Contacts of the helix formed by residues 114 - 126 (chain g) 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 g).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76g TYR* 2.9 21.2 + - - +
112g ASN 3.7 2.5 + - - +
113g ALA* 1.3 69.4 - - - +
115g PRO* 1.3 62.7 - - - +
116g GLN* 2.8 23.3 + - - +
117g VAL* 2.7 45.9 + - + +
118g LEU* 3.0 10.3 + - - +
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Residues in contact with PRO 115 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104g LYS* 5.0 2.8 - - - +
108g ILE* 3.9 31.0 - - + -
113g ALA 3.2 10.0 - - - +
114g ASN* 1.3 88.9 - - - +
116g GLN* 1.3 56.6 + - - +
118g LEU* 3.2 15.6 + - + +
119g ASP* 2.9 37.1 + - - +
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Residues in contact with GLN 116 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66g TYR* 2.9 44.7 + - - -
114g ASN* 2.8 19.0 + - - +
115g PRO* 1.3 74.8 - - - +
117g VAL* 1.3 70.0 + - - +
119g ASP* 3.3 10.1 + - - +
120g ALA* 3.1 17.0 + - - +
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Residues in contact with VAL 117 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62g VAL* 5.3 0.7 - - + -
63g LEU* 4.1 13.0 - - + -
66g TYR* 4.1 27.6 - - + -
68g ILE* 4.9 7.6 - - + -
76g TYR* 3.7 38.4 - - + +
114g ASN* 2.7 27.8 + - + +
116g GLN* 1.3 83.7 - - - +
118g LEU* 1.3 65.0 - - - +
120g ALA* 2.9 17.4 + - + +
121g VAL* 3.0 14.4 + - + +
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Residues in contact with LEU 118 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76g TYR* 3.6 24.2 - - + -
79g PHE* 3.3 52.1 - - + -
104g LYS* 4.4 11.7 - - + +
107g TYR* 4.4 8.1 - - + -
108g ILE* 3.3 36.1 - - + -
113g ALA* 3.8 16.6 - - + -
114g ASN 3.0 11.5 + - - +
115g PRO* 3.4 13.0 - - + +
117g VAL* 1.3 77.0 - - - +
119g ASP* 1.3 62.4 + - - +
121g VAL* 3.1 4.1 + - - +
122g VAL* 3.0 19.7 + - - +
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Residues in contact with ASP 119 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104g LYS* 2.7 36.8 + - - +
115g PRO* 2.9 19.6 + - - +
116g GLN* 3.6 11.2 - - - +
117g VAL 3.2 0.2 - - - -
118g LEU* 1.3 72.8 - - - +
120g ALA* 1.3 60.5 + - - +
122g VAL* 3.2 7.7 + - - +
123g ASN* 2.8 30.1 + - - +
129g PRO* 4.3 25.7 - - + +
130g THR 5.6 0.9 + - - -
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Residues in contact with ALA 120 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62g VAL* 4.0 8.8 - - + +
66g TYR* 3.5 40.6 - - + +
116g GLN* 3.1 11.0 + - - +
117g VAL 2.9 12.4 + - - +
119g ASP* 1.3 76.8 - - - +
121g VAL* 1.3 60.3 + - - +
123g ASN* 3.3 20.6 + - - +
124g ILE* 3.4 14.6 - - - +
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Residues in contact with VAL 121 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59g VAL* 4.0 26.7 - - + -
62g VAL* 5.0 8.3 - - + -
63g LEU* 5.1 1.1 - - + -
76g TYR* 4.4 20.0 - - + +
79g PHE* 3.8 12.6 - - + -
80g GLY* 3.6 31.4 - - - +
117g VAL* 3.0 22.7 + - + +
118g LEU* 3.1 8.7 + - - +
120g ALA* 1.3 75.8 - - - +
122g VAL* 1.3 63.4 + - + +
124g ILE* 3.0 17.4 + - - +
125g ILE* 3.2 19.2 + - + +
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Residues in contact with VAL 122 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79g PHE* 3.6 23.8 - - + -
83g VAL* 4.5 7.0 - - + -
100g ILE* 4.2 21.1 - - + -
104g LYS* 5.0 1.1 - - + -
118g LEU 3.0 14.2 + - - +
119g ASP* 3.6 13.5 - - - +
121g VAL* 1.3 76.5 - - - +
123g ASN* 1.3 55.9 + - - +
124g ILE 2.9 1.4 + - - -
125g ILE* 4.6 4.5 - - - +
126g THR* 2.6 53.5 + - + +
128g SER 3.2 18.8 - - - +
129g PRO* 3.9 10.3 - - + -
130g THR* 4.1 7.4 - - - +
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Residues in contact with ASN 123 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119g ASP 2.8 17.9 + - - +
120g ALA* 3.4 11.2 - - - +
121g VAL 3.2 0.4 - - - -
122g VAL* 1.3 75.4 - - - +
124g ILE* 1.3 68.4 + - - +
127g GLY* 3.1 33.6 + - - +
128g SER* 3.4 17.0 + - - +
129g PRO* 3.5 11.4 - - + +
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Residues in contact with ILE 124 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58g ASN* 3.7 37.7 - - + +
59g VAL* 5.0 3.1 - - + +
62g VAL* 3.6 25.8 - - + -
120g ALA 3.4 13.9 - - - +
121g VAL* 3.0 7.4 + - - +
122g VAL 3.0 0.8 - - - -
123g ASN* 1.3 93.9 - - - +
125g ILE* 1.3 72.2 + - + +
126g THR 3.4 0.2 - - - -
127g GLY* 3.6 7.0 + - - -
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Residues in contact with ILE 125 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55g VAL* 3.9 24.5 - - + -
59g VAL* 4.4 5.6 - - + -
80g GLY* 3.2 42.4 - - - +
83g VAL* 3.7 27.4 - - + -
84g ALA* 4.5 14.6 - - + +
87g LEU* 4.8 16.6 - - + +
121g VAL* 3.2 20.0 + - + +
122g VAL* 4.2 1.6 - - - +
124g ILE* 1.3 81.8 - - + +
126g THR* 1.3 61.5 + - + +
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Residues in contact with THR 126 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83g VAL* 4.3 12.3 - - + -
87g LEU* 6.1 3.4 - - + -
96g LEU* 4.6 12.3 - - + -
100g ILE* 4.1 19.1 - - + -
122g VAL* 2.6 29.1 + - + +
124g ILE 4.2 0.4 - - - -
125g ILE* 1.3 79.8 - - + +
127g GLY* 1.3 57.4 + - - +
128g SER* 2.4 34.6 + - - -
134g 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