Contacts of the helix formed by residues 49 - 66 (chain j) 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 j).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2118 A 3.9 28.5 - - + +
10i TYR* 3.8 9.4 - - + -
13i ARG* 3.7 27.3 + - - +
45j PHE* 3.0 63.8 + - + +
48j ASN* 1.3 70.4 - - - +
50j PRO* 1.4 61.3 - - + +
51j LYS 3.0 4.7 - - - -
52j PHE* 2.8 31.2 + - - +
53j THR 3.2 6.4 + - - -
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Residues in contact with PRO 50 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E PRO* 5.8 2.0 - - + -
9F SER* 6.4 2.5 - - - -
10F TYR* 4.1 20.4 - - + -
11F SER* 5.7 0.4 - - - -
10i TYR* 3.5 35.6 - - + -
46j GLN 3.1 25.6 - - - +
47j THR 3.7 6.1 - - - +
48j ASN 3.4 2.0 - - - -
49j VAL* 1.4 96.2 - - + +
51j LYS* 1.3 65.4 + - + +
52j PHE 3.2 0.2 - - - -
53j THR* 3.7 5.1 - - - +
54j SER* 3.1 25.1 + - - -
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Residues in contact with LYS 51 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47j THR* 3.4 28.5 + - - +
48j ASN* 3.0 32.8 + - - +
50j PRO* 1.3 79.5 - - + +
52j PHE* 1.3 63.1 + - + +
54j SER* 2.9 19.3 + - - -
55j VAL* 3.4 12.3 - - - +
84j ALA* 5.7 0.6 - - - +
88j ASN* 3.8 29.5 + - - +
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Residues in contact with PHE 52 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2108 T 3.6 24.7 - - + -
2118 A 3.5 28.5 - - - +
13i ARG* 4.6 6.5 - - - +
48j ASN* 3.1 28.9 - - + -
49j VAL* 2.8 7.5 + - + +
51j LYS* 1.3 76.0 - - + +
53j THR* 1.3 66.4 + - - +
54j SER 3.2 0.4 - - - -
55j VAL* 3.1 8.4 + - - +
56j ASN* 3.0 27.4 + - - -
81j LEU* 3.5 46.2 - - + +
84j ALA* 3.6 13.7 - - + -
85j ARG* 3.5 13.7 - - - -
88j ASN* 3.4 28.5 - - - -
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Residues in contact with THR 53 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8i ARG 4.8 2.9 - - - +
9i SER* 4.3 5.2 - - - -
10i TYR* 3.5 42.2 - - + +
13i ARG* 2.8 37.5 + - - +
49j VAL 3.2 8.1 + - - -
50j PRO 3.3 7.8 + - - -
52j PHE* 1.3 78.5 - - - +
54j SER* 1.3 62.6 + - - +
56j ASN* 3.1 18.4 + - + +
57j GLU* 3.1 13.0 + - + +
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Residues in contact with SER 54 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E PRO 5.3 0.9 - - - -
54E SER* 3.3 36.9 - - - -
58E ASN* 5.3 5.0 + - - -
50j PRO 3.1 12.3 + - - -
51j LYS* 2.9 21.7 + - - -
53j THR* 1.3 77.3 - - - +
55j VAL* 1.3 63.1 + - - +
57j GLU* 3.4 10.3 + - - +
58j ASN* 3.2 28.2 + - - +
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Residues in contact with VAL 55 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51j LYS 3.4 17.3 - - - +
52j PHE* 3.1 14.2 + - - +
54j SER* 1.3 84.8 + - - +
56j ASN* 1.3 58.5 + - - +
58j ASN* 3.3 3.9 + - - +
59j VAL* 2.8 53.0 + - + +
77j GLN* 5.4 0.9 - - - +
80j GLY 4.5 8.1 - - - +
81j LEU* 4.5 12.8 - - + -
84j ALA* 4.2 18.4 - - + -
124j ILE* 6.1 1.6 - - - -
125j ILE* 4.0 25.1 - - + -
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Residues in contact with ASN 56 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1407 T 5.2 5.3 + - - +
1417 A 4.4 31.6 + - - +
13i ARG* 4.3 13.9 - - - +
52j PHE* 3.0 16.9 + - - +
53j THR* 3.1 15.6 + - + +
55j VAL* 1.3 76.5 - - - +
57j GLU* 1.3 56.7 + - - +
60j SER* 2.9 33.7 + - - -
77j GLN* 3.4 21.1 + - - +
81j LEU* 3.4 31.2 - - - +
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Residues in contact with GLU 57 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E LYS* 4.2 31.0 - - - +
54E SER* 5.7 0.5 + - - -
87E LEU* 5.8 3.8 - - - +
88E ASN* 5.2 4.2 - - - +
53j THR* 3.1 11.3 + - + +
54j SER* 3.7 11.2 - - - +
55j VAL 3.2 0.2 - - - -
56j ASN* 1.3 77.4 - - - +
58j ASN* 1.3 71.1 + - - +
60j SER* 3.6 4.3 - - - -
61j ALA* 3.0 23.5 + - + +
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Residues in contact with ASN 58 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E SER* 5.5 5.1 + - - -
55E VAL* 6.4 0.2 - - - +
