Contacts of the helix formed by residues 114 - 126 (chain Z) 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 Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76Z TYR* 2.9 21.6 + - - +
112Z ASN 3.7 2.5 + - - +
113Z ALA* 1.3 71.1 - - - +
115Z PRO* 1.4 63.8 - - - +
116Z GLN* 2.8 26.9 + - - +
117Z VAL* 2.7 39.5 + - + +
118Z LEU* 3.0 10.7 + - - +
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Residues in contact with PRO 115 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104Z LYS* 4.5 8.7 - - - +
108Z ILE* 3.9 28.9 - - + -
113Z ALA 3.3 10.5 - - - +
114Z ASN* 1.4 90.1 - - - +
116Z GLN* 1.3 55.4 + - - +
118Z LEU* 3.3 14.0 + - + +
119Z ASP* 2.9 38.7 + - - +
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Residues in contact with GLN 116 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66Z TYR* 3.2 36.1 + - + -
114Z ASN* 2.8 23.3 + - - +
115Z PRO* 1.3 75.4 - - - +
117Z VAL* 1.3 62.0 + - + +
119Z ASP* 3.4 10.1 + - - +
120Z ALA* 3.1 17.7 + - - +
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Residues in contact with VAL 117 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62Z VAL* 5.5 0.4 - - + -
63Z LEU* 3.6 30.1 - - + -
66Z TYR* 3.9 29.4 - - + -
68Z ILE* 4.3 15.0 - - + -
76Z TYR* 3.7 29.4 - - + +
114Z ASN* 2.7 21.5 + - + +
116Z GLN* 1.3 71.9 - - + +
118Z LEU* 1.3 66.5 - - - +
120Z ALA* 3.0 9.5 + - + +
121Z VAL* 2.9 22.7 + - + +
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Residues in contact with LEU 118 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76Z TYR* 3.7 21.1 - - + -
79Z PHE* 3.3 52.6 - - + -
104Z LYS* 4.0 18.6 - - + +
107Z TYR* 4.4 2.0 - - + -
108Z ILE* 3.3 35.4 - - + +
113Z ALA* 3.8 18.6 - - + -
114Z ASN 3.0 11.3 + - - +
115Z PRO* 3.5 14.1 - - + +
117Z VAL* 1.3 77.7 - - - +
119Z ASP* 1.3 61.5 + - - +
121Z VAL* 3.2 2.9 + - - +
122Z VAL* 3.1 20.1 + - - +
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Residues in contact with ASP 119 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104Z LYS* 2.7 37.1 + - - +
115Z PRO* 2.9 22.3 + - - +
116Z GLN* 3.6 11.9 - - - +
117Z VAL 3.2 0.2 - - - -
118Z LEU* 1.3 72.7 - - - +
120Z ALA* 1.3 60.8 + - - +
122Z VAL* 3.1 9.4 + - - +
123Z ASN* 2.8 41.6 + - - +
129Z PRO* 5.4 13.5 - - + +
130Z THR* 5.2 3.8 + - - +
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Residues in contact with ALA 120 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62Z VAL* 3.8 11.8 - - + +
66Z TYR* 3.5 39.5 - - + +
116Z GLN* 3.1 5.7 + - - +
117Z VAL 3.0 10.4 + - - +
119Z ASP* 1.3 79.8 - - - +
121Z VAL* 1.3 62.8 + - - +
123Z ASN* 3.1 21.1 + - - +
124Z ILE* 3.3 17.7 + - - +
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Residues in contact with VAL 121 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59Z VAL* 4.1 27.1 - - + -
62Z VAL* 5.4 4.7 - - + -
63Z LEU* 5.0 2.5 - - + -
76Z TYR* 4.2 21.8 - - + +
79Z PHE* 3.8 12.6 - - + -
80Z GLY* 3.5 32.3 - - - -
117Z VAL* 2.9 20.6 + - + +
118Z LEU* 3.5 8.3 - - - +
119Z ASP 3.2 0.2 - - - -
120Z ALA* 1.3 76.5 - - + +
122Z VAL* 1.3 62.6 + - - +
124Z ILE* 3.0 17.8 + - - +
125Z ILE* 3.2 19.4 + - + +
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Residues in contact with VAL 122 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79Z PHE* 3.7 23.6 - - + -
83Z VAL* 4.6 7.6 - - + -
100Z ILE* 4.3 21.3 - - + -
104Z LYS* 6.0 1.8 - - + -
118Z LEU 3.1 14.2 + - - +
119Z ASP* 3.5 11.9 - - - +
121Z VAL* 1.3 75.2 - - - +
123Z ASN* 1.3 55.8 + - - +
124Z ILE 3.0 0.6 + - - -
125Z ILE* 4.6 4.9 - - - +
126Z THR* 2.5 53.1 + - + +
128Z SER 3.2 21.8 - - - +
129Z PRO* 4.3 7.2 - - + -
130Z THR* 4.4 8.3 - - + +
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Residues in contact with ASN 123 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119Z ASP* 2.8 29.0 + - - +
120Z ALA* 3.1 13.1 + - - +
122Z VAL* 1.3 73.8 - - - +
124Z ILE* 1.3 64.1 + - + +
127Z GLY* 3.2 27.2 - - - +
128Z SER* 3.1 1.1 - - - -
129Z PRO* 3.0 45.0 - - - +
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Residues in contact with ILE 124 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55Z VAL* 5.6 1.1 - - - +
58Z ASN* 3.6 39.3 - - + +
59Z VAL* 4.7 5.6 - - + +
62Z VAL* 3.7 30.5 - - + -
120Z ALA 3.3 15.3 - - - +
121Z VAL* 3.0 8.0 + - - +
122Z VAL 3.0 0.6 - - - -
123Z ASN* 1.3 86.8 - - + +
125Z ILE* 1.3 72.4 + - + +
126Z THR 4.4 0.2 - - - -
127Z GLY* 3.9 5.6 + - - -
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Residues in contact with ILE 125 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55Z VAL* 4.0 26.0 - - + -
59Z VAL* 4.7 1.6 - - + -
80Z GLY* 3.1 43.3 - - - +
83Z VAL* 3.8 26.0 - - + -
84Z ALA* 4.4 14.8 - - + +
87Z LEU* 4.5 19.7 - - + +
121Z VAL* 3.2 17.8 + - + +
122Z VAL 4.2 1.3 - - - +
124Z ILE* 1.3 84.7 - - + +
126Z THR* 1.3 61.5 + - + +
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Residues in contact with THR 126 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83Z VAL* 4.5 4.0 - - + -
87Z LEU* 6.0 2.7 - - + -
96Z LEU* 4.8 10.3 - - + -
100Z ILE* 4.1 20.4 - - + -
122Z VAL* 2.5 36.3 + - + +
124Z ILE 4.4 0.4 - - - -
125Z ILE* 1.3 86.1 - - + +
127Z GLY* 1.3 58.1 + - - +
128Z SER* 2.5 31.5 + - - -
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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