Contacts of the helix formed by residues 114 - 126 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76X TYR* 2.9 20.8 + - + +
112X ASN 3.7 2.3 + - - +
113X ALA* 1.3 70.8 - - - +
115X PRO* 1.4 62.3 - - - +
116X GLN* 2.8 26.9 + - - +
117X VAL* 2.7 39.2 + - + +
118X LEU* 3.0 10.1 + - - +
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Residues in contact with PRO 115 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104X LYS* 4.5 8.3 - - - +
108X ILE* 3.9 28.7 - - + -
113X ALA 3.3 10.5 - - - +
114X ASN* 1.4 90.5 - - - +
116X GLN* 1.3 56.5 + - - +
118X LEU* 3.5 13.5 - - + +
119X ASP* 2.9 38.1 + - - +
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Residues in contact with GLN 116 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66X TYR* 3.2 36.3 + - + -
114X ASN* 2.8 23.1 + - - +
115X PRO* 1.3 75.7 - - - +
117X VAL* 1.3 62.9 + - + +
119X ASP* 3.4 8.9 + - - +
120X ALA* 3.1 18.1 + - - +
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Residues in contact with VAL 117 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62X VAL* 5.5 0.4 - - + -
63X LEU* 3.6 30.5 - - + -
66X TYR* 3.9 29.4 - - + -
68X ILE* 4.3 14.8 - - + -
76X TYR* 3.7 29.4 - - + +
114X ASN* 2.7 22.8 + - + +
116X GLN* 1.3 72.7 - - + +
118X LEU* 1.3 66.7 + - - +
120X ALA* 3.0 9.7 + - + +
121X VAL* 2.9 22.2 + - + +
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Residues in contact with LEU 118 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76X TYR* 3.7 20.9 - - + -
79X PHE* 3.3 53.4 - - + -
104X LYS* 4.0 18.8 - - + +
107X TYR* 4.4 2.7 - - + -
108X ILE* 3.3 35.2 - - + +
113X ALA* 3.8 18.6 - - + -
114X ASN 3.0 11.8 + - - +
115X PRO* 3.5 14.1 - - + +
117X VAL* 1.3 77.6 - - - +
119X ASP* 1.3 61.8 + - - +
121X VAL* 3.2 2.1 + - - -
122X VAL* 3.1 20.1 + - - +
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Residues in contact with ASP 119 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104X LYS* 2.7 37.7 + - - +
115X PRO* 2.9 22.6 + - - +
116X GLN* 3.6 11.7 - - - +
118X LEU* 1.3 72.5 - - - +
120X ALA* 1.3 60.7 + - - +
122X VAL* 3.1 9.5 + - - +
123X ASN* 2.8 43.7 + - - +
129X PRO* 5.4 13.4 - - + +
130X THR* 5.2 3.6 - - - +
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Residues in contact with ALA 120 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62X VAL* 3.8 12.5 - - + +
66X TYR* 3.5 39.7 - - + +
116X GLN* 3.1 5.9 + - - +
117X VAL* 3.0 10.4 + - - +
119X ASP* 1.3 78.5 - - - +
121X VAL* 1.3 62.7 + - - +
123X ASN* 3.1 20.5 + - - +
124X ILE* 3.3 18.0 + - - +
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Residues in contact with VAL 121 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59X VAL* 4.1 26.7 - - + -
62X VAL* 5.4 4.7 - - + -
63X LEU* 5.0 2.7 - - + -
76X TYR* 4.2 21.1 - - + +
79X PHE* 3.8 13.2 - - + -
80X GLY* 3.5 32.8 - - - +
117X VAL* 2.9 22.7 + - + +
118X LEU* 3.5 8.1 - - - +
120X ALA* 1.3 75.7 - - + +
122X VAL* 1.3 62.5 + - - +
124X ILE* 3.0 18.8 + - - +
125X ILE* 3.2 19.1 + - + +
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Residues in contact with VAL 122 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79X PHE* 3.7 23.6 - - + -
83X VAL* 4.6 7.0 - - + -
100X ILE* 4.3 20.9 - - + -
104X LYS* 6.0 1.8 - - + -
118X LEU 3.1 14.9 + - - +
119X ASP* 3.5 12.1 - - - +
121X VAL* 1.3 77.1 - - - +
123X ASN* 1.3 55.5 + - - +
124X ILE 3.0 0.7 + - - -
125X ILE* 4.6 4.9 - - - +
126X THR* 2.5 53.3 + - + +
128X SER 3.2 22.9 - - - +
129X PRO* 4.3 7.0 - - + -
130X THR* 4.4 7.9 - - + +
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Residues in contact with ASN 123 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119X ASP* 2.8 29.8 + - - +
120X ALA* 3.1 11.9 + - - +
122X VAL* 1.3 74.2 - - - +
124X ILE* 1.3 64.3 + - + +
127X GLY* 3.2 26.4 - - - +
128X SER* 3.1 1.6 - - - -
129X PRO* 3.0 44.3 - - - +
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Residues in contact with ILE 124 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55X VAL* 5.6 1.8 - - - +
58X ASN* 3.6 39.3 - - + +
59X VAL* 4.7 6.1 - - + +
62X VAL* 3.7 28.3 - - + -
120X ALA 3.3 15.9 - - - +
121X VAL* 3.4 9.2 - - - +
122X VAL 3.0 0.8 - - - -
123X ASN* 1.3 85.6 - - + +
125X ILE* 1.3 71.0 + - + +
126X THR 3.4 0.7 - - - -
127X GLY* 3.9 5.0 + - - -
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Residues in contact with ILE 125 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55X VAL* 4.0 25.4 - - + -
59X VAL* 4.7 2.0 - - + -
80X GLY* 3.1 42.6 - - - +
83X VAL* 3.9 25.8 - - + -
84X ALA* 4.4 15.9 - - + +
87X LEU* 4.5 18.8 - - + +
121X VAL* 3.2 19.8 + - + +
122X VAL 4.2 1.8 - - - +
124X ILE* 1.3 83.5 - - + +
126X THR* 1.3 62.5 + - + +
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Residues in contact with THR 126 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83X VAL* 4.5 4.0 - - + -
87X LEU* 6.0 3.1 - - + -
96X LEU* 4.8 11.0 - - + -
100X ILE* 4.1 20.4 - - + -
122X VAL* 2.5 36.1 + - + +
124X ILE 4.4 0.2 - - - -
125X ILE* 1.3 84.7 - - + +
127X GLY* 1.3 58.6 + - - +
128X SER* 2.5 31.7 + - - -
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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