Contacts of the helix formed by residues 114 - 128 (chain A) in PDB entry 1NR5
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 GLY 114 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ASP* 5.9 0.2 + - - -
47A ILE* 4.6 3.2 - - - +
113A GLY* 1.3 74.7 - - - +
115A GLY* 1.3 61.7 + - - -
116A VAL 3.3 0.3 + - - -
117A ILE* 3.3 3.4 + - - +
118A GLY* 2.9 26.3 + - - -
139A THR* 3.5 3.8 + - - -
140A THR* 3.7 17.3 - - - +
143A ALA* 3.8 7.2 - - - -
147A SER* 4.3 0.2 - - - -
400A NAD 3.1 27.5 + - - -
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Residues in contact with GLY 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A GLY* 1.3 68.9 - - - -
116A VAL* 1.3 60.0 + - - +
118A GLY* 3.8 2.2 - - - -
119A ASP* 2.9 36.0 + - - +
143A ALA* 4.0 0.6 - - - +
147A SER* 3.3 24.9 + - - -
400A NAD 2.9 35.5 + - - +
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Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A PRO 5.5 0.2 - - - +
80A GLY 3.3 36.8 - - - +
81A GLU* 3.9 19.3 - - - +
83A SER* 4.3 12.8 - - - -
84A LYS* 3.9 23.0 - - + +
115A GLY* 1.3 76.8 - - - +
117A ILE* 1.3 72.2 + - + +
120A LEU* 3.1 24.5 + - + +
400A NAD 3.1 39.8 + - - +
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Residues in contact with ILE 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 3.6 29.8 - - + +
43A THR* 4.0 18.6 - - - +
44A ASP* 4.0 28.5 - - + +
77A ARG* 4.5 11.9 - - + -
78A PRO 5.5 2.0 - - - +
79A PRO* 6.2 0.7 - - + -
83A SER* 5.8 0.9 - - - -
111A ALA* 4.4 2.2 - - + -
112A LEU 3.9 16.2 - - - +
113A GLY* 4.1 12.1 - - - +
114A GLY 3.3 8.3 + - - +
116A VAL* 1.3 85.5 - - + +
118A GLY* 1.3 56.8 + - - +
120A LEU* 4.7 10.3 - - + -
121A THR* 2.7 44.4 + - - +
400A NAD 4.2 1.7 + - - +
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Residues in contact with GLY 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ALA* 4.1 5.8 - - - -
113A GLY 5.1 1.3 - - - -
114A GLY 2.9 16.7 + - - -
115A GLY* 4.0 2.0 - - - -
117A ILE* 1.3 77.8 - - - +
119A ASP* 1.3 58.1 + - - +
121A THR* 4.2 0.2 - - - -
122A GLY* 2.9 28.6 + - - -
134A TYR* 4.7 0.2 - - - -
136A GLN* 3.5 35.2 + - - -
147A SER* 5.8 1.3 - - - -
153A THR* 4.5 1.6 - - - +
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Residues in contact with ASP 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LYS* 2.8 29.0 + - + -
115A GLY* 2.9 23.6 + - - +
118A GLY* 1.3 76.5 - - - +
120A LEU* 1.3 61.9 + - - +
123A PHE* 3.2 24.9 + - - +
136A GLN* 5.7 0.2 + - - -
147A SER* 4.7 3.5 - - - +
152A LYS 3.8 2.7 - - - +
153A THR* 3.4 9.9 - - - +
154A ALA* 3.5 25.3 + - - +
162A ASN* 4.3 4.3 + - - +
400A NAD 2.9 42.9 + - - -
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 5.3 0.7 - - + -
77A ARG* 4.7 5.2 - - + -
83A SER* 3.7 26.2 - - - +
84A LYS* 4.6 6.5 - - + +
85A SER 4.2 3.8 - - - +
88A THR* 3.4 23.3 - - + -
89A LYS* 3.8 34.3 - - + +
92A ILE* 3.9 18.2 - - + -
116A VAL 3.1 16.9 + - - +
117A ILE* 4.0 11.7 - - + +
119A ASP* 1.3 77.3 - - - +
121A THR* 1.3 62.0 + - - +
123A PHE* 3.3 5.1 + - - +
124A VAL* 3.0 31.2 + - + +
154A ALA 4.3 5.1 + - - -
155A ILE* 4.3 8.7 - - + -
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Residues in contact with THR 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 3.4 31.3 - - + +
