Contacts of the helix formed by residues 114 - 126 (chain Q) 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 Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76Q TYR* 2.9 22.8 + - - +
112Q ASN 3.7 2.1 + - - +
113Q ALA* 1.3 70.9 - - - +
115Q PRO* 1.3 62.1 - - - +
116Q GLN* 2.8 24.4 + - - +
117Q VAL* 2.7 44.8 + - + +
118Q LEU* 3.0 10.6 + - - +
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Residues in contact with PRO 115 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104Q LYS* 5.0 3.1 - - - +
108Q ILE* 3.9 31.4 - - + -
113Q ALA 3.2 9.8 - - - +
114Q ASN* 1.3 91.8 - - - +
116Q GLN* 1.3 56.4 + - - +
118Q LEU* 3.2 15.5 + - + +
119Q ASP* 2.9 37.3 + - - +
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Residues in contact with GLN 116 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66Q TYR* 2.9 44.5 + - - -
114Q ASN* 2.8 18.4 + - - +
115Q PRO* 1.3 75.5 - - - +
117Q VAL* 1.3 67.6 + - - +
119Q ASP* 3.3 9.8 + - + +
120Q ALA* 3.1 17.1 + - - +
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Residues in contact with VAL 117 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62Q VAL* 5.3 0.2 - - + -
63Q LEU* 4.1 13.7 - - + -
66Q TYR* 4.1 27.1 - - + -
68Q ILE* 4.9 8.5 - - + -
76Q TYR* 3.7 38.1 - - + +
114Q ASN* 2.7 28.7 + - + +
116Q GLN* 1.3 83.6 - - - +
118Q LEU* 1.3 65.5 + - - +
120Q ALA* 2.9 17.1 + - + +
121Q VAL* 3.0 14.6 + - + +
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Residues in contact with LEU 118 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76Q TYR* 3.6 24.2 - - + -
79Q PHE* 3.3 51.6 - - + -
104Q LYS* 4.4 12.1 - - + +
107Q TYR* 4.4 8.1 - - + -
108Q ILE* 3.3 35.2 - - + -
113Q ALA* 3.8 18.4 - - + -
114Q ASN 3.0 11.3 + - - +
115Q PRO* 3.4 12.6 - - + +
116Q GLN 3.2 0.2 - - - -
117Q VAL* 1.3 77.5 - - - +
119Q ASP* 1.3 62.0 + - - +
121Q VAL* 3.1 4.3 + - - +
122Q VAL* 3.0 20.3 + - - +
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Residues in contact with ASP 119 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104Q LYS* 2.7 36.9 + - - +
115Q PRO* 2.9 20.4 + - - +
116Q GLN* 3.6 10.5 - - + +
118Q LEU* 1.3 72.1 - - - +
120Q ALA* 1.3 61.3 + - - +
122Q VAL* 3.2 7.5 + - - +
123Q ASN* 2.8 30.2 + - - +
129Q PRO* 4.3 26.1 - - + +
130Q THR 5.6 0.3 + - - -
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Residues in contact with ALA 120 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62Q VAL* 4.0 9.4 - - + +
66Q TYR* 3.5 40.2 - - + +
116Q GLN* 3.1 10.1 + - - +
117Q VAL 2.9 12.4 + - - +
119Q ASP* 1.3 76.8 - - - +
121Q VAL* 1.3 60.2 + - - +
123Q ASN* 3.3 19.6 + - - +
124Q ILE* 3.4 14.4 - - - +
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Residues in contact with VAL 121 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59Q VAL* 4.0 28.4 - - + +
62Q VAL* 5.0 8.5 - - + -
63Q LEU* 5.1 0.9 - - + -
76Q TYR* 4.4 19.3 - - + +
79Q PHE* 3.8 12.6 - - + -
80Q GLY* 3.6 31.2 - - - -
117Q VAL* 3.0 22.0 + - + +
118Q LEU* 3.1 8.7 + - - +
120Q ALA* 1.3 76.1 - - - +
122Q VAL* 1.3 62.4 + - - +
124Q ILE* 3.0 17.0 + - - +
125Q ILE* 3.2 19.6 + - + +
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Residues in contact with VAL 122 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79Q PHE* 3.6 22.9 - - + -
83Q VAL* 4.5 7.9 - - + -
100Q ILE* 4.2 21.5 - - + -
104Q LYS* 5.0 1.3 - - + -
118Q LEU 3.0 16.1 + - - +
119Q ASP* 3.6 13.5 - - - +
121Q VAL* 1.3 75.2 - - - +
123Q ASN* 1.3 55.3 + - - +
124Q ILE 2.9 1.9 + - - -
125Q ILE* 3.2 5.3 + - - +
126Q THR* 2.6 52.0 + - + +
128Q SER 3.2 20.0 - - - +
129Q PRO* 3.9 10.3 - - + -
130Q THR* 4.1 7.0 - - + +
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Residues in contact with ASN 123 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119Q ASP 2.8 16.2 + - - +
120Q ALA* 3.4 11.8 + - - +
122Q VAL* 1.3 76.0 - - - +
124Q ILE* 1.3 60.1 + - - +
127Q GLY* 3.1 33.4 + - - +
128Q SER* 3.4 16.4 - - - +
129Q PRO* 3.5 11.4 - - + +
123v ASN* 3.8 16.5 + - - +
127v GLY 3.4 24.4 + - - -
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Residues in contact with ILE 124 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58Q ASN* 3.7 35.4 - - + +
59Q VAL* 5.0 3.4 - - + +
62Q VAL* 3.6 25.1 - - + -
120Q ALA 3.4 14.6 - - - +
121Q VAL* 3.0 7.1 + - - +
122Q VAL 3.0 0.8 - - - -
123Q ASN* 1.3 89.2 - - - +
125Q ILE* 1.3 72.5 + - + +
126Q THR 4.2 0.2 - - - -
127Q GLY 3.6 5.1 + - - -
58v ASN* 4.3 10.6 + - - +
123v ASN 3.9 4.7 - - - +
124v ILE* 4.1 25.0 - - - +
126v THR 4.8 0.7 - - - +
127v GLY* 3.3 33.7 - - - -
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Residues in contact with ILE 125 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55Q VAL* 3.9 25.6 - - + -
59Q VAL* 4.4 5.2 - - + -
80Q GLY* 3.2 41.7 - - - +
83Q VAL* 3.7 26.7 - - + -
84Q ALA* 4.5 14.4 - - + +
87Q LEU* 4.8 17.4 - - + +
121Q VAL* 3.2 19.8 + - + +
122Q VAL* 4.2 1.3 - - - +
124Q ILE* 1.3 81.8 - - + +
126Q THR* 1.3 60.5 + - + +
58v ASN* 4.2 17.2 - - - +
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Residues in contact with THR 126 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83Q VAL* 4.3 13.0 - - + -
87Q LEU* 6.1 2.7 - - + -
96Q LEU* 4.6 12.6 - - + -
100Q ILE* 4.1 18.4 - - + -
122Q VAL* 2.6 29.3 + - + +
124Q ILE 4.2 0.4 - - - -
125Q ILE* 1.3 78.2 - - + +
127Q GLY* 1.3 58.0 + - - +
128Q SER* 2.4 34.1 + - - -
134Q SER* 5.1 6.6 - - - +
61v ALA* 5.9 2.8 - - - +
62v VAL* 5.0 6.6 - - - +
65v GLN* 6.0 0.9 - - - +
124v 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