Contacts of the strand formed by residues 65 - 72 (chain A) in PDB entry 5X11
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 LEU 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ILE* 3.3 4.7 - - - +
61A GLN* 2.8 48.4 + - + +
63A THR 4.0 0.2 - - - -
64A LYS* 1.3 76.1 - - - +
66A GLU* 1.3 73.6 + - - +
6I C 4.2 7.9 - - - +
7I A 4.0 32.5 - - - +
8I T 6.3 0.2 - - - -
23J G 3.7 25.4 - - + +
24J T 3.5 32.1 - - - +
25J T 3.5 18.0 + - - +
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A THR* 3.8 24.0 - - + +
59A THR 3.5 4.5 - - - -
60A ILE* 4.2 16.0 - - + +
64A LYS 3.8 5.8 + - - +
65A LEU* 1.3 86.2 - - - +
67A LYS* 1.3 63.4 + - - +
68A LYS* 6.0 2.0 - - + -
7I A 4.0 2.9 - - - +
8I T 3.9 17.1 - - - +
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Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A SER* 3.9 13.7 - - - -
21A ASP* 5.4 2.1 + - - -
58A THR* 3.3 4.3 - - - -
59A THR* 2.8 44.7 + - - +
61A GLN* 3.2 30.8 + - + -
66A GLU* 1.3 77.6 - - - +
68A LYS* 1.3 64.2 + - - +
69A MET* 3.6 28.8 + - - +
7I A 3.0 60.1 + - - +
8I T 3.5 6.3 - - - +
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Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A SER* 3.3 21.3 - - - -
19A GLY 4.1 0.2 + - - -
56A PHE* 3.5 41.5 - - + -
57A ARG 3.3 5.2 - - - +
58A THR* 4.1 10.5 - - + +
66A GLU* 6.0 1.1 - - - -
67A LYS* 1.3 73.0 - - - +
69A MET* 1.3 63.8 + - - +
70A TYR* 3.6 33.7 + - + +
8I T 2.9 18.7 + - - +
9I G 2.6 40.8 + - - +
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Residues in contact with MET 69 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A GLU* 3.7 57.1 - - + +
17A LEU* 3.4 4.5 - - - -
18A SER* 3.8 16.4 - - - -
21A ASP* 4.2 7.4 - - - +
56A PHE* 3.2 3.6 - - - -
57A ARG* 3.0 39.6 + - + +
59A THR* 4.5 21.8 - - - -
67A LYS* 3.6 30.3 - - - +
68A LYS* 1.3 72.0 - - - +
70A TYR* 1.3 62.6 + - - +
71A THR* 4.0 1.9 + - - -
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Residues in contact with TYR 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 3.6 25.3 - - + +
16A GLU* 3.1 23.5 - - - -
17A LEU 2.7 21.4 + - - +
18A SER 4.9 0.2 - - - -
19A GLY 4.6 4.0 - - - -
22A ILE* 5.4 0.7 - - + -
42A TYR* 6.1 0.9 - + - -
45A LEU* 3.6 47.0 - - + +
46A LYS* 4.7 1.9 + - - -
49A THR* 3.4 20.6 + - - -
54A ILE* 3.6 19.5 - - + -
55A THR 3.2 16.4 - - - +
56A PHE* 3.5 21.3 - + + -
68A LYS* 3.6 40.0 + - + +
69A MET* 1.3 74.7 - - - +
71A THR* 1.3 60.7 + - - +
9I G 4.6 6.7 + - - -
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Residues in contact with THR 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 4.9 2.5 - - - +
15A GLY* 5.4 5.8 - - - -
16A GLU* 4.0 23.3 + - + +
54A ILE* 3.2 7.1 - - - -
55A THR* 2.8 47.3 + - - +
57A ARG* 5.9 1.2 - - - +
69A MET 4.6 2.3 + - - -
70A TYR* 1.3 76.7 + - - +
72A LEU* 1.3 76.9 + - + +
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 3.7 42.6 - - + +
12A LEU* 3.5 28.6 + - + +
13A ARG* 3.8 13.2 - - - +
53A PHE 3.7 13.0 - - - +
54A ILE* 4.2 7.8 - - + +
55A THR* 5.3 1.7 - - - +
71A THR* 1.3 89.9 - - + +
73A THR* 1.3 65.4 + - - +
76A GLY 4.0 13.0 - - - +
77A LYS* 3.9 31.6 - - + -
80A LEU* 4.5 8.7 - - + -
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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