Contacts of the helix formed by residues 114 - 126 (chain D) in PDB entry 3J9X
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 ASN 114 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76D TYR* 2.9 20.6 + - - +
112D ASN 3.7 2.5 + - - +
113D ALA* 1.3 70.2 - - - +
115D PRO* 1.4 62.7 - - - +
116D GLN* 2.8 26.1 + - - +
117D VAL* 2.7 39.1 + - + +
118D LEU* 3.0 10.5 + - - +
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Residues in contact with PRO 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D LYS* 4.5 8.3 - - - +
108D ILE* 3.9 29.6 - - + -
113D ALA 3.3 9.6 - - - +
114D ASN* 1.4 90.5 - - - +
116D GLN* 1.3 56.2 + - - +
118D LEU* 3.3 14.2 + - + +
119D ASP* 2.9 38.3 + - - +
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Residues in contact with GLN 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D TYR* 3.2 36.1 + - + -
114D ASN* 2.8 21.8 + - - +
115D PRO* 1.3 74.6 - - - +
117D VAL* 1.3 61.7 + - + +
119D ASP* 3.4 9.3 + - - +
120D ALA* 3.1 17.7 + - - +
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Residues in contact with VAL 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D VAL* 5.5 0.7 - - + -
63D LEU* 3.6 31.0 - - + -
66D TYR* 3.9 29.2 - - + -
68D ILE* 4.3 15.0 - - + -
76D TYR* 3.7 30.1 - - + +
114D ASN* 2.7 22.7 + - + +
116D GLN* 1.3 72.0 - - + +
118D LEU* 1.3 66.1 + - - +
120D ALA* 3.0 9.3 + - + +
121D VAL* 2.9 22.5 + - + +
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Residues in contact with LEU 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D TYR* 3.7 21.3 - - + -
79D PHE* 3.3 52.7 - - + -
104D LYS* 4.0 17.9 - - + +
107D TYR* 4.4 1.8 - - + -
108D ILE* 3.3 35.4 - - + +
113D ALA* 3.8 18.4 - - + -
114D ASN 3.0 11.3 + - - +
115D PRO* 3.5 14.6 - - + +
116D GLN 3.2 0.2 - - - -
117D VAL* 1.3 77.1 - - - +
119D ASP* 1.3 61.2 + - - +
121D VAL* 3.2 3.4 + - - +
122D VAL* 3.1 21.2 + - - +
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Residues in contact with ASP 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D LYS* 2.7 36.3 + - - +
115D PRO* 2.9 22.8 + - - +
116D GLN* 3.6 11.5 - - - +
118D LEU* 1.3 72.9 - - - +
120D ALA* 1.3 60.7 + - - +
122D VAL* 3.1 8.4 + - - +
123D ASN* 2.8 42.7 + - - +
129D PRO* 5.4 13.9 - - + +
130D THR* 5.2 3.8 - - - +
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Residues in contact with ALA 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D VAL* 3.8 11.7 - - + -
66D TYR* 3.5 40.2 - - + +
116D GLN* 3.1 5.7 + - - +
117D VAL 3.0 10.4 + - - +
119D ASP* 1.3 79.1 - - - +
121D VAL* 1.3 62.6 + - - +
123D ASN* 3.1 20.2 + - - +
124D ILE* 3.3 18.2 + - - +
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Residues in contact with VAL 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D VAL* 4.1 25.6 - - + -
62D VAL* 5.4 4.9 - - + -
63D LEU* 5.0 2.0 - - + -
76D TYR* 4.2 22.4 - - + +
79D PHE* 3.8 12.8 - - + -
80D GLY* 3.5 32.8 - - - -
117D VAL* 2.9 21.2 + - + +
118D LEU* 3.5 8.1 - - - +
119D ASP 3.2 0.2 - - - -
120D ALA* 1.3 77.0 - - + +
122D VAL* 1.3 62.1 + - - +
124D ILE* 3.0 17.9 + - - +
125D ILE* 3.2 19.4 + - + +
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Residues in contact with VAL 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D PHE* 3.7 23.6 - - + -
83D VAL* 4.6 7.4 - - + -
100D ILE* 4.3 21.1 - - + -
104D LYS* 6.0 1.6 - - + -
118D LEU 3.1 14.2 + - - +
119D ASP* 3.1 12.3 + - - +
121D VAL* 1.3 75.7 - - - +
123D ASN* 1.3 54.9 + - - +
124D ILE 3.0 0.9 + - - -
125D ILE* 4.6 4.9 - - - +
126D THR* 2.5 53.1 + - + +
128D SER 3.2 22.2 - - - +
129D PRO* 4.3 7.0 - - + -
130D THR* 4.4 8.1 - - + +
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Residues in contact with ASN 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D ASP* 2.8 28.6 + - - +
120D ALA* 3.1 12.1 + - - +
122D VAL* 1.3 76.8 - - - +
124D ILE* 1.3 62.8 + - + +
127D GLY* 3.2 26.4 - - - +
128D SER* 3.1 1.2 - - - -
129D PRO* 3.0 44.9 - - - +
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Residues in contact with ILE 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D VAL* 6.1 1.6 - - - -
58D ASN* 3.6 40.2 - - + +
59D VAL* 4.7 5.4 - - + +
62D VAL* 3.7 29.2 - - + -
120D ALA 3.3 15.0 - - - +
121D VAL* 3.0 8.9 + - - +
122D VAL 3.0 0.6 - - - -
123D ASN* 1.3 86.2 - - + +
125D ILE* 1.3 72.1 + - + +
126D THR 3.4 0.4 - - - -
127D GLY* 3.9 4.2 + - - -
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Residues in contact with ILE 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D VAL* 4.0 25.6 - - + -
59D VAL* 4.7 1.8 - - + -
80D GLY* 3.1 42.8 - - - +
83D VAL* 3.9 26.7 - - + -
84D ALA* 4.4 15.3 - - + +
87D LEU* 4.5 19.3 - - + +
121D VAL* 3.2 18.9 + - + +
122D VAL 4.2 1.1 - - - +
124D ILE* 1.3 84.2 - - + +
126D THR* 1.3 62.5 + - + +
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Residues in contact with THR 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D VAL* 4.5 4.3 - - + -
87D LEU* 6.0 3.1 - - + -
96D LEU* 4.8 11.2 - - + -
100D ILE* 4.1 20.4 - - + -
122D VAL* 2.5 36.0 + - + +
124D ILE 4.4 0.4 - - - -
125D ILE* 1.3 84.9 - - + +
127D GLY* 1.3 58.8 + - - +
128D SER* 2.5 31.2 + - - +
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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