Contacts of the helix formed by residues 114 - 126 (chain k) 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 k).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76k TYR* 2.9 21.5 + - - +
112k ASN 3.7 2.3 + - - +
113k ALA* 1.3 69.8 - - - +
115k PRO* 1.3 63.1 - - - +
116k GLN* 2.8 23.4 + - - +
117k VAL* 2.7 45.7 + - + +
118k LEU* 3.0 10.5 + - - +
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Residues in contact with PRO 115 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104k LYS* 5.0 2.4 - - - +
108k ILE* 3.9 31.4 - - + -
113k ALA 3.2 9.5 - - - +
114k ASN* 1.3 90.1 - - - +
116k GLN* 1.3 56.6 + - - +
118k LEU* 3.2 15.5 + - + +
119k ASP* 2.9 37.6 + - - +
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Residues in contact with GLN 116 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66k TYR* 2.9 44.2 + - - -
114k ASN* 2.8 19.2 + - - +
115k PRO* 1.3 74.8 - - - +
117k VAL* 1.3 68.5 + - - +
119k ASP* 3.3 9.8 + - - +
120k ALA* 3.1 16.9 + - - +
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Residues in contact with VAL 117 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62k VAL* 5.3 0.7 - - + -
63k LEU* 4.1 12.8 - - + -
66k TYR* 4.1 27.8 - - + -
68k ILE* 4.9 7.9 - - + -
76k TYR* 3.7 37.7 - - + +
114k ASN* 2.7 28.7 + - + +
116k GLN* 1.3 84.3 - - - +
118k LEU* 1.3 66.0 - - - +
120k ALA* 3.0 16.7 + - + +
121k VAL* 3.0 14.5 + - + +
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Residues in contact with LEU 118 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76k TYR* 3.6 24.7 - - + -
79k PHE* 3.3 51.2 - - + -
104k LYS* 4.4 12.3 - - + +
107k TYR* 4.4 7.9 - - + -
108k ILE* 3.3 35.2 - - + -
113k ALA* 3.8 18.4 - - + -
114k ASN 3.0 11.3 + - - +
115k PRO* 3.4 12.8 - - + +
117k VAL* 1.3 76.9 - - - +
119k ASP* 1.3 62.1 + - - +
121k VAL* 3.1 4.4 + - - +
122k VAL* 3.0 20.4 + - - +
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Residues in contact with ASP 119 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104k LYS* 2.7 37.7 + - - +
115k PRO* 2.9 19.7 + - - +
116k GLN* 3.6 11.2 - - - +
118k LEU* 1.3 72.6 - - - +
120k ALA* 1.3 60.5 + - - +
122k VAL* 3.2 8.3 + - - +
123k ASN* 2.8 29.7 + - - +
129k PRO* 4.3 25.4 - - + +
130k THR* 5.6 0.9 + - - +
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Residues in contact with ALA 120 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62k VAL* 4.0 9.3 - - + +
66k TYR* 3.5 40.6 - - + +
116k GLN* 3.1 11.1 + - - +
117k VAL 3.0 12.7 + - - +
119k ASP* 1.3 77.5 - - - +
121k VAL* 1.3 60.5 + - - +
123k ASN* 3.3 19.4 + - - +
124k ILE* 3.4 14.8 - - - +
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Residues in contact with VAL 121 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59k VAL* 4.0 28.3 - - + -
62k VAL* 5.0 8.5 - - + -
63k LEU* 5.1 0.9 - - + -
76k TYR* 4.4 19.3 - - + +
79k PHE* 3.8 13.5 - - + -
80k GLY* 3.6 31.4 - - - +
117k VAL* 3.0 22.9 + - + +
118k LEU* 3.1 8.5 + - - +
120k ALA* 1.3 76.0 - - - +
122k VAL* 1.3 63.0 + - - +
124k ILE* 3.0 17.5 + - - +
125k ILE* 3.2 19.8 + - + +
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Residues in contact with VAL 122 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79k PHE* 3.6 24.2 - - + -
83k VAL* 4.5 7.2 - - + -
100k ILE* 4.2 20.6 - - + -
104k LYS* 5.0 1.1 - - + -
118k LEU 3.0 13.8 + - - +
119k ASP* 3.6 13.7 - - - +
121k VAL* 1.3 74.8 - - - +
123k ASN* 1.3 55.6 + - - +
124k ILE 2.9 1.2 + - - -
125k ILE* 4.6 5.2 - - - +
126k THR* 2.6 52.0 + - + +
128k SER 3.2 19.7 - - - +
129k PRO* 3.9 10.1 - - + -
130k THR* 4.1 7.9 - - + +
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Residues in contact with ASN 123 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119k ASP 2.8 18.3 + - - +
120k ALA* 3.4 11.6 - - - +
121k VAL 3.2 0.4 - - - -
122k VAL* 1.3 75.0 - - - +
124k ILE* 1.3 69.0 + - - +
127k GLY* 3.1 33.4 + - - +
128k SER* 3.4 16.0 - - - +
129k PRO* 3.5 11.4 - - + +
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Residues in contact with ILE 124 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58k ASN* 3.7 37.0 - - + +
59k VAL* 5.0 3.1 - - + +
62k VAL* 3.6 25.8 - - + -
120k ALA 3.4 14.6 - - - +
121k VAL* 3.0 6.9 + - - +
122k VAL 3.0 1.0 - - - -
123k ASN* 1.3 95.7 - - - +
125k ILE* 1.3 70.6 + - + +
126k THR 4.2 0.2 - - - -
127k GLY* 3.6 7.3 + - - -
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Residues in contact with ILE 125 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55k VAL* 3.9 25.8 - - + -
59k VAL* 4.4 5.4 - - + -
80k GLY* 3.2 42.0 - - - +
83k VAL* 3.7 27.4 - - + -
84k ALA* 4.5 14.6 - - + +
87k LEU* 4.8 16.5 - - + +
121k VAL* 3.2 20.5 + - + +
122k VAL* 4.2 1.3 - - - +
124k ILE* 1.3 81.9 - - + +
126k THR* 1.3 61.6 + - + +
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Residues in contact with THR 126 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83k VAL* 4.3 12.3 - - + -
87k LEU* 6.1 2.9 - - + -
96k LEU* 4.6 11.9 - - + -
100k ILE* 4.1 18.8 - - + -
122k VAL* 2.6 29.9 + - + +
124k ILE 4.2 0.2 - - - -
125k ILE* 1.3 79.0 - - + +
127k GLY* 1.3 57.5 + - - +
128k SER* 2.4 34.0 + - - -
130k THR* 6.3 0.2 - - - -
134k SER* 5.1 6.8 - - - +
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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