Contacts of the helix formed by residues 49 - 66 (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 VAL 49 (chain r).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2598 A 3.9 28.0 - - + +
10q TYR* 3.8 10.1 - - + -
13q ARG* 3.7 27.6 - - + +
45r PHE* 3.0 63.2 + - + +
48r ASN* 1.3 71.5 - - - +
50r PRO* 1.4 61.1 - - + +
51r LYS 3.0 4.0 - - - -
52r PHE* 2.8 31.0 + - + +
53r THR* 3.2 6.9 + - - -
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Residues in contact with PRO 50 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50M PRO* 5.8 1.8 - - + -
9N SER* 6.4 2.5 - - - -
10N TYR* 4.1 20.2 - - + -
11N SER* 5.7 0.7 - - - -
10q TYR* 3.5 36.0 - - + +
46r GLN 3.1 25.4 - - - +
47r THR 3.7 6.1 - - - +
48r ASN 3.4 2.5 - - - -
49r VAL* 1.4 96.4 - - + +
51r LYS* 1.3 65.1 + - + +
53r THR* 3.7 5.3 - - - +
54r SER* 3.1 24.9 + - - -
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Residues in contact with LYS 51 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47r THR* 3.4 27.3 + - - +
48r ASN* 3.0 34.9 + - - +
49r VAL 2.9 0.2 + - - -
50r PRO* 1.3 80.2 - - + +
52r PHE* 1.3 63.0 + - + +
54r SER* 2.9 19.9 + - - -
55r VAL* 3.4 12.0 - - - +
84r ALA* 5.7 0.4 - - - +
88r ASN* 3.8 30.4 + - - +
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Residues in contact with PHE 52 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2588 T 3.6 23.1 - - + +
2598 A 3.5 29.4 - - - +
13q ARG* 4.6 5.6 - - - +
48r ASN* 3.1 28.5 - - + -
49r VAL* 2.8 7.3 + - - +
51r LYS* 1.3 77.6 - - + +
53r THR* 1.3 66.5 + - - +
54r SER 3.2 1.6 - - - -
55r VAL* 3.1 7.3 + - - +
56r ASN* 3.0 26.5 + - - +
81r LEU* 3.5 45.5 - - + +
84r ALA* 3.6 13.5 - - + -
85r ARG* 3.5 14.1 - - - -
88r ASN* 3.4 28.0 - - - -
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Residues in contact with THR 53 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8q ARG 4.8 2.9 - - - +
9q SER* 4.3 5.2 - - - -
10q TYR* 3.5 41.2 - - + +
13q ARG* 2.8 37.8 + - - +
49r VAL 3.2 8.4 + - - -
50r PRO* 3.7 8.1 - - - -
52r PHE* 1.3 78.0 - - - +
54r SER* 1.3 63.2 + - - +
56r ASN* 3.1 17.9 + - + +
57r GLU* 3.1 12.9 + - + +
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Residues in contact with SER 54 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50M PRO 5.3 1.6 - - - -
54M SER* 3.3 35.7 - - - -
58M ASN* 5.3 5.6 + - - -
50r PRO 3.1 12.5 + - - -
51r LYS* 2.9 21.7 + - - -
53r THR* 1.3 77.1 - - - +
55r VAL* 1.3 63.6 + - - +
57r GLU* 3.4 10.4 + - - +
58r ASN* 3.2 27.9 + - - +
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Residues in contact with VAL 55 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51r LYS 3.4 17.3 - - - +
52r PHE* 3.1 13.4 + - - +
54r SER* 1.3 81.6 + - - +
56r ASN* 1.3 61.8 + - - +
58r ASN* 3.3 4.3 + - - +
59r VAL* 2.8 53.3 + - + +
77r GLN* 5.4 0.7 - - - +
80r GLY 4.5 7.9 - - - +
81r LEU* 4.5 12.8 - - + +
84r ALA* 4.2 17.9 - - + -
124r ILE* 6.1 0.9 - - - -
125r ILE* 4.0 25.6 - - + -
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Residues in contact with ASN 56 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927 T 5.2 5.5 + - - +
937 A 4.4 31.6 + - - +
13q ARG* 4.3 13.5 - - - +
52r PHE* 3.0 16.4 + - - +
53r THR* 3.1 15.1 + - + +
55r VAL* 1.3 77.0 - - - +
57r GLU* 1.3 57.5 + - - +
60r SER* 2.9 33.8 + - - -
77r GLN* 3.4 20.7 + - - +
81r LEU* 3.4 29.9 - - - +
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Residues in contact with GLU 57 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51M LYS* 4.2 31.4 - - - +
54M SER* 5.7 0.5 + - - -
87M LEU* 5.8 3.6 - - - +
88M ASN* 5.2 4.3 - - - +
53r THR* 3.1 11.9 + - + +
54r SER* 3.7 11.0 - - - +
55r VAL 3.2 0.4 - - - -
56r ASN* 1.3 78.3 - - - +
58r ASN* 1.3 69.8 + - - +
60r SER* 3.6 3.7 - - - -
61r ALA* 3.0 22.5 + - + +
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Residues in contact with ASN 58 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54M SER* 5.5 4.2 + - - -
