Contacts of the helix formed by residues 49 - 66 (chain X) 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 X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1398 A 3.9 28.7 - - + +
10W TYR* 3.8 10.8 - - + -
13W ARG* 3.7 26.2 - - - +
45X PHE* 3.0 62.3 + - + +
48X ASN* 1.3 71.7 - - - +
50X PRO* 1.4 62.1 - - + +
51X LYS 3.0 4.0 - - - -
52X PHE* 2.8 30.1 + - + +
53X THR 3.2 6.9 + - - -
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Residues in contact with PRO 50 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10W TYR* 3.5 37.9 - - + -
46X GLN 3.1 24.9 - - - +
47X THR 3.7 6.1 - - - +
48X ASN 3.4 2.5 - - - -
49X VAL* 1.4 96.4 - - + +
51X LYS* 1.3 64.1 + - + +
52X PHE 3.2 0.2 - - - -
53X THR* 3.7 4.6 - - - +
54X SER* 3.1 25.3 + - - -
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Residues in contact with LYS 51 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47X THR* 3.4 27.3 + - - +
48X ASN* 3.0 34.9 + - - +
50X PRO* 1.3 81.1 - - + +
52X PHE* 1.3 63.2 + - + +
54X SER* 2.9 19.3 + - - -
55X VAL* 3.4 12.7 - - - +
84X ALA* 6.2 0.4 - - - -
88X ASN* 3.8 29.7 + - - +
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Residues in contact with PHE 52 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1388 T 3.6 24.9 - - + +
1398 A 3.5 29.2 - - - +
13W ARG* 4.9 5.8 - - - +
48X ASN* 3.1 29.6 - - + -
49X VAL* 2.8 7.3 + - - +
51X LYS* 1.3 77.0 - - + +
53X THR* 1.3 65.8 + - - +
54X SER 3.2 0.4 - - - -
55X VAL* 3.1 7.3 + - - +
56X ASN* 3.0 27.5 + - - +
81X LEU* 3.5 44.8 - - + +
84X ALA* 3.6 13.2 - - + -
85X ARG* 3.5 13.9 - - - -
88X ASN* 3.4 28.7 - - - -
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Residues in contact with THR 53 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8W ARG 4.8 2.9 - - - +
9W SER* 4.3 5.4 - - - -
10W TYR* 3.5 42.5 - - + +
13W ARG* 2.8 36.9 + - - +
49X VAL 3.2 8.2 + - - -
50X PRO 3.3 8.0 + - - -
52X PHE* 1.3 78.3 - - - +
54X SER* 1.3 61.4 + - - +
56X ASN* 3.1 18.1 + - + +
57X GLU* 3.1 13.0 + - + +
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Residues in contact with SER 54 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50X PRO 3.1 12.7 + - - -
51X LYS* 2.9 22.0 + - - -
53X THR* 1.3 77.3 - - - +
55X VAL* 1.3 63.0 + - - +
57X GLU* 3.4 10.4 + - - +
58X ASN* 3.2 28.9 + - - +
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Residues in contact with VAL 55 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51X LYS 3.4 17.3 - - - +
52X PHE* 3.1 13.4 + - - +
54X SER* 1.3 81.4 + - - +
56X ASN* 1.3 61.3 - - - +
58X ASN* 3.3 3.6 + - - +
59X VAL* 2.8 52.9 + - + +
77X GLN* 5.4 0.4 - - - +
80X GLY* 4.5 8.3 - - - +
81X LEU* 4.5 13.0 - - + +
84X ALA* 4.2 18.2 - - + -
124X ILE* 6.1 1.3 - - - -
125X ILE* 4.0 25.8 - - + -
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Residues in contact with ASN 56 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2127 T 5.2 5.1 + - - +
2137 A 4.4 30.8 + - - +
13W ARG* 4.3 13.9 - - - +
52X PHE 3.0 16.9 + - - -
53X THR* 3.4 14.4 - - + +
55X VAL* 1.3 77.0 - - - +
57X GLU* 1.3 57.4 + - - +
60X SER* 2.9 33.3 + - - -
77X GLN* 3.4 19.7 + - - +
81X LEU* 3.4 30.9 - - - +
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Residues in contact with GLU 57 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53X THR* 3.1 12.6 + - + +
54X SER* 3.7 11.4 - - - +
55X VAL 3.2 0.2 - - - -
56X ASN* 1.3 77.4 - - - +
58X ASN* 1.3 70.2 + - - +
60X SER* 3.6 4.3 - - - -
61X ALA* 3.0 23.3 + - + +
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Residues in contact with ASN 58 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54X SER* 3.2 16.9 + - - +
