Contacts of the helix formed by residues 114 - 126 (chain a) 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 a).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76a TYR* 2.9 21.7 + - - +
112a ASN 3.7 1.8 + - - +
113a ALA* 1.3 69.6 - - - +
115a PRO* 1.3 62.6 - - - +
116a GLN* 2.8 23.8 + - - +
117a VAL* 2.7 45.6 + - + +
118a LEU* 3.0 10.9 + - - +
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Residues in contact with PRO 115 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104a LYS* 5.0 2.4 - - - -
108a ILE* 3.9 30.3 - - + -
113a ALA 3.2 9.8 - - - +
114a ASN* 1.3 90.2 - - - +
116a GLN* 1.3 55.9 + - - +
118a LEU* 3.2 14.6 + - + +
119a ASP* 2.9 37.2 + - - +
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Residues in contact with GLN 116 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66a TYR* 2.9 44.3 + - - -
114a ASN* 2.8 18.6 + - - +
115a PRO* 1.3 75.8 - - - +
117a VAL* 1.3 69.4 + - - +
119a ASP* 3.3 9.3 + - - +
120a ALA* 3.1 16.8 + - - +
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Residues in contact with VAL 117 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62a VAL* 5.3 0.9 - - + -
63a LEU* 4.1 12.8 - - + -
66a TYR* 4.1 27.8 - - + -
68a ILE* 4.9 7.9 - - + -
76a TYR* 3.7 37.7 - - + +
114a ASN* 2.7 29.0 + - + +
116a GLN* 1.3 83.3 - - - +
118a LEU* 1.3 66.7 + - - +
120a ALA* 2.9 16.4 + - + +
121a VAL* 3.0 14.2 + - + +
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Residues in contact with LEU 118 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76a TYR* 3.6 24.7 - - + -
79a PHE* 3.3 51.8 - - + -
104a LYS* 4.4 12.1 - - + +
107a TYR* 4.4 7.9 - - + -
108a ILE* 3.3 35.2 - - + -
113a ALA* 3.8 17.9 - - + -
114a ASN 3.0 10.2 + - - +
115a PRO* 3.4 12.6 - - + +
117a VAL* 1.3 77.5 - - - +
119a ASP* 1.3 62.4 + - - +
121a VAL* 3.1 4.3 + - - +
122a VAL* 3.0 19.8 + - - +
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Residues in contact with ASP 119 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104a LYS* 2.7 37.6 + - - +
115a PRO* 2.9 19.3 + - - +
116a GLN* 3.6 11.6 - - + +
117a VAL 3.2 0.2 - - - -
118a LEU* 1.3 73.8 - - - +
120a ALA* 1.3 60.1 + - - +
122a VAL* 3.2 8.1 + - - +
123a ASN* 2.8 29.9 + - - +
129a PRO* 4.3 26.6 - - + +
130a THR 5.6 0.5 + - - -
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Residues in contact with ALA 120 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62a VAL* 4.0 9.7 - - + +
66a TYR* 3.5 39.7 - - + +
116a GLN* 3.1 10.6 + - - +
117a VAL 2.9 11.8 + - - +
119a ASP* 1.3 77.1 - - - +
121a VAL* 1.3 60.0 + - - +
123a ASN* 3.3 20.1 + - - +
124a ILE* 3.4 14.6 - - - +
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Residues in contact with VAL 121 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59a VAL* 4.0 26.5 - - + -
62a VAL* 5.0 8.3 - - + -
63a LEU* 5.1 1.1 - - + -
76a TYR* 4.4 19.3 - - + +
79a PHE* 3.8 13.0 - - + -
80a GLY* 3.6 31.2 - - - +
117a VAL* 3.0 22.3 + - + +
118a LEU* 3.1 8.3 + - - +
120a ALA* 1.3 76.1 - - - +
122a VAL* 1.3 62.4 + - - +
124a ILE* 3.0 18.1 + - - +
125a ILE* 3.2 19.7 + - + +
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Residues in contact with VAL 122 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79a PHE* 3.6 23.6 - - + -
83a VAL* 4.5 7.6 - - + -
100a ILE* 4.2 21.1 - - + -
104a LYS* 5.0 1.1 - - + -
118a LEU 3.0 15.4 + - - +
119a ASP* 3.6 13.2 - - - +
121a VAL* 1.3 76.0 - - - +
123a ASN* 1.3 55.8 + - - +
124a ILE 2.9 1.4 + - - -
125a ILE* 4.6 5.4 - - - +
126a THR* 2.6 51.8 + - + +
128a SER 3.2 20.0 - - - +
129a PRO* 3.9 9.9 - - + -
130a THR* 4.1 8.5 - - + +
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Residues in contact with ASN 123 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1236 ASN* 3.8 16.1 + - - +
1246 ILE* 4.4 0.2 - - - +
1276 GLY 3.4 23.8 + - - -
119a ASP 2.8 18.9 + - - +
120a ALA* 3.4 11.8 + - - +
121a VAL 3.2 0.4 - - - -
122a VAL* 1.3 74.6 - - - +
124a ILE* 1.3 59.1 + - - +
127a GLY* 3.1 34.2 + - - +
128a SER* 3.4 17.2 + - - +
129a PRO* 3.5 11.2 - - + +
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Residues in contact with ILE 124 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586 ASN* 4.3 10.6 + - - +
1236 ASN 3.9 4.3 - - - +
1246 ILE* 4.1 25.0 - - - +
1266 THR 4.8 0.9 - - - +
1276 GLY* 3.3 34.3 - - - +
58a ASN* 3.7 35.4 - - + +
59a VAL* 5.0 3.4 - - + +
62a VAL* 3.6 24.5 - - + -
120a ALA 3.4 14.8 - - - +
121a VAL* 3.0 6.7 + - - +
122a VAL 3.0 0.6 - - - -
123a ASN* 1.3 89.6 - - - +
125a ILE* 1.3 72.7 + - + +
126a THR 3.4 0.6 + - - -
127a GLY 3.6 4.5 + - - -
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Residues in contact with ILE 125 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586 ASN* 4.2 16.9 - - - +
55a VAL* 3.9 25.4 - - + -
59a VAL* 4.4 5.4 - - + -
80a GLY* 3.2 41.5 - - - +
83a VAL* 3.7 27.8 - - + -
84a ALA* 4.5 15.3 - - + +
87a LEU* 4.8 16.1 - - + +
121a VAL* 3.2 20.4 + - + +
122a VAL* 4.2 1.1 - - - +
124a ILE* 1.3 82.3 - - + +
126a THR* 1.3 62.0 + - + +
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Residues in contact with THR 126 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616 ALA* 5.9 2.9 - - - +
626 VAL* 5.0 6.6 - - - +
656 GLN* 6.0 0.9 - - - +
1246 ILE* 5.0 1.5 - - - +
83a VAL* 4.3 13.5 - - + -
87a LEU* 6.1 2.7 - - + -
96a LEU* 4.6 12.1 - - + -
100a ILE* 4.1 18.6 - - + -
122a VAL* 2.6 28.3 + - + +
124a ILE 4.2 0.2 - - - -
125a ILE* 1.3 79.2 - - + +
127a GLY* 1.3 57.5 + - - +
128a SER* 2.4 35.4 + - - -
134a SER* 5.1 6.4 - - - +
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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