Contacts of the helix formed by residues 114 - 126 (chain U) 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 U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76U TYR* 2.9 21.2 + - - +
112U ASN 3.7 2.0 + - - +
113U ALA* 1.3 70.9 - - - +
115U PRO* 1.3 62.5 - - - +
116U GLN* 2.8 23.6 + - - +
117U VAL* 2.7 44.9 + - + +
118U LEU* 3.0 10.3 + - - +
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Residues in contact with PRO 115 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104U LYS* 5.0 2.4 - - - +
108U ILE* 3.9 31.4 - - + -
113U ALA 3.2 10.4 - - - +
114U ASN* 1.3 88.1 - - - +
116U GLN* 1.3 56.0 + - - +
118U LEU* 3.2 15.0 + - + +
119U ASP* 2.9 36.6 + - - +
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Residues in contact with GLN 116 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66U TYR* 2.9 45.5 + - - -
114U ASN* 2.8 18.8 + - - +
115U PRO* 1.3 75.0 - - - +
117U VAL* 1.3 69.4 + - - +
119U ASP* 3.3 9.7 + - - +
120U ALA* 3.1 17.0 + - - +
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Residues in contact with VAL 117 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62U VAL* 5.3 0.7 - - + -
63U LEU* 4.1 13.5 - - + -
66U TYR* 4.1 27.6 - - + -
68U ILE* 4.9 7.6 - - + -
76U TYR* 3.7 37.5 - - + +
114U ASN* 2.7 28.0 + - + +
116U GLN* 1.3 83.7 - - - +
118U LEU* 1.3 65.5 + - - +
120U ALA* 3.0 16.8 + - + +
121U VAL* 3.0 14.2 + - + +
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Residues in contact with LEU 118 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76U TYR* 3.6 24.5 - - + -
79U PHE* 3.3 50.9 - - + -
104U LYS* 4.4 11.9 - - + +
107U TYR* 4.4 7.6 - - + -
108U ILE* 3.3 36.1 - - + -
113U ALA* 3.8 17.5 - - + -
114U ASN 3.0 10.2 + - - +
115U PRO* 3.4 12.3 - - + +
117U VAL* 1.3 77.7 - - - +
119U ASP* 1.3 62.4 + - - +
121U VAL* 3.1 4.3 + - - -
122U VAL* 3.0 20.1 + - - +
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Residues in contact with ASP 119 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104U LYS* 2.7 37.2 + - - +
115U PRO* 2.9 19.9 + - - +
116U GLN* 3.6 11.8 - - + +
117U VAL 3.2 0.2 - - - -
118U LEU* 1.3 72.8 - - - +
120U ALA* 1.3 61.4 + - - +
122U VAL* 3.2 8.0 + - - +
123U ASN* 2.8 31.0 + - - +
129U PRO* 4.3 26.2 - - + +
130U THR* 5.6 0.7 + - - +
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Residues in contact with ALA 120 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62U VAL* 4.0 9.0 - - + +
66U TYR* 3.5 39.7 - - + +
116U GLN* 3.1 10.4 + - - +
117U VAL 3.0 12.4 + - - +
119U ASP* 1.3 76.5 - - - +
121U VAL* 1.3 60.3 + - - +
123U ASN* 3.3 20.0 + - - +
124U ILE* 3.4 14.8 - - - +
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Residues in contact with VAL 121 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59U VAL* 4.0 26.9 - - + -
62U VAL* 5.0 9.0 - - + -
63U LEU* 5.1 0.9 - - + -
76U TYR* 4.4 20.0 - - + +
79U PHE* 3.8 13.0 - - + -
80U GLY* 3.6 31.6 - - - +
117U VAL* 3.0 21.0 + - + +
118U LEU* 3.1 8.5 + - - +
120U ALA* 1.3 77.0 - - - +
122U VAL* 1.3 62.2 + - - +
124U ILE* 3.0 17.3 + - - +
125U ILE* 3.2 19.2 + - + +
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Residues in contact with VAL 122 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79U PHE* 3.6 23.6 - - + -
83U VAL* 4.5 7.2 - - + -
100U ILE* 4.2 20.9 - - + -
104U LYS* 5.0 1.6 - - + -
118U LEU 3.0 15.4 + - - +
119U ASP* 3.2 13.9 + - - +
121U VAL* 1.3 75.5 - - - +
123U ASN* 1.3 55.5 + - - +
124U ILE 2.9 1.4 + - - -
125U ILE* 4.6 4.9 - - - +
126U THR* 2.6 52.8 + - + +
128U SER 3.2 20.0 - - - +
129U PRO* 3.9 9.4 - - + -
130U THR* 4.1 7.4 - - - +
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Residues in contact with ASN 123 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119U ASP 2.8 17.3 + - - +
120U ALA* 3.4 11.6 + - - +
121U VAL 3.2 0.2 - - - -
122U VAL* 1.3 75.0 - - - +
124U ILE* 1.3 59.1 + - - +
127U GLY* 3.1 33.6 + - - +
128U SER* 3.4 16.7 - - - +
129U PRO* 3.5 11.6 - - + +
123z ASN* 3.8 16.7 + - - +
127z GLY 3.4 23.8 + - - -
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Residues in contact with ILE 124 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58U ASN* 3.7 35.4 - - + +
59U VAL* 5.0 3.4 - - + +
62U VAL* 3.6 24.0 - - + -
120U ALA 3.4 14.8 - - - +
121U VAL* 3.0 7.1 + - - +
122U VAL 3.0 0.8 - - - -
123U ASN* 1.3 88.3 - - - +
125U ILE* 1.3 72.0 + - + +
126U THR 3.4 0.4 + - - -
127U GLY 3.6 4.2 + - - -
58z ASN* 4.3 10.6 + - - +
123z ASN 3.9 4.3 - - - +
124z ILE* 4.1 25.5 - - - +
126z THR 4.8 0.7 - - - +
127z GLY* 3.3 34.3 - - - -
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Residues in contact with ILE 125 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55U VAL* 3.9 24.7 - - + -
59U VAL* 4.4 5.2 - - + -
80U GLY* 3.2 42.2 - - - +
83U VAL* 3.7 26.5 - - + -
84U ALA* 4.5 15.5 - - + +
87U LEU* 4.8 16.6 - - + +
121U VAL* 3.2 20.2 + - + +
122U VAL* 4.2 1.6 - - - +
124U ILE* 1.3 81.6 - - + +
126U THR* 1.3 61.0 + - + +
58z ASN* 4.2 16.8 - - - +
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Residues in contact with THR 126 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83U VAL* 4.3 12.8 - - + -
87U LEU* 6.1 2.2 - - + -
96U LEU* 4.6 13.0 - - + -
100U ILE* 4.1 18.8 - - + -
122U VAL* 2.6 28.6 + - + +
124U ILE 4.2 0.2 - - - -
125U ILE* 1.3 80.5 - - + +
127U GLY* 1.3 57.0 + - - +
128U SER* 2.4 34.6 + - - -
130U THR* 6.3 0.4 - - - -
134U SER* 5.1 6.6 - - - +
61z ALA* 5.9 2.8 - - - +
62z VAL* 5.0 6.2 - - - +
65z GLN* 6.0 1.0 - - - +
124z ILE* 5.0 1.4 - - - +
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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