Contacts of the helix formed by residues 123 - 133 (chain A) in PDB entry 3NA0
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 ILE 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A PHE* 4.0 5.1 + - + -
122A LEU* 1.3 72.8 - - - +
124A PRO* 1.3 68.2 - - + +
125A PRO* 3.6 25.8 - - + -
126A TRP* 3.0 57.1 + - + +
127A VAL* 3.0 14.1 + - - +
141A LEU* 5.6 1.6 - - - +
248A LEU* 4.3 10.1 - - + -
499A LEU* 3.5 42.6 - - + -
602A 2DC 4.0 31.4 - - + -
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Residues in contact with PRO 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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96A VAL* 6.1 1.8 - - + -
121A PHE* 3.9 21.3 - - + -
122A LEU 3.3 9.8 - - - +
123A ILE* 1.3 83.5 - - + +
125A PRO* 1.4 73.6 - - + +
127A VAL* 3.2 7.7 + - + +
128A ALA* 2.9 25.8 + - - +
247A MET 5.0 0.2 - - - +
248A LEU* 4.1 14.6 - - + +
250A LEU 4.0 11.4 - - - +
251A PRO* 5.5 0.4 - - + -
252A PRO* 4.9 9.3 - - + +
255A PHE* 3.8 15.9 - - + -
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Residues in contact with PRO 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ILE* 3.6 14.6 - - + -
124A PRO* 1.4 97.8 - - + +
126A TRP* 1.3 65.4 + - + +
128A ALA 3.5 0.2 + - - -
129A TYR* 3.1 23.9 + - - +
244A SER* 4.1 22.0 - - - +
247A MET* 4.1 24.5 - - + +
248A LEU* 4.9 1.8 - - - -
255A PHE* 3.6 22.8 - - + -
263A TRP* 3.7 6.1 - - + -
266A HIS* 3.8 21.4 + - + +
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Residues in contact with TRP 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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123A ILE* 3.0 38.8 + - + +
125A PRO* 1.3 76.9 - - + +
127A VAL* 1.3 60.7 + - - +
129A TYR* 3.4 2.1 + - - +
130A HIS* 2.8 36.4 + + + +
140A LEU* 3.8 31.9 - - + -
141A LEU* 4.8 9.9 - - + -
240A MET* 3.2 13.6 - - + -
241A PHE* 3.5 31.6 - + - -
244A SER* 2.8 21.4 + - - -
266A HIS* 3.6 16.8 - + - -
270A TRP* 3.7 25.6 - + + +
499A LEU* 3.4 28.9 - - + -
602A 2DC 4.2 23.1 - - + -
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Residues in contact with VAL 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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122A LEU* 3.8 33.7 - - + -
123A ILE 3.0 17.5 + - - +
124A PRO* 3.2 8.9 + - + +
126A TRP* 1.3 77.0 - - - +
128A ALA* 1.3 57.3 + - - +
130A HIS* 3.2 4.9 + - - +
131A GLN* 3.0 53.6 + - + +
141A LEU* 4.1 22.7 - - + -
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Residues in contact with ALA 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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124A PRO 2.9 17.8 + - - +
125A PRO 3.9 0.7 - - - +
127A VAL* 1.3 74.1 - - - +
129A TYR* 1.3 60.0 + - - +
131A GLN* 3.9 9.1 - - - +
132A TYR* 2.8 36.5 + - + +
252A PRO* 4.3 15.9 - - + -
255A PHE* 4.1 13.7 - - + -
263A TRP* 3.9 18.4 - - + -
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Residues in contact with TYR 129 (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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125A PRO 3.1 17.6 + - - +
126A TRP 3.6 3.8 - - - +
128A ALA* 1.3 75.2 - - - +
130A HIS* 1.3 74.2 + - - +
133A TYR* 3.1 43.8 + + - +
135A ARG* 3.3 35.1 + - + -
263A TRP* 3.6 12.5 - - + -
266A HIS* 5.0 0.7 - - + -
267A VAL* 3.7 33.0 - - + -
270A TRP* 3.2 49.6 + + + -
271A ASP* 2.7 33.1 + - - -
274A PHE* 3.6 11.3 - + - -
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Residues in contact with HIS 130 (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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126A TRP* 2.8 22.4 + - + -
127A VAL 3.2 8.3 + - - +
129A TYR* 1.3 86.1 - + - +
131A GLN* 1.3 58.6 + - + +
134A GLN* 3.0 8.8 + - - -
135A ARG* 2.9 37.1 + - + +
136A PRO 4.0 5.1 + - - -
137A ILE* 3.8 30.1 - - + -
140A LEU* 6.4 0.9 - - + -
141A LEU* 3.3 23.0 - - + +
270A TRP* 3.9 31.9 - + - -
274A PHE* 3.3 34.3 - + - -
322A GLU* 4.9 8.5 + - + +
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Residues in contact with GLN 131 (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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127A VAL* 3.0 40.3 + - + +
128A ALA* 3.9 6.7 - - - +
130A HIS* 1.3 77.5 - - + +
132A TYR* 1.3 64.5 + - - +
134A GLN* 3.2 22.6 + - - +
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Residues in contact with TYR 132 (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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128A ALA* 2.8 22.6 + - + +
131A GLN* 1.3 75.0 - - - +
133A TYR* 1.3 96.3 + + + +
134A GLN* 3.3 5.4 + - - +
263A TRP* 5.3 7.2 - + + -
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Residues in contact with TYR 133 (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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129A TYR* 3.1 36.4 + + + +
132A TYR* 1.3 107.1 - + + +
134A GLN* 1.3 71.8 + - - +
135A ARG* 3.4 36.0 + - + +
263A TRP* 4.4 11.3 + + - -
267A VAL* 3.7 38.5 - - + +
271A ASP* 5.5 2.5 - - - -
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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