58E ASN* 4.2 18.4 - - - +
124E ILE* 4.3 9.4 + - - +
125E ILE* 4.2 16.3 + - - +
54j SER* 3.2 15.9 + - - +
55j VAL* 4.0 2.2 - - - +
57j GLU* 1.3 85.3 - - - +
59j VAL* 1.3 66.0 + - - +
61j ALA* 3.2 9.1 + - - +
62j VAL* 3.1 26.5 + - - +
124j ILE* 3.6 29.0 - - + +
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Residues in contact with VAL 59 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55j VAL* 2.8 41.7 + - + +
56j ASN 4.2 0.2 - - - +
58j ASN* 1.3 72.5 - - - +
60j SER* 1.3 62.8 + - - +
62j VAL* 3.1 9.6 + - - +
63j LEU* 3.0 30.7 + - + +
76j TYR 4.4 7.2 - - - +
77j GLN* 3.3 27.1 - - - +
80j GLY* 5.0 1.6 - - - -
121j VAL* 4.1 37.5 - - + +
124j ILE* 4.9 8.1 - - + -
125j ILE* 4.6 6.5 - - + -
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Residues in contact with SER 60 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1417 A 4.8 1.3 - - - -
1427 T 2.9 19.3 + - - -
89h ARG 4.5 4.3 + - - -
90h ILE 4.9 2.1 + - - -
56j ASN 2.9 21.5 + - - -
57j GLU* 3.6 4.9 - - - -
59j VAL* 1.3 77.9 - - - +
61j ALA* 1.3 61.7 + - - +
63j LEU* 3.1 3.8 + - - -
64j THR* 3.0 10.2 + - - -
73j ARG* 2.7 41.9 + - - +
77j GLN* 3.5 8.9 - - - +
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Residues in contact with ALA 61 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E THR 5.9 2.9 - - - +
90h ILE 5.8 0.7 - - - -
57j GLU* 3.0 14.5 + - + +
58j ASN* 3.4 13.0 - - - +
60j SER* 1.3 76.9 - - - +
62j VAL* 1.3 62.9 + - + +
64j THR* 3.2 10.6 + - - -
65j GLN* 3.1 26.2 + - + +
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Residues in contact with VAL 62 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E THR 5.0 8.7 - - - +
127E GLY* 5.1 1.8 - - - -
58j ASN 3.1 13.5 + - - +
59j VAL* 3.3 10.1 - - + +
61j ALA* 1.3 76.8 - - + +
63j LEU* 1.3 62.8 + - + +
65j GLN* 2.9 11.7 + - + +
66j TYR* 2.9 50.2 + - + -
117j VAL* 5.5 0.4 - - + -
120j ALA* 3.8 18.6 - - + +
121j VAL* 5.0 4.3 - - + +
124j ILE* 3.7 32.8 - - + -
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Residues in contact with LEU 63 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59j VAL* 3.0 34.5 + - + +
60j SER* 3.1 7.6 + - - +
62j VAL* 1.3 76.3 - - + +
64j THR* 1.3 61.1 + - - +
66j TYR* 3.2 3.5 + - - +
67j GLY 3.0 4.2 + - - -
68j ILE* 2.9 38.9 + - + -
73j ARG* 3.5 47.8 - - + +
76j TYR* 3.6 31.4 - - + -
77j GLN* 4.0 10.5 - - - +
117j VAL* 3.6 18.8 - - + -
121j VAL* 5.0 3.4 - - + -
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Residues in contact with THR 64 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90h ILE* 2.6 28.9 + - + +
91h GLY* 3.6 13.7 - - - +
92h SER 3.4 27.4 - - - +
93h GLY* 4.5 1.6 - - - -
94h PRO* 3.3 4.8 - - + +
95h ALA* 3.2 19.5 + - + +
60j SER 3.0 5.7 + - - -
61j ALA* 3.4 11.4 - - - -
62j VAL 3.1 0.2 - - - -
63j LEU* 1.3 77.4 - - - +
65j GLN* 1.3 64.3 + - - +
67j GLY 3.1 10.2 + - - -
73j ARG* 2.9 22.6 + - - +
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Residues in contact with GLN 65 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E SER* 4.4 16.4 + - - -
126E THR 6.0 0.7 - - - +
133E VAL* 3.9 20.4 - - - +
134E SER* 3.0 43.4 + - - +
92h SER 4.9 7.9 + - - -
93h GLY* 5.3 0.8 - - - -
94h PRO* 3.4 32.2 - - - +
61j ALA* 3.1 17.7 + - + +
62j VAL* 2.9 11.5 + - - +
64j THR* 1.3 78.1 - - - +
66j TYR* 1.3 63.9 + - + +
67j GLY 3.3 0.2 - - - -
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Residues in contact with TYR 66 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E SER* 5.9 5.4 - - - -
94h PRO* 4.7 0.9 - - - -
62j VAL* 2.9 34.3 + - + +
63j LEU* 3.2 6.0 + - - +
65j GLN* 1.3 80.6 - - + +
67j GLY* 1.3 62.1 + - - +
68j ILE* 3.2 20.8 + - + +
116j GLN* 3.2 41.5 + - + -
117j VAL* 3.9 18.8 - - + -
120j ALA* 3.5 30.8 - - + +
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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
------------------------------------------------------------
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