.9 7.6 - - - +
135M GLY* 2.7 29.6 + - - -
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Residues in contact with LYS 132 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699A C 3.0 24.0 + - - -
700A A 5.6 0.2 + - - -
66M VAL* 4.5 6.1 - - + -
110M GLY* 2.9 28.4 + - - +
112M GLY 2.5 35.3 + - - +
113M GLN* 5.0 2.0 - - - -
114M VAL* 3.8 20.3 - - + +
128M GLY* 3.0 24.5 + - - +
129M ALA* 3.9 3.6 - - - +
131M GLU* 1.3 78.8 - - + +
133M VAL* 1.3 63.5 + - - +
135M GLY* 3.2 2.5 + - - -
136M ALA* 3.1 24.3 + - - +
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Residues in contact with VAL 133 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66M VAL* 4.3 13.2 - - + -
114M VAL* 4.6 15.3 - - + -
118M LEU* 3.2 31.5 + - + +
120M LEU* 3.5 27.4 - - + -
129M ALA* 3.0 22.0 + - + +
130M ARG 3.9 2.0 - - - +
132M LYS* 1.3 75.4 - - - +
134M GLU* 1.3 58.2 + - + +
136M ALA* 3.8 5.0 + - - +
138M GLY* 2.8 27.9 + - - -
139M SER 3.5 20.0 - - - +
140M VAL* 4.0 11.2 - - + -
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Residues in contact with GLU 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130M ARG* 2.9 36.0 + - - +
131M GLU* 3.9 6.3 - - - +
133M VAL* 1.3 75.1 - - + +
135M GLY* 1.3 55.0 + - - +
136M ALA 2.9 4.3 - - - -
137M GLY* 2.7 26.7 + - - -
138M GLY 3.2 20.3 + - - +
139M SER* 4.9 4.8 - - - -
140M VAL* 5.2 8.3 + - + +
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Residues in contact with GLY 135 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131M GLU 2.7 19.0 + - - -
132M LYS* 3.2 3.3 + - - -
134M GLU* 1.3 77.0 - - - +
136M ALA* 1.3 56.1 + - - +
137M GLY 3.2 2.8 + - - -
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Residues in contact with ALA 136 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114M VAL* 3.4 25.4 - - + +
115M ARG 5.1 0.7 - - - -
116M HIS 3.3 21.4 - - - +
117M GLU* 3.3 18.9 + - - +
132M LYS 3.1 12.8 + - - +
133M VAL 4.3 2.5 - - - +
134M GLU 2.9 1.6 + - - -
135M GLY* 1.3 75.3 - - - +
137M GLY* 1.3 63.8 + - - +
138M GLY 3.3 1.1 - - - -
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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