Contacts of the helix formed by residues 114 - 126 (chain m) 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 m).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76m TYR* 2.9 21.7 + - - +
112m ASN 3.7 2.0 + - - +
113m ALA* 1.3 69.8 - - - +
115m PRO* 1.3 62.1 - - - +
116m GLN* 2.8 23.1 + - - +
117m VAL* 2.7 44.9 + - + +
118m LEU* 3.0 10.6 + - - +
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Residues in contact with PRO 115 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104m LYS* 5.0 3.0 - - - +
108m ILE* 3.9 31.9 - - + -
113m ALA 3.2 10.0 - - - +
114m ASN* 1.3 88.7 - - - +
116m GLN* 1.3 56.9 + - - +
118m LEU* 3.2 15.1 + - + +
119m ASP* 2.9 37.4 + - - +
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Residues in contact with GLN 116 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66m TYR* 2.9 44.9 + - - -
114m ASN* 2.8 19.1 + - - +
115m PRO* 1.3 74.8 - - - +
117m VAL* 1.3 69.9 + - - +
119m ASP* 3.3 9.3 + - - +
120m ALA* 3.1 16.9 + - - +
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Residues in contact with VAL 117 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62m VAL* 5.3 0.7 - - + -
63m LEU* 4.1 13.5 - - + -
66m TYR* 4.1 28.0 - - + -
68m ILE* 4.9 7.6 - - + -
76m TYR* 3.7 37.5 - - + +
114m ASN* 2.7 28.2 + - + +
116m GLN* 1.3 83.1 - - - +
118m LEU* 1.3 67.0 + - - +
120m ALA* 2.9 16.6 + - + +
121m VAL* 3.0 14.7 + - + +
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Residues in contact with LEU 118 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76m TYR* 3.6 24.0 - - + -
79m PHE* 3.3 51.2 - - + -
104m LYS* 4.4 12.1 - - + +
107m TYR* 4.4 8.1 - - + -
108m ILE* 3.3 36.1 - - + -
113m ALA* 3.8 17.5 - - + -
114m ASN 3.0 10.9 + - - +
115m PRO* 3.4 12.3 - - + +
117m VAL* 1.3 77.5 - - - +
119m ASP* 1.3 62.2 + - - +
121m VAL* 3.1 3.8 + - - -
122m VAL* 3.0 20.1 + - - +
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Residues in contact with ASP 119 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104m LYS* 2.7 36.9 + - - +
115m PRO* 2.9 19.0 + - - +
116m GLN* 3.6 11.2 - - - +
117m VAL 3.2 0.2 - - - -
118m LEU* 1.3 73.4 - - - +
120m ALA* 1.3 60.6 + - - +
122m VAL* 3.2 8.1 + - - +
123m ASN* 2.8 31.0 + - - +
129m PRO* 4.3 26.0 - - + +
130m THR* 5.6 0.7 + - - +
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Residues in contact with ALA 120 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62m VAL* 4.0 9.5 - - + +
66m TYR* 3.5 39.9 - - + +
116m GLN* 3.1 10.6 + - - +
117m VAL 2.9 12.2 + - - +
119m ASP* 1.3 77.4 - - - +
121m VAL* 1.3 60.5 + - - +
123m ASN* 3.3 19.5 + - - +
124m ILE* 3.4 14.6 - - - +
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Residues in contact with VAL 121 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59m VAL* 4.0 26.2 - - + -
62m VAL* 5.0 9.2 - - + -
63m LEU* 5.1 0.7 - - + -
76m TYR* 4.4 20.2 - - + +
79m PHE* 3.8 13.0 - - + -
80m GLY* 3.6 31.2 - - - +
117m VAL* 3.0 21.4 + - + +
118m LEU* 3.1 8.7 + - - +
120m ALA* 1.3 76.9 - - - +
122m VAL* 1.3 62.6 + - - +
124m ILE* 3.0 17.7 + - - +
125m ILE* 3.2 19.2 + - + +
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Residues in contact with VAL 122 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79m PHE* 3.6 23.3 - - + -
83m VAL* 4.5 7.2 - - + -
100m ILE* 4.2 20.9 - - + -
104m LYS* 5.0 1.1 - - + -
118m LEU 3.0 15.6 + - - +
119m ASP* 3.2 13.9 + - - +
121m VAL* 1.3 76.4 - - - +
123m ASN* 1.3 55.2 + - - +
124m ILE 2.9 1.2 + - - -
125m ILE* 4.6 4.9 - - - +
126m THR* 2.6 53.2 + - + +
128m SER 3.2 20.9 - - - +
129m PRO* 3.9 9.4 - - + -
130m THR* 4.1 7.4 - - - +
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Residues in contact with ASN 123 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119m ASP 2.8 17.5 + - - +
120m ALA* 3.4 11.4 + - - +
121m VAL 3.2 0.2 - - - -
122m VAL* 1.3 75.2 - - - +
124m ILE* 1.3 68.1 + - - +
127m GLY* 3.1 33.4 + - - +
128m SER* 3.4 16.2 - - - +
129m PRO* 3.5 12.0 - - + +
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Residues in contact with ILE 124 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58m ASN* 3.7 37.7 - - + +
59m VAL* 5.0 3.6 - - + +
62m VAL* 3.6 25.6 - - + -
120m ALA 3.4 14.4 - - - +
121m VAL* 3.0 6.9 + - - +
122m VAL 3.0 0.8 - - - -
123m ASN* 1.3 93.9 - - - +
125m ILE* 1.3 71.8 + - + +
126m THR 3.4 0.6 + - - -
127m GLY* 3.6 5.9 + - - -
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Residues in contact with ILE 125 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55m VAL* 3.9 24.7 - - + -
59m VAL* 4.4 4.9 - - + -
80m GLY* 3.2 42.2 - - - +
83m VAL* 3.7 26.2 - - + -
84m ALA* 4.5 15.3 - - + +
87m LEU* 4.8 16.9 - - + +
121m VAL* 3.2 20.5 + - + +
122m VAL* 4.2 1.6 - - - +
124m ILE* 1.3 81.8 - - + +
126m THR* 1.3 61.4 + - + +
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Residues in contact with THR 126 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83m VAL* 4.3 12.6 - - + -
87m LEU* 6.1 2.9 - - + -
96m LEU* 4.6 12.8 - - + -
100m ILE* 4.1 18.2 - - + -
122m VAL* 2.6 28.8 + - + +
124m ILE 4.2 0.2 - - - -
125m ILE* 1.3 80.5 - - + +
127m GLY* 1.3 57.5 + - - +
128m SER* 2.4 34.5 + - - -
130m THR* 6.3 0.4 - - - -
134m SER* 5.1 6.4 - - - +
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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