Contacts of the helix formed by residues 114 - 126 (chain W) 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 W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76W TYR* 2.9 22.1 + - - +
112W ASN 3.7 1.8 + - - +
113W ALA* 1.3 70.9 - - - +
115W PRO* 1.3 63.9 - - - +
116W GLN* 2.8 23.5 + - - +
117W VAL* 2.7 45.1 + - + +
118W LEU* 3.0 10.7 + - - +
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Residues in contact with PRO 115 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104W LYS* 5.0 2.9 - - - +
108W ILE* 3.9 32.8 - - + -
113W ALA 3.2 10.0 - - - +
114W ASN* 1.3 91.2 - - - +
116W GLN* 1.3 54.9 + - - +
118W LEU* 3.2 15.3 + - + +
119W ASP* 2.9 37.7 + - - +
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Residues in contact with GLN 116 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66W TYR* 2.9 44.4 + - - -
114W ASN* 2.8 18.5 + - - +
115W PRO* 1.3 75.2 - - - +
117W VAL* 1.3 69.9 + - - +
119W ASP* 3.3 10.2 + - + +
120W ALA* 3.1 16.8 + - - +
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Residues in contact with VAL 117 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62W VAL* 5.3 0.9 - - + -
63W LEU* 4.1 12.8 - - + -
66W TYR* 4.1 28.3 - - + -
68W ILE* 4.9 8.1 - - + -
76W TYR* 3.7 37.9 - - + +
114W ASN* 2.7 28.1 + - + +
116W GLN* 1.3 85.5 - - - +
118W LEU* 1.3 65.9 - - - +
120W ALA* 2.9 16.0 + - + +
121W VAL* 3.0 14.0 + - + +
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Residues in contact with LEU 118 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76W TYR* 3.6 23.8 - - + -
79W PHE* 3.3 51.8 - - + -
104W LYS* 4.4 11.4 - - + +
107W TYR* 4.4 7.9 - - + -
108W ILE* 3.3 35.7 - - + -
113W ALA* 3.8 18.2 - - + -
114W ASN 3.0 10.8 + - - +
115W PRO* 3.4 12.3 - - + +
117W VAL* 1.3 77.4 - - - +
119W ASP* 1.3 63.8 + - - +
121W VAL* 3.1 4.7 + - - +
122W VAL* 3.0 19.6 + - - +
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Residues in contact with ASP 119 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104W LYS* 2.7 37.0 + - - +
115W PRO* 2.9 18.5 + - - +
116W GLN* 3.6 10.2 - - - +
118W LEU* 1.3 73.5 - - - +
120W ALA* 1.3 61.0 + - - +
122W VAL* 3.2 8.3 + - - +
123W ASN* 2.8 29.7 + - - +
129W PRO* 4.3 26.2 - - + +
130W THR* 5.6 0.9 + - - +
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Residues in contact with ALA 120 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62W VAL* 4.0 9.0 - - + +
66W TYR* 3.5 39.7 - - + +
116W GLN* 3.1 10.5 + - - +
117W VAL 2.9 12.2 + - - +
119W ASP* 1.3 77.5 - - - +
121W VAL* 1.3 60.9 + - - +
123W ASN* 3.3 20.1 + - - +
124W ILE* 3.4 15.0 - - - +
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Residues in contact with VAL 121 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59W VAL* 4.0 27.6 - - + -
62W VAL* 5.0 8.3 - - + -
63W LEU* 5.1 0.9 - - + -
76W TYR* 4.4 19.3 - - + +
79W PHE* 3.8 13.5 - - + -
80W GLY* 3.6 30.5 - - - +
117W VAL* 3.0 22.7 + - + +
118W LEU* 3.4 8.3 - - - +
120W ALA* 1.3 75.9 - - - +
122W VAL* 1.3 62.7 + - - +
124W ILE* 3.0 17.3 + - - +
125W ILE* 3.2 20.4 + - + +
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Residues in contact with VAL 122 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79W PHE* 3.6 24.5 - - + -
83W VAL* 4.5 7.2 - - + -
100W ILE* 4.2 20.6 - - + -
104W LYS* 5.0 1.3 - - + -
118W LEU 3.0 15.6 + - - +
119W ASP* 3.6 13.5 - - - +
121W VAL* 1.3 74.6 - - - +
123W ASN* 1.3 54.4 + - - +
124W ILE 2.9 1.9 + - - -
125W ILE* 3.2 5.3 + - - +
126W THR* 2.6 52.6 + - + +
128W SER 3.2 19.5 - - - +
129W PRO* 3.9 10.1 - - + -
130W THR* 4.1 7.9 - - + +
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Residues in contact with ASN 123 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1232 ASN* 3.8 17.0 + - - +
1272 GLY 3.4 24.2 + - - -
119W ASP 2.8 18.5 + - - +
120W ALA* 3.4 11.0 - - - +
121W VAL 3.2 0.4 - - - -
122W VAL* 1.3 74.3 - - - +
124W ILE* 1.3 59.8 + - - +
127W GLY* 3.1 33.3 + - - +
128W SER* 3.4 16.6 - - - +
129W PRO* 3.5 10.8 - - + +
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Residues in contact with ILE 124 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582 ASN* 4.3 10.9 + - - +
1232 ASN 3.9 3.8 - - - +
1242 ILE* 4.1 25.4 - - - +
1262 THR 4.8 0.9 - - - +
1272 GLY* 3.3 34.8 - - - +
58W ASN* 3.7 35.7 - - + +
59W VAL* 5.0 2.9 - - + +
62W VAL* 3.6 24.7 - - + -
120W ALA 3.4 14.1 - - - +
121W VAL* 3.0 7.3 + - - +
122W VAL 3.0 0.8 - - - -
123W ASN* 1.3 89.3 - - - +
125W ILE* 1.3 71.0 + - + +
126W THR 3.4 0.6 + - - -
127W GLY 3.6 4.7 + - - -
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Residues in contact with ILE 125 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582 ASN* 4.2 17.3 - - - +
55W VAL* 3.9 25.4 - - + -
59W VAL* 4.4 5.2 - - + -
80W GLY* 3.2 42.6 - - - +
83W VAL* 3.7 26.9 - - + -
84W ALA* 4.5 13.9 - - + +
87W LEU* 4.8 16.3 - - + +
121W VAL* 3.2 20.3 + - + +
122W VAL* 4.2 1.6 - - - +
124W ILE* 1.3 81.2 - - + +
126W THR* 1.3 60.9 + - + +
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Residues in contact with THR 126 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612 ALA* 5.9 3.1 - - - +
622 VAL* 5.0 6.9 - - - +
652 GLN* 6.0 1.2 - - - +
1242 ILE* 5.0 1.4 - - - +
83W VAL* 4.3 13.0 - - + -
87W LEU* 6.1 2.2 - - + -
96W LEU* 4.6 12.3 - - + -
100W ILE* 4.1 18.2 - - + -
122W VAL* 2.6 30.1 + - + +
124W ILE 4.2 0.4 - - - -
125W ILE* 1.3 80.0 - - + +
127W GLY* 1.3 56.8 + - - +
128W SER* 2.4 34.1 + - - -
134W SER* 5.1 6.6 - - - +
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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