Contacts of the helix formed by residues 114 - 126 (chain V) 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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76V TYR* 2.9 21.0 + - - +
112V ASN 3.7 2.5 + - - +
113V ALA* 1.3 70.2 - - - +
115V PRO* 1.4 62.7 - - - +
116V GLN* 2.8 27.1 + - - +
117V VAL* 2.7 38.9 + - + +
118V LEU* 3.0 10.6 + - - +
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Residues in contact with PRO 115 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104V LYS* 4.5 8.5 - - - +
108V ILE* 3.9 28.7 - - + -
113V ALA 3.3 9.6 - - - +
114V ASN* 1.4 90.9 - - - +
116V GLN* 1.3 56.2 + - - +
118V LEU* 3.3 14.2 + - + +
119V ASP* 2.9 37.9 + - - +
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Residues in contact with GLN 116 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66V TYR* 3.2 35.5 + - + -
114V ASN* 2.8 22.2 + - - +
115V PRO* 1.3 73.8 - - - +
117V VAL* 1.3 62.4 + - + +
119V ASP* 3.4 9.5 + - - +
120V ALA* 3.1 17.7 + - - +
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Residues in contact with VAL 117 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62V VAL* 5.5 0.7 - - + -
63V LEU* 3.6 31.0 - - + -
66V TYR* 3.9 28.9 - - + -
68V ILE* 4.3 14.8 - - + -
76V TYR* 3.7 29.8 - - + +
114V ASN* 2.7 22.1 + - + +
116V GLN* 1.3 71.1 - - + +
118V LEU* 1.3 66.6 + - - +
120V ALA* 3.0 9.3 + - + +
121V VAL* 2.9 22.7 + - + +
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Residues in contact with LEU 118 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76V TYR* 3.7 21.1 - - + -
79V PHE* 3.3 53.9 - - + -
104V LYS* 4.0 17.9 - - + +
107V TYR* 4.4 1.8 - - + -
108V ILE* 3.3 35.4 - - + +
113V ALA* 3.8 18.2 - - + -
114V ASN 3.0 11.8 + - - +
115V PRO* 3.5 14.8 - - + +
116V GLN 3.2 0.2 - - - -
117V VAL* 1.3 77.7 - - - +
119V ASP* 1.3 61.6 + - - +
121V VAL* 3.2 3.3 + - - +
122V VAL* 3.1 20.4 + - - +
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Residues in contact with ASP 119 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104V LYS* 2.7 36.9 + - - +
115V PRO* 2.9 22.0 + - - +
116V GLN* 3.6 11.7 - - - +
118V LEU* 1.3 73.3 - - - +
120V ALA* 1.3 60.7 + - - +
122V VAL* 3.1 9.4 + - - +
123V ASN* 2.8 43.0 + - - +
129V PRO* 5.4 13.9 - - + +
130V THR* 5.2 3.8 - - - +
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Residues in contact with ALA 120 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62V VAL* 3.8 11.6 - - + +
66V TYR* 3.5 39.9 - - + +
116V GLN* 3.1 5.4 + - - +
117V VAL* 3.0 10.4 + - - +
119V ASP* 1.3 78.5 - - - +
121V VAL* 1.3 62.9 + - - +
123V ASN* 3.1 19.8 + - - +
124V ILE* 3.3 17.8 + - - +
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Residues in contact with VAL 121 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59V VAL* 4.1 26.5 - - + -
62V VAL* 5.4 4.9 - - + -
63V LEU* 5.0 2.0 - - + -
76V TYR* 4.2 21.8 - - + +
79V PHE* 3.8 13.0 - - + -
80V GLY* 3.5 32.8 - - - -
117V VAL* 2.9 21.6 + - + +
118V LEU* 3.5 8.5 - - - +
119V ASP 3.2 0.2 - - - -
120V ALA* 1.3 77.0 - - + +
122V VAL* 1.3 62.8 + - - +
124V ILE* 3.0 17.7 + - - +
125V ILE* 3.2 18.8 + - + +
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Residues in contact with VAL 122 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79V PHE* 3.7 23.3 - - + -
83V VAL* 4.6 7.4 - - + -
100V ILE* 4.3 21.1 - - + -
104V LYS* 6.0 1.6 - - + -
118V LEU 3.1 14.4 + - - +
119V ASP* 3.1 12.8 + - - +
121V VAL* 1.3 75.0 - - - +
123V ASN* 1.3 55.2 + - - +
124V ILE 3.0 0.9 + - - -
125V ILE* 4.6 5.6 - - - +
126V THR* 2.5 52.6 + - + +
128V SER 3.2 22.2 - - - +
129V PRO* 4.3 7.0 - - + -
130V THR* 4.4 8.1 - - + +
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Residues in contact with ASN 123 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119V ASP* 2.8 28.6 + - - +
120V ALA* 3.1 12.8 + - - +
122V VAL* 1.3 75.9 - - - +
124V ILE* 1.3 62.4 + - + +
127V GLY* 3.2 26.6 - - - +
128V SER* 3.1 1.1 - - - -
129V PRO* 3.0 44.7 - - - +
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Residues in contact with ILE 124 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55V VAL* 6.1 1.3 - - - -
58V ASN* 3.6 39.7 - - + +
59V VAL* 4.7 5.4 - - + +
62V VAL* 3.7 29.8 - - + -
120V ALA 3.3 14.6 - - - +
121V VAL* 3.0 8.7 + - - +
122V VAL 3.0 0.6 - - - -
123V ASN* 1.3 86.1 - - + +
125V ILE* 1.3 72.6 + - + +
126V THR 3.4 0.6 + - - -
127V GLY* 3.9 4.7 + - - -
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Residues in contact with ILE 125 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55V VAL* 4.0 26.0 - - + -
59V VAL* 4.7 1.8 - - + -
80V GLY* 3.1 42.6 - - - +
83V VAL* 3.9 26.7 - - + -
84V ALA* 4.4 15.3 - - + +
87V LEU* 4.5 19.0 - - + +
121V VAL* 3.2 18.7 + - + +
122V VAL 4.2 1.3 - - - +
124V ILE* 1.3 84.4 - - + +
126V THR* 1.3 63.5 + - + +
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Residues in contact with THR 126 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83V VAL* 4.5 4.5 - - + -
87V LEU* 6.0 2.9 - - + -
96V LEU* 4.8 11.2 - - + -
100V ILE* 4.1 20.6 - - + -
122V VAL* 2.5 36.1 + - + +
124V ILE 4.4 0.4 - - - -
125V ILE* 1.3 85.3 - - + +
127V GLY* 1.3 58.0 + - - +
128V SER* 2.5 31.3 + - - +
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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