Contacts of the strand formed by residues 113 - 122 (chain N) 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 ARG 113 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106N ASN* 3.9 0.4 - - - +
111N ASN 4.8 1.3 + - - +
112N LEU* 1.3 80.6 - - - +
114N VAL* 1.3 65.2 + - - +
115N LEU 3.4 0.3 + - - -
133N LEU* 3.3 4.5 - - - -
134N ILE* 2.9 32.9 + - - +
136N PRO* 3.8 24.6 - - + +
150N ILE* 2.7 50.5 + - + +
151N SER* 3.2 12.8 + - - +
152N ARG 2.7 23.7 + - - -
153N THR* 4.5 1.6 - - - +
155N HIS* 3.4 20.1 + - - +
156N ARG* 3.0 41.3 - - - +
157N LEU 4.6 6.7 - - - +
158N ARG* 4.4 3.4 - - - -
8518N CL 3.9 8.1 - - + -
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Residues in contact with VAL 114 (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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102N GLU* 4.0 14.8 - - - +
106N ASN* 3.2 28.3 - - + +
113N ARG* 1.3 70.1 - - - +
115N LEU* 1.3 62.1 + - - +
116N ASN 3.8 10.5 - - - +
131N VAL* 3.8 24.0 - - + -
132N ILE 3.8 3.1 - - - -
133N LEU* 4.5 3.4 - - + +
150N ILE* 4.0 0.8 - - - +
158N ARG* 3.0 30.0 + - - -
159N THR* 3.1 36.8 - - + +
164N THR* 3.7 10.3 - - - +
8518N CL 3.4 5.6 - - + +
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Residues in contact with LEU 115 (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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432A G 4.9 9.7 + - - +
52N LEU 3.0 32.5 - - - +
53N GLY* 4.0 9.9 - - - -
113N ARG 3.4 1.2 + - - -
114N VAL* 1.3 75.7 - - - +
116N ASN* 1.3 77.4 + - + +
132N ILE* 2.7 24.5 + - + +
134N ILE* 3.7 25.6 - - + -
147N LEU* 4.4 15.5 - - + -
149N TRP* 3.5 32.8 - - + -
150N ILE* 3.9 8.3 - - + -
158N ARG* 4.1 8.2 + - - +
164N THR* 4.9 1.3 + - - -
165N SER* 4.8 2.4 + - - -
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Residues in contact with ASN 116 (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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431A G 3.1 38.0 + - - -
432A G 3.5 9.7 + - - -
52N LEU* 3.4 31.7 + - + +
102N GLU* 3.9 3.4 - - - -
114N VAL* 3.6 5.6 - - - +
115N LEU* 1.3 92.9 + - + +
117N SER* 1.3 71.2 + - - +
131N VAL* 3.7 3.8 - - - +
132N ILE* 2.9 26.5 + - + +
165N SER* 2.6 33.1 + - - -
169N ARG* 4.4 2.6 + - - -
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Residues in contact with SER 117 (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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431A G 5.4 0.7 + - - -
48N ARG* 5.3 1.2 + - - -
52N LEU* 3.4 13.1 - - - +
98N GLN* 2.6 34.8 + - - +
102N GLU* 2.4 39.4 + - - +
116N ASN* 1.3 86.2 + - - +
118N TYR* 1.3 66.7 + - - +
129N HIS* 5.1 2.6 - - - +
130N GLU 3.3 14.6 - - - -
131N VAL* 3.9 9.6 - - - -
132N ILE* 4.6 0.9 - - - +
169N ARG* 5.3 1.7 + - - -
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Residues in contact with TYR 118 (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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381A G 5.0 0.4 - - - +
43N PRO* 3.5 19.4 - - - +
44N THR 3.5 2.1 + - - -
45N ARG* 3.6 28.7 + - + +
48N ARG* 3.9 28.5 - - + +
49N ALA* 4.1 20.9 - - + -
52N LEU* 3.9 14.4 - - + -
62N VAL* 4.7 2.1 - - + +
98N GLN* 3.9 5.4 - - - +
117N SER* 1.3 80.8 - - - +
119N SER* 1.3 70.0 + - - +
120N VAL* 3.5 22.0 - - + -
129N HIS* 3.1 9.0 - - - -
130N GLU* 2.6 65.7 + - + +
132N ILE* 4.4 9.2 - - + -
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Residues in contact with SER 119 (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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381A G 4.5 22.9 + - - +
12N TRP* 4.4 1.6 - - - -
45N ARG* 2.8 34.5 + - - +
98N GLN* 4.8 1.4 - - - +
118N TYR* 1.3 75.4 - - - +
120N VAL* 1.3 60.5 + - - +
121N GLY* 3.3 15.0 + - - -
128N TRP 3.7 2.1 + - - -
129N HIS* 3.5 24.9 - - - -
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Residues in contact with VAL 120 (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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12N TRP* 3.7 16.3 - - + -
24N MET* 3.0 18.2 - - - +
31N TRP* 3.3 23.9 - - + -
44N THR* 4.2 9.0 - - - -
45N ARG* 4.2 4.9 - - + -
64N ARG* 4.4 3.4 - - + -
118N TYR* 3.5 32.3 - - + -
119N SER* 1.3 71.6 - - - +
121N GLY* 1.3 56.5 + - - +
128N TRP* 2.9 40.0 + - + +
129N HIS* 3.8 6.3 - - - +
130N GLU* 3.5 24.9 - - + +
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Residues in contact with GLY 121 (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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12N TRP* 4.1 6.5 - - - -
15N PRO* 6.2 2.0 - - - -
24N MET* 3.9 9.9 - - - -
28N MET* 4.2 0.4 - - - -
119N SER* 3.3 12.7 + - - -
120N VAL* 1.3 80.5 - - - +
122N GLU* 1.3 63.4 + - - +
127N LYS* 3.8 0.5 - - - +
128N TRP* 2.9 32.1 + - - +
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Residues in contact with GLU 122 (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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404A G 3.2 23.7 + - - -
2131A G 5.0 0.7 + - - -
2132A C 5.5 2.8 - - - +
28N MET* 3.3 18.7 - - - +
69N LYS* 3.3 18.9 + - - -
121N GLY* 1.3 76.5 - - - +
123N ASP* 1.3 63.2 + - - +
126N HIS 3.1 18.4 - - - +
127N LYS* 3.1 30.2 - - + +
128N TRP* 3.7 7.2 - - - -
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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