58M ASN* 4.2 17.6 - - - +
124M ILE* 4.3 10.0 + - - +
125M ILE* 4.2 18.4 + - - +
54r SER* 3.2 16.7 + - - +
55r VAL* 4.0 2.2 - - - +
57r GLU* 1.3 86.6 - - - +
59r VAL* 1.3 66.8 + - - +
61r ALA* 3.2 9.1 + - - +
62r VAL* 3.1 26.3 + - - +
124r ILE* 3.6 28.6 - - + +
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Residues in contact with VAL 59 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55r VAL* 2.8 41.7 + - + +
58r ASN* 1.3 71.0 - - - +
60r SER* 1.3 62.2 + - - +
62r VAL* 3.1 9.2 + - - +
63r LEU* 3.0 30.5 + - + +
76r TYR 4.4 7.0 - - - +
77r GLN* 3.3 27.1 - - - +
80r GLY* 5.0 1.6 - - - -
121r VAL* 4.1 37.5 - - + +
124r ILE* 4.9 9.0 - - + -
125r ILE* 4.6 6.3 - - + -
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Residues in contact with SER 60 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937 A 4.8 0.9 - - - -
947 T 2.9 19.9 + - - -
89p ARG 4.5 4.0 + - - -
90p ILE 4.9 2.3 + - - -
56r ASN 2.9 20.9 + - - -
57r GLU* 3.6 4.7 - - - -
59r VAL* 1.3 78.0 - - - +
61r ALA* 1.3 62.3 + - - +
63r LEU* 3.1 3.9 + - - -
64r THR* 3.0 10.1 + - - -
73r ARG* 2.7 41.8 + - - +
77r GLN* 3.5 8.2 - - - +
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Residues in contact with ALA 61 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126M THR 5.9 2.9 - - - +
90p ILE 5.8 0.7 - - - -
57r GLU* 3.0 14.7 + - + +
58r ASN* 3.4 12.3 - - - +
60r SER* 1.3 76.3 - - - +
62r VAL* 1.3 63.4 + - + +
64r THR* 3.2 9.8 + - - -
65r GLN* 3.1 26.2 + - + +
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Residues in contact with VAL 62 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126M THR 5.0 8.3 - - - +
127M GLY* 5.1 1.6 - - - -
58r ASN 3.1 13.1 + - - +
59r VAL* 3.1 10.3 + - + +
61r ALA* 1.3 76.8 - - + +
63r LEU* 1.3 63.6 + - + +
65r GLN* 2.9 11.2 + - + +
66r TYR* 2.9 51.7 + - + -
117r VAL* 5.5 0.4 - - + +
120r ALA* 3.8 17.7 - - + +
121r VAL* 5.0 4.7 - - + +
124r ILE* 3.7 32.8 - - + -
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Residues in contact with LEU 63 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59r VAL* 3.0 33.2 + - + +
60r SER* 3.1 7.8 + - - +
62r VAL* 1.3 76.3 - - + +
64r THR* 1.3 61.3 + - - +
66r TYR* 3.2 2.7 + - - +
67r GLY 3.0 4.5 + - - -
68r ILE* 2.9 38.9 + - + -
73r ARG* 3.5 48.5 - - + +
76r TYR* 3.6 31.9 - - + -
77r GLN* 4.0 10.3 - - - +
117r VAL* 3.6 19.1 - - + -
121r VAL* 5.0 2.9 - - + -
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Residues in contact with THR 64 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90p ILE* 2.6 27.9 + - + +
91p GLY* 3.6 13.9 - - - +
92p SER 3.4 27.6 - - - +
93p GLY* 4.5 1.6 - - - -
94p PRO* 3.3 4.3 - - + +
95p ALA* 3.2 19.8 + - + +
60r SER 3.0 5.4 + - - -
61r ALA* 3.4 11.2 - - - -
62r VAL 3.1 0.2 - - - -
63r LEU* 1.3 77.2 - - - +
65r GLN* 1.3 64.1 + - - +
67r GLY 3.1 10.0 + - - -
73r ARG* 2.9 22.5 + - - +
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Residues in contact with GLN 65 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92M SER* 4.4 17.2 + - - -
126M THR 6.0 1.3 - - - +
133M VAL* 3.9 20.7 - - - +
134M SER* 3.0 42.9 + - - +
92p SER 4.9 7.7 + - - -
93p GLY* 5.3 1.2 - - - -
94p PRO* 3.4 32.4 - - - +
61r ALA* 3.1 18.2 + - + +
62r VAL* 2.9 12.3 + - + +
64r THR* 1.3 76.6 - - - +
66r TYR* 1.3 63.9 + - + +
67r GLY 3.3 0.2 - - - -
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Residues in contact with TYR 66 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134M SER* 5.9 4.9 - - - -
94p PRO* 4.7 0.7 - - - -
62r VAL* 2.9 36.1 + - + +
63r LEU* 3.2 6.0 + - - +
65r GLN* 1.3 80.1 - - + +
67r GLY* 1.3 62.0 + - - +
68r ILE* 3.2 20.9 + - + +
116r GLN* 3.2 42.3 + - + -
117r VAL* 3.9 20.2 - - + -
120r ALA* 3.5 30.5 - - + +
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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
------------------------------------------------------------
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