55X VAL* 4.0 2.4 - - - +
57X GLU* 1.3 84.5 - - - +
59X VAL* 1.3 66.5 + - - +
61X ALA* 3.2 9.5 + - - +
62X VAL* 3.1 25.8 + - - +
124X ILE* 3.6 28.6 - - + +
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Residues in contact with VAL 59 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55X VAL* 2.8 41.9 + - + +
56X ASN 4.2 0.2 - - - +
58X ASN* 1.3 71.6 - - - +
60X SER* 1.3 64.0 + - - +
62X VAL* 3.1 10.1 + - - +
63X LEU* 3.0 30.5 + - + +
76X TYR 4.4 6.5 - - - +
77X GLN* 3.3 27.8 - - - +
80X GLY* 5.0 1.8 - - - -
121X VAL* 4.1 38.4 - - + +
124X ILE* 4.9 8.1 - - + -
125X ILE* 4.6 6.1 - - + -
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Residues in contact with SER 60 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2137 A 4.8 1.3 - - - -
2147 T 2.9 19.9 + - - -
89V ARG 4.5 4.2 + - - -
90V ILE 4.9 2.0 + - - -
56X ASN 2.9 21.1 + - - -
57X GLU* 3.6 5.2 - - - -
59X VAL* 1.3 77.1 - - - +
61X ALA* 1.3 63.2 + - - +
63X LEU* 3.1 3.6 + - - -
64X THR* 3.0 9.9 + - - -
73X ARG* 2.7 42.3 + - - +
77X GLN* 3.5 8.7 - - - +
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Residues in contact with ALA 61 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90V ILE 5.8 0.7 - - - -
57X GLU* 3.0 14.9 + - + +
58X ASN* 3.2 12.5 + - - +
60X SER* 1.3 76.5 - - - +
62X VAL* 1.3 62.8 + - + +
64X THR* 3.2 10.1 + - - -
65X GLN* 3.1 26.0 + - + +
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Residues in contact with VAL 62 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58X ASN 3.1 15.0 + - - +
59X VAL* 3.3 10.1 - - + +
61X ALA* 1.3 77.0 - - + +
63X LEU* 1.3 63.6 + - + +
65X GLN* 2.9 11.8 + - - +
66X TYR* 2.9 50.5 + - + -
117X VAL* 5.5 0.4 - - + +
120X ALA* 3.8 18.6 - - + -
121X VAL* 5.0 4.0 - - + +
124X ILE* 3.7 32.1 - - + -
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Residues in contact with LEU 63 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59X VAL* 3.0 33.4 + - + +
60X SER* 3.1 8.0 + - - +
62X VAL* 1.3 77.2 - - + +
64X THR* 1.3 61.7 + - - +
66X TYR* 3.2 3.6 + - - +
67X GLY 3.0 4.7 + - - -
68X ILE* 2.9 38.1 + - + +
73X ARG* 3.5 48.2 - - + +
76X TYR* 3.6 32.1 - - + -
77X GLN* 4.0 10.3 - - - +
117X VAL* 3.6 19.7 - - + -
121X VAL* 5.0 2.9 - - + -
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Residues in contact with THR 64 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90V ILE* 2.6 27.1 + - + +
91V GLY* 3.6 14.4 - - - +
92V SER 3.4 27.8 - - - +
93V GLY* 4.5 1.8 - - - -
94V PRO* 3.3 4.1 - - + +
95V ALA* 3.2 19.4 + - + +
60X SER 3.0 5.8 + - - -
61X ALA* 3.4 10.5 - - - -
62X VAL 3.1 0.2 - - - -
63X LEU* 1.3 76.8 - - - +
65X GLN* 1.3 63.3 + - - +
67X GLY 3.1 10.2 + - - -
73X ARG* 2.9 23.3 + - - +
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Residues in contact with GLN 65 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92V SER 4.9 8.3 + - - -
93V GLY* 5.3 0.8 - - - -
94V PRO* 3.4 31.7 - - - +
61X ALA 3.1 17.9 + - - +
62X VAL* 2.9 12.8 + - + +
64X THR* 1.3 77.3 - - - +
66X TYR* 1.3 63.6 + - + +
67X GLY 3.3 0.2 - - - -
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Residues in contact with TYR 66 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94V PRO* 4.7 1.1 - - - -
62X VAL* 2.9 35.6 + - + +
63X LEU* 3.2 5.8 + - - +
65X GLN* 1.3 79.7 - - + +
67X GLY* 1.3 61.9 + - - +
68X ILE* 3.2 21.2 + - + +
116X GLN* 3.2 41.9 + - + -
117X VAL* 3.9 18.6 - - + -
120X ALA* 3.5 30.1 - - + +
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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