Contacts of the helix formed by residues 114 - 126 (chain y) 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 y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76y TYR* 2.9 21.2 + - - +
112y ASN 3.7 2.3 + - - +
113y ALA* 1.3 68.7 - - - +
115y PRO* 1.3 63.4 - - - +
116y GLN* 2.8 23.1 + - - +
117y VAL* 2.7 46.1 + - + +
118y LEU* 3.0 10.5 + - - +
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Residues in contact with PRO 115 (chain y).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104y LYS* 5.0 2.6 - - - +
108y ILE* 3.9 31.0 - - + -
113y ALA 3.2 9.8 - - - +
114y ASN* 1.3 90.4 - - - +
116y GLN* 1.3 56.8 + - - +
118y LEU* 3.2 15.0 + - + +
119y ASP* 2.9 37.4 + - - +
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Residues in contact with GLN 116 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66y TYR* 2.9 45.1 + - - -
114y ASN* 2.8 18.8 + - - +
115y PRO* 1.3 75.0 - - - +
117y VAL* 1.3 68.5 + - - +
119y ASP* 3.3 9.2 + - - +
120y ALA* 3.1 16.9 + - - +
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Residues in contact with VAL 117 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62y VAL* 5.3 0.7 - - + -
63y LEU* 4.1 13.2 - - + -
66y TYR* 4.1 27.8 - - + -
68y ILE* 4.9 7.4 - - + -
76y TYR* 3.7 37.9 - - + +
114y ASN* 2.7 28.5 + - + +
116y GLN* 1.3 83.5 - - - +
118y LEU* 1.3 65.3 - - - +
120y ALA* 3.0 16.6 + - + +
121y VAL* 3.0 14.4 + - + +
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Residues in contact with LEU 118 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76y TYR* 3.6 24.9 - - + -
79y PHE* 3.3 51.7 - - + -
104y LYS* 4.4 12.3 - - + +
107y TYR* 4.4 7.9 - - + -
108y ILE* 3.3 35.9 - - + -
113y ALA* 3.8 16.8 - - + -
114y ASN 3.0 10.9 + - - +
115y PRO* 3.4 12.6 - - + +
117y VAL* 1.3 77.5 - - - +
119y ASP* 1.3 61.4 + - - +
121y VAL* 3.1 3.8 + - - +
122y VAL* 3.0 20.1 + - - +
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Residues in contact with ASP 119 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104y LYS* 2.7 37.0 + - - +
115y PRO* 2.9 19.4 + - - +
116y GLN* 3.6 11.2 - - - +
117y VAL 3.2 0.2 - - - -
118y LEU* 1.3 73.4 - - - +
120y ALA* 1.3 59.9 + - - +
122y VAL* 3.2 7.9 + - - +
123y ASN* 2.8 29.9 + - - +
129y PRO* 4.3 25.0 - - + +
130y THR 5.6 0.9 + - - -
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Residues in contact with ALA 120 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62y VAL* 4.0 9.5 - - + +
66y TYR* 3.5 40.4 - - + +
116y GLN* 3.1 10.3 + - - +
117y VAL 3.0 12.6 + - - +
119y ASP* 1.3 77.0 - - - +
121y VAL* 1.3 60.5 + - - +
123y ASN* 3.3 20.2 + - - +
124y ILE* 3.4 14.6 - - - +
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Residues in contact with VAL 121 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59y VAL* 4.0 26.9 - - + -
62y VAL* 5.0 8.7 - - + -
63y LEU* 5.1 1.1 - - + -
76y TYR* 4.4 19.7 - - + +
79y PHE* 3.8 13.0 - - + -
80y GLY* 3.6 31.6 - - - +
117y VAL* 3.0 22.3 + - + +
118y LEU* 3.1 8.7 + - - +
120y ALA* 1.3 75.3 - - - +
122y VAL* 1.3 63.0 + - - +
124y ILE* 3.0 17.7 + - - +
125y ILE* 3.2 19.8 + - + +
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Residues in contact with VAL 122 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79y PHE* 3.6 24.0 - - + -
83y VAL* 4.5 7.0 - - + -
100y ILE* 4.2 21.3 - - + -
104y LYS* 5.0 1.1 - - + -
118y LEU 3.0 14.6 + - - +
119y ASP* 3.6 13.5 - - - +
121y VAL* 1.3 75.4 - - - +
123y ASN* 1.3 56.3 + - - +
124y ILE 2.9 1.2 + - - -
125y ILE* 4.6 4.9 - - - +
126y THR* 2.6 52.8 + - + +
128y SER 3.2 19.3 - - - +
129y PRO* 3.9 10.3 - - + -
130y THR* 4.1 7.4 - - - +
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Residues in contact with ASN 123 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119y ASP 2.8 17.9 + - - +
120y ALA* 3.4 11.6 - - - +
121y VAL 3.2 0.4 - - - -
122y VAL* 1.3 75.2 - - - +
124y ILE* 1.3 68.4 + - - +
127y GLY* 3.1 33.6 + - - +
128y SER* 3.4 16.7 + - - +
129y PRO* 3.5 11.6 - - + +
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Residues in contact with ILE 124 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58y ASN* 3.7 37.5 - - + +
59y VAL* 5.0 3.1 - - + +
62y VAL* 3.6 25.8 - - + -
120y ALA 3.4 14.4 - - - +
121y VAL* 3.0 7.4 + - - +
122y VAL 3.0 0.8 - - - -
123y ASN* 1.3 94.8 - - - +
125y ILE* 1.3 72.0 + - + +
126y THR 3.4 0.4 - - - -
127y GLY* 3.6 6.8 + - - -
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Residues in contact with ILE 125 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55y VAL* 3.9 24.7 - - + -
59y VAL* 4.4 5.8 - - + -
80y GLY* 3.2 42.2 - - - +
83y VAL* 3.7 26.9 - - + -
84y ALA* 4.5 14.6 - - + +
87y LEU* 4.8 16.7 - - + +
121y VAL* 3.2 20.0 + - + +
122y VAL* 4.2 1.8 - - - +
124y ILE* 1.3 81.8 - - + +
126y THR* 1.3 61.8 + - + +
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Residues in contact with THR 126 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83y VAL* 4.3 12.3 - - + -
87y LEU* 6.1 3.1 - - + -
96y LEU* 4.6 11.9 - - + -
100y ILE* 4.1 18.8 - - + -
122y VAL* 2.6 30.0 + - + +
124y ILE 4.2 0.4 - - - -
125y ILE* 1.3 79.5 - - + +
127y GLY* 1.3 57.2 + - - +
128y SER* 2.4 35.4 + - - -
134y SER* 5.1 6.1 - - - +
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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