Contacts of the helix formed by residues 114 - 126 (chain r) 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 r).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76r TYR* 2.9 22.1 + - + +
112r ASN 3.7 2.3 + - - +
113r ALA* 1.3 70.7 - - - +
115r PRO* 1.4 64.5 - - - +
116r GLN* 2.8 26.2 + - - +
117r VAL* 2.7 39.2 + - + +
118r LEU* 3.0 10.3 + - - +
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Residues in contact with PRO 115 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104r LYS* 4.5 8.7 - - - +
108r ILE* 3.9 29.4 - - + -
113r ALA 3.3 10.3 - - - +
114r ASN* 1.4 90.1 - - - +
116r GLN* 1.3 55.4 + - - +
118r LEU* 3.3 13.8 + - + +
119r ASP* 2.9 38.3 + - - +
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Residues in contact with GLN 116 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66r TYR* 3.2 35.9 + - + -
114r ASN* 2.8 22.8 + - - +
115r PRO* 1.3 74.3 - - - +
117r VAL* 1.3 61.9 + - + +
119r ASP* 3.4 9.9 + - - +
120r ALA* 3.1 18.0 + - - +
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Residues in contact with VAL 117 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62r VAL* 5.5 0.7 - - + -
63r LEU* 3.6 30.3 - - + -
66r TYR* 3.9 29.2 - - + -
68r ILE* 4.3 15.3 - - + -
76r TYR* 3.7 28.9 - - + +
114r ASN* 2.7 21.7 + - + +
116r GLN* 1.3 72.4 - - + +
118r LEU* 1.3 66.3 - - - +
120r ALA* 3.0 9.2 + - + +
121r VAL* 2.9 23.0 + - + +
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Residues in contact with LEU 118 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76r TYR* 3.7 21.8 - - + -
79r PHE* 3.3 52.1 - - + -
104r LYS* 4.0 17.7 - - + +
107r TYR* 4.4 2.5 - - + -
108r ILE* 3.3 35.4 - - + +
113r ALA* 3.8 18.4 - - + -
114r ASN 3.0 11.2 + - - +
115r PRO* 3.5 14.8 - - + +
117r VAL* 1.3 77.3 - - - +
119r ASP* 1.3 62.0 + - - +
121r VAL* 3.2 2.9 + - - +
122r VAL* 3.1 20.3 + - - +
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Residues in contact with ASP 119 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104r LYS* 2.7 37.2 + - - +
115r PRO* 2.9 21.8 + - - +
116r GLN* 3.6 12.5 - - - +
117r VAL 3.2 0.2 - - - -
118r LEU* 1.3 72.5 - - - +
120r ALA* 1.3 61.5 + - - +
122r VAL* 3.1 9.8 + - - +
123r ASN* 2.8 42.7 + - - +
129r PRO* 5.4 13.5 - - + +
130r THR* 5.2 3.8 + - - +
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Residues in contact with ALA 120 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62r VAL* 3.8 12.5 - - + +
66r TYR* 3.5 39.3 - - + +
116r GLN* 3.1 6.1 + - - +
117r VAL 3.0 10.4 + - - +
119r ASP* 1.3 79.5 - - - +
121r VAL* 1.3 63.0 + - - +
123r ASN* 3.1 20.8 + - - +
124r ILE* 3.3 17.7 + - - +
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Residues in contact with VAL 121 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59r VAL* 4.1 27.4 - - + -
62r VAL* 5.4 4.5 - - + -
63r LEU* 5.0 2.7 - - + -
76r TYR* 4.2 22.0 - - + +
79r PHE* 3.8 12.8 - - + -
80r GLY* 3.5 32.1 - - - -
117r VAL* 2.9 21.2 + - + +
118r LEU* 3.5 8.3 - - - +
119r ASP 3.2 0.2 - - - -
120r ALA* 1.3 75.9 - - + +
122r VAL* 1.3 62.6 + - - +
124r ILE* 3.0 18.5 + - - +
125r ILE* 3.2 19.4 + - + +
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Residues in contact with VAL 122 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79r PHE* 3.7 23.8 - - + -
83r VAL* 4.6 7.9 - - + -
100r ILE* 4.3 21.1 - - + -
104r LYS* 6.0 1.6 - - + -
118r LEU 3.1 14.6 + - - +
119r ASP* 3.5 11.7 - - - +
121r VAL* 1.3 75.6 - - - +
123r ASN* 1.3 56.0 + - - +
124r ILE 3.0 0.6 + - - -
125r ILE* 4.6 5.2 - - - +
126r THR* 2.5 53.2 + - + +
128r SER 3.2 22.2 - - - +
129r PRO* 4.3 7.0 - - + -
130r THR* 4.4 8.7 - - + +
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Residues in contact with ASN 123 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123M ASN* 3.8 21.1 + - - +
124M ILE* 3.9 0.5 - - - +
127M GLY 5.3 5.4 - - - +
119r ASP* 2.8 28.8 + - - +
120r ALA* 3.1 13.1 + - - +
122r VAL* 1.3 74.2 - - - +
124r ILE* 1.3 60.1 + - + +
127r GLY* 3.2 25.9 - - - +
128r SER* 3.1 1.2 - - - -
129r PRO* 3.0 45.9 - - - +
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Residues in contact with ILE 124 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58M ASN* 4.7 7.3 + - - +
124M ILE* 4.1 26.9 - - - +
126M THR 5.0 0.9 - - - +
127M GLY* 3.4 34.5 - - - +
55r VAL* 6.1 1.1 - - - -
58r ASN* 3.6 38.8 - - + +
59r VAL* 4.7 6.3 - - + +
62r VAL* 3.7 26.7 - - + -
120r ALA 3.3 14.8 - - - +
121r VAL* 3.0 7.8 + - - +
122r VAL 3.0 0.6 - - - -
123r ASN* 1.3 85.0 - - - +
125r ILE* 1.3 72.0 + - + +
126r THR 4.4 0.2 - - - -
127r GLY 3.9 4.0 + - - -
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Residues in contact with ILE 125 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58M ASN* 4.8 10.5 - - - +
55r VAL* 4.0 25.8 - - + -
59r VAL* 4.7 1.8 - - + -
80r GLY* 3.1 43.3 - - - +
83r VAL* 3.9 26.0 - - + -
84r ALA* 4.4 15.0 - - + +
87r LEU* 4.5 19.3 - - + +
121r VAL* 3.2 18.3 + - + +
122r VAL 4.2 1.1 - - - +
124r ILE* 1.3 84.8 - - + +
126r THR* 1.3 62.1 + - + +
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Residues in contact with THR 126 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61M ALA* 5.7 4.0 - - - +
62M VAL* 5.4 4.0 - - - +
65M GLN* 3.9 22.4 + - - +
124M ILE* 4.8 1.7 - - - +
83r VAL* 4.5 4.0 - - + -
87r LEU* 6.0 2.2 - - + -
96r LEU* 4.8 10.5 - - + -
100r ILE* 4.1 20.4 - - + -
122r VAL* 2.5 36.9 + - + +
124r ILE 4.4 0.7 - - - -
125r ILE* 1.3 85.9 - - + +
127r GLY* 1.3 58.2 + - - +
128r SER* 2.5 29.6 + - - -
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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
------------------------------------------------------------
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