Contacts of the helix formed by residues 114 - 126 (chain j) 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 j).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76j TYR* 2.9 20.8 + - + +
112j ASN 3.7 2.3 + - - +
113j ALA* 1.3 70.4 - - - +
115j PRO* 1.4 62.0 - - - +
116j GLN* 2.8 27.4 + - - +
117j VAL* 2.7 38.5 + - + +
118j LEU* 3.0 10.3 + - - +
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Residues in contact with PRO 115 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104j LYS* 4.5 9.0 - - - +
108j ILE* 3.9 28.7 - - + -
113j ALA 3.3 10.2 - - - +
114j ASN* 1.4 89.0 - - - +
116j GLN* 1.3 56.2 + - - +
118j LEU* 3.3 13.4 + - + +
119j ASP* 2.9 38.0 + - - +
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Residues in contact with GLN 116 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66j TYR* 3.2 37.4 + - + -
114j ASN* 2.8 22.4 + - - +
115j PRO* 1.3 75.7 - - - +
117j VAL* 1.3 61.4 + - + +
119j ASP* 3.4 8.9 + - - +
120j ALA* 3.1 18.1 + - - +
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Residues in contact with VAL 117 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62j VAL* 5.5 0.9 - - + -
63j LEU* 3.6 31.0 - - + -
66j TYR* 3.9 29.6 - - + -
68j ILE* 4.3 14.8 - - + -
76j TYR* 3.7 29.6 - - + +
114j ASN* 2.7 22.8 + - + +
116j GLN* 1.3 71.4 - - + +
118j LEU* 1.3 66.3 + - - +
120j ALA* 3.0 9.0 + - + +
121j VAL* 2.9 21.5 + - + +
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Residues in contact with LEU 118 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76j TYR* 3.7 21.3 - - + -
79j PHE* 3.3 51.6 - - + -
104j LYS* 4.0 17.7 - - + +
107j TYR* 4.4 1.8 - - + -
108j ILE* 3.3 35.4 - - + +
113j ALA* 3.8 18.2 - - + -
114j ASN 3.0 11.3 + - - +
115j PRO* 3.5 14.4 - - + +
117j VAL* 1.3 77.7 - - - +
119j ASP* 1.3 61.8 + - - +
121j VAL* 3.2 3.4 + - - +
122j VAL* 3.1 21.0 + - - +
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Residues in contact with ASP 119 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104j LYS* 2.7 36.7 + - - +
115j PRO* 2.9 22.6 + - - +
116j GLN* 3.6 11.7 - - - +
118j LEU* 1.3 72.2 - - - +
120j ALA* 1.3 60.4 + - - +
122j VAL* 3.1 8.6 + - - +
123j ASN* 2.8 42.3 + - - +
129j PRO* 5.4 13.5 - - + +
130j THR* 5.2 3.5 - - - +
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Residues in contact with ALA 120 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62j VAL* 3.8 11.7 - - + -
66j TYR* 3.5 40.4 - - + +
116j GLN* 3.1 5.2 + - - +
117j VAL* 3.0 10.6 + - - +
119j ASP* 1.3 79.9 - - - +
121j VAL* 1.3 62.8 + - - +
123j ASN* 3.1 19.3 + - - +
124j ILE* 3.3 18.4 + - - +
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Residues in contact with VAL 121 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59j VAL* 4.1 26.0 - - + -
62j VAL* 5.4 4.7 - - + -
63j LEU* 5.0 2.5 - - + -
76j TYR* 4.2 21.8 - - + +
79j PHE* 3.8 13.0 - - + -
80j GLY* 3.5 32.5 - - - -
117j VAL* 2.9 21.4 + - + +
118j LEU* 3.5 7.2 - - - +
119j ASP 3.2 0.2 - - - -
120j ALA* 1.3 77.0 - - + +
122j VAL* 1.3 62.4 + - - +
124j ILE* 3.0 18.8 + - - +
125j ILE* 3.2 18.7 + - + +
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Residues in contact with VAL 122 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79j PHE* 3.7 23.3 - - + -
83j VAL* 4.6 7.4 - - + -
100j ILE* 4.3 20.9 - - + -
104j LYS* 6.0 1.8 - - + -
118j LEU 3.1 14.2 + - - +
119j ASP* 3.1 12.5 + - - +
121j VAL* 1.3 76.3 - - - +
123j ASN* 1.3 55.6 + - - +
124j ILE 3.0 0.5 + - - -
125j ILE* 4.6 4.9 - - - +
126j THR* 2.5 52.7 + - + +
128j SER 3.2 22.7 - - - +
129j PRO* 4.3 7.0 - - + -
130j THR* 4.4 8.3 - - + +
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Residues in contact with ASN 123 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E ASN* 3.8 20.8 + - - +
124E ILE* 3.9 0.7 - - - +
127E GLY 5.1 5.1 - - - +
119j ASP* 2.8 28.9 + - - +
120j ALA* 3.1 12.5 + - - +
122j VAL* 1.3 75.1 - - - +
124j ILE* 1.3 59.4 + - + +
127j GLY* 3.2 26.2 - - - +
128j SER* 3.1 1.2 - - - -
129j PRO* 3.0 44.4 - - - +
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Residues in contact with ILE 124 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E ASN* 4.7 6.4 + - - +
124E ILE* 4.1 27.5 - - + +
126E THR 5.0 0.4 - - - +
127E GLY* 3.4 34.1 - - - +
55j VAL* 6.1 1.6 - - - -
58j ASN* 3.6 39.3 - - + +
59j VAL* 4.7 5.6 - - + +
62j VAL* 3.7 25.4 - - + -
120j ALA 3.3 15.5 - - - +
121j VAL* 3.4 8.1 - - - +
122j VAL 3.0 0.6 - - - -
123j ASN* 1.3 85.0 - - + +
125j ILE* 1.3 73.1 + - + +
126j THR 3.4 0.4 + - - -
127j GLY 3.9 3.1 + - - -
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Residues in contact with ILE 125 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E ASN* 4.8 11.0 - - - +
55j VAL* 4.0 25.6 - - + -
59j VAL* 4.7 1.8 - - + -
80j GLY* 3.1 42.6 - - - +
83j VAL* 3.9 25.6 - - + -
84j ALA* 4.4 15.0 - - + +
87j LEU* 4.5 19.9 - - + +
121j VAL* 3.2 19.3 + - + +
122j VAL 4.2 1.3 - - - +
124j ILE* 1.3 83.6 - - + +
126j THR* 1.3 62.9 + - + +
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Residues in contact with THR 126 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E ALA* 5.7 3.8 - - - +
62E VAL* 5.4 3.8 - - - +
65E GLN* 3.9 22.7 + - - +
124E ILE* 4.8 2.1 - - - +
83j VAL* 4.5 4.3 - - + -
87j LEU* 6.0 2.9 - - + -
96j LEU* 4.8 11.0 - - + -
100j ILE* 4.1 20.6 - - + -
122j VAL* 2.5 36.4 + - + +
124j ILE 4.4 0.4 - - - -
125j ILE* 1.3 85.7 - - + +
127j GLY* 1.3 57.9 + - - +
128j SER* 2.5 29.8 + - - -
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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