Contacts of the helix formed by residues 114 - 126 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76I TYR* 2.9 21.9 + - - +
112I ASN 3.7 2.3 + - - +
113I ALA* 1.3 69.2 - - - +
115I PRO* 1.3 63.0 - - - +
116I GLN* 2.8 23.8 + - - +
117I VAL* 2.7 45.4 + - + +
118I LEU* 3.0 10.8 + - - +
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Residues in contact with PRO 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104I LYS* 5.0 3.0 - - - +
108I ILE* 3.9 30.1 - - + -
113I ALA 3.2 9.3 - - - +
114I ASN* 1.3 89.7 - - - +
116I GLN* 1.3 55.9 + - - +
118I LEU* 3.2 14.9 + - + +
119I ASP* 2.9 37.5 + - - +
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Residues in contact with GLN 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66I TYR* 2.9 44.9 + - - -
114I ASN* 2.8 18.2 + - - +
115I PRO* 1.3 75.9 - - - +
117I VAL* 1.3 69.8 + - - +
119I ASP* 3.3 9.4 + - - +
120I ALA* 3.1 17.0 + - - +
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Residues in contact with VAL 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62I VAL* 5.3 0.7 - - + -
63I LEU* 4.1 12.6 - - + -
66I TYR* 4.1 28.0 - - + -
68I ILE* 4.9 8.3 - - + -
76I TYR* 3.7 37.2 - - + +
114I ASN* 2.7 29.0 + - + +
116I GLN* 1.3 83.9 - - - +
118I LEU* 1.3 66.4 - - - +
120I ALA* 3.0 16.6 + - + +
121I VAL* 3.0 14.4 + - + +
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Residues in contact with LEU 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76I TYR* 3.6 24.2 - - + -
79I PHE* 3.3 52.1 - - + -
104I LYS* 4.4 12.1 - - + +
107I TYR* 4.4 7.4 - - + -
108I ILE* 3.3 35.2 - - + -
113I ALA* 3.8 18.2 - - + -
114I ASN 3.0 11.0 + - - +
115I PRO* 3.4 12.8 - - + +
116I GLN 3.2 0.2 - - - -
117I VAL* 1.3 77.4 - - - +
119I ASP* 1.3 62.4 + - - +
121I VAL* 3.1 4.1 + - - +
122I VAL* 3.0 19.6 + - - +
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Residues in contact with ASP 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104I LYS* 2.7 36.9 + - - +
115I PRO* 2.9 19.1 + - - +
116I GLN* 3.6 11.2 - - - +
117I VAL 3.2 0.2 - - - -
118I LEU* 1.3 73.8 - - - +
120I ALA* 1.3 60.0 + - - +
122I VAL* 3.2 7.9 + - - +
123I ASN* 2.8 29.9 + - - +
129I PRO* 4.3 26.7 - - + +
130I THR 5.6 0.5 + - - -
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Residues in contact with ALA 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62I VAL* 4.0 8.8 - - + +
66I TYR* 3.5 39.9 - - + +
116I GLN* 3.1 10.8 + - - +
117I VAL 3.0 12.0 + - - +
119I ASP* 1.3 76.8 - - - +
121I VAL* 1.3 60.6 + - - +
123I ASN* 3.3 20.4 + - - +
124I ILE* 3.4 14.4 - - - +
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Residues in contact with VAL 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I VAL* 4.0 27.4 - - + -
62I VAL* 5.0 8.1 - - + -
63I LEU* 5.1 0.9 - - + -
76I TYR* 4.4 19.3 - - + +
79I PHE* 3.8 13.2 - - + -
80I GLY* 3.6 30.5 - - - -
117I VAL* 3.0 22.9 + - + +
118I LEU* 3.1 8.7 + - - +
120I ALA* 1.3 75.9 - - - +
122I VAL* 1.3 63.6 + - - +
124I ILE* 3.0 17.6 + - - +
125I ILE* 3.2 19.3 + - + +
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Residues in contact with VAL 122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I PHE* 3.6 23.6 - - + -
83I VAL* 4.5 7.2 - - + -
100I ILE* 4.2 21.8 - - + -
104I LYS* 5.0 1.1 - - + -
118I LEU 3.0 15.7 + - - +
119I ASP* 3.6 13.0 - - - +
121I VAL* 1.3 75.6 - - - +
123I ASN* 1.3 55.0 + - - +
124I ILE 2.9 1.6 + - - -
125I ILE* 4.6 4.9 - - - +
126I THR* 2.6 52.5 + - + +
128I SER 3.2 19.7 - - - +
129I PRO* 3.9 10.3 - - + -
130I THR* 4.1 8.3 - - + +
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Residues in contact with ASN 123 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119I ASP 2.8 18.7 + - - +
120I ALA* 3.4 11.8 + - - +
121I VAL 3.2 0.4 - - - -
122I VAL* 1.3 73.9 - - - +
124I ILE* 1.3 59.2 + - - +
127I GLY* 3.1 33.8 + - - +
128I SER* 3.4 17.1 + - - +
129I PRO* 3.5 11.2 - - + +
123n ASN* 3.8 16.5 + - - +
124n ILE* 4.4 0.2 - - - +
127n GLY 3.4 23.8 + - - -
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Residues in contact with ILE 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58I ASN* 3.7 35.9 - - + +
59I VAL* 5.0 3.1 - - + +
62I VAL* 3.6 24.5 - - + -
120I ALA 3.4 14.4 - - - +
121I VAL* 3.0 6.3 + - - +
122I VAL 3.0 0.8 - - - -
123I ASN* 1.3 88.5 - - - +
125I ILE* 1.3 72.5 + - + +
126I THR 3.4 0.6 + - - -
127I GLY 3.6 4.5 + - - -
58n ASN* 4.3 10.5 + - - +
123n ASN 3.9 4.5 - - - +
124n ILE* 4.1 25.7 - - - +
126n THR 4.8 0.9 - - - +
127n GLY* 3.3 34.5 - - - +
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Residues in contact with ILE 125 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55I VAL* 3.9 25.4 - - + -
59I VAL* 4.4 5.4 - - + -
80I GLY* 3.2 41.7 - - - +
83I VAL* 3.7 27.6 - - + -
84I ALA* 4.5 15.3 - - + +
87I LEU* 4.8 16.4 - - + +
121I VAL* 3.2 20.9 + - + +
122I VAL* 4.2 1.3 - - - +
124I ILE* 1.3 82.1 - - + +
126I THR* 1.3 61.0 + - + +
58n ASN* 4.2 16.8 - - - +
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Residues in contact with THR 126 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83I VAL* 4.3 12.8 - - + -
87I LEU* 6.1 3.1 - - + -
96I LEU* 4.6 12.1 - - + -
100I ILE* 4.1 18.6 - - + -
122I VAL* 2.6 29.1 + - + +
124I ILE 4.2 0.2 - - - -
125I ILE* 1.3 79.0 - - + +
127I GLY* 1.3 58.2 + - - +
128I SER* 2.4 34.4 + - - -
134I SER* 5.1 6.8 - - - +
61n ALA* 5.9 2.8 - - - +
62n VAL* 5.0 6.4 - - - +
65n GLN* 6.0 0.9 - - - +
124n ILE* 5.0 1.8 - - - +
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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