92A ILE* 5.8 0.7 - - - -
109A VAL* 3.2 33.5 - - + +
111A ALA* 3.8 24.7 - - + +
117A ILE* 2.7 26.1 + - - +
120A LEU* 1.3 78.1 - - - +
122A GLY* 1.3 58.8 + - - +
124A VAL* 3.3 7.4 + - + +
125A ALA* 2.9 27.2 + - - +
134A TYR* 4.8 4.5 - - + -
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Residues in contact with GLY 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A GLY 2.9 18.5 + - - -
121A THR* 1.3 76.6 - - - +
123A PHE* 1.3 57.3 + - - +
125A ALA* 3.4 3.2 + - - +
126A SER* 3.0 27.9 + - - -
134A TYR* 3.6 26.9 - - - -
153A THR* 3.6 14.0 - - - +
168A TRP* 4.0 4.5 - - - -
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Residues in contact with PHE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LYS* 3.5 31.0 - - + -
119A ASP 3.2 20.0 + - - +
120A LEU* 3.7 4.7 - - - +
122A GLY* 1.3 75.2 - - - +
124A VAL* 1.3 65.8 + - - +
126A SER* 2.7 30.4 + - - -
127A THR* 3.4 20.8 + - + -
153A THR* 3.4 14.0 - - - +
154A ALA 4.2 1.3 - - - +
155A ILE* 3.9 28.9 - - + -
164A ILE* 3.8 30.1 - - + -
165A GLY* 3.6 31.9 - - - -
166A ALA* 4.2 1.6 - - + -
603A CL 3.9 10.5 - - + -
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Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LYS* 4.0 37.5 - - + +
92A ILE* 4.0 35.9 - - + -
93A GLU* 4.1 14.2 - - + +
96A MET* 4.1 16.8 - - + -
109A VAL* 5.8 4.5 - - + -
120A LEU* 3.0 21.1 + - + +
121A THR* 3.6 10.5 - - + +
123A PHE* 1.3 78.2 - - - +
125A ALA* 1.3 64.0 + - - +
127A THR* 3.2 2.5 + - - -
128A TYR* 3.0 25.0 + - + +
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Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A VAL* 4.5 6.9 - - + +
121A THR 2.9 17.3 + - - +
122A GLY 3.5 4.9 - - - +
124A VAL* 1.3 81.1 - - - +
126A SER* 1.3 59.0 + - - +
127A THR 3.2 0.7 + - - -
128A TYR* 3.5 2.0 + - - -
131A GLY* 3.3 1.7 - - - -
132A VAL* 2.9 51.1 + - + +
134A TYR* 3.8 31.6 - - + -
168A TRP* 3.9 2.0 - - - -
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Residues in contact with SER 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A GLY 3.0 12.7 + - - -
123A PHE* 2.7 33.8 + - - -
125A ALA* 1.3 76.8 - - - +
127A THR* 1.3 63.2 + - - +
130A ARG 3.7 4.2 - - - +
131A GLY* 3.5 13.0 + - - -
166A ALA* 3.7 14.4 - - - +
168A TRP* 3.4 43.3 - - - +
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Residues in contact with THR 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LYS* 2.9 30.5 + - - +
93A GLU* 3.7 4.0 + - - -
123A PHE* 3.5 18.4 + - + -
124A VAL 3.2 3.6 + - - -
126A SER* 1.3 91.6 + - - +
128A TYR* 1.3 65.2 + - - +
129A MET 3.0 4.5 + - - -
130A ARG* 3.1 13.0 + - - +
131A GLY 4.2 0.4 - - - +
166A ALA* 5.6 1.8 - - + -
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Residues in contact with TYR 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A GLU* 4.0 20.6 - - + -
96A MET* 3.6 43.9 - - + -
97A LEU* 3.4 43.5 + - + +
103A CYS* 2.7 41.7 + - - +
104A GLY 4.1 5.4 - - - -
107A THR* 5.2 0.2 - - - -
124A VAL* 3.0 17.9 + - + +
125A ALA* 3.5 7.1 + - - +
127A THR* 1.3 72.0 - - - +
129A MET* 1.3 85.6 + - + +
131A GLY* 2.8 19.6 + - - -
132A VAL* 3.7 22.5 - - + +
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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