Contacts of the strand formed by residues 67 - 73 (chain A) in PDB entry 2XOA
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 PHE 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A GLU* 3.2 6.2 - - - +
20A VAL* 2.6 43.2 + - + +
21A VAL* 5.4 2.2 - - - -
22A LEU* 5.4 7.4 - - + -
37A LEU* 3.9 29.2 - - + -
39A ALA 5.4 2.9 - - - -
47A CYS* 5.3 2.7 - - - -
64A ILE 4.7 0.9 - - - -
65A CYS* 3.2 28.3 - - - -
66A CYS* 1.3 73.3 - - - +
68A THR* 1.3 60.6 + - - +
109A LEU* 3.9 33.0 - - + -
110A ARG 3.2 6.3 - - - -
111A HIS* 3.6 46.9 - + + -
112A ALA* 4.4 0.9 - - - +
118A LEU* 4.0 29.2 - - + -
137A LEU* 4.0 11.9 - - + -
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Residues in contact with THR 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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17A ASP* 4.3 21.9 + - + +
18A ASP 3.7 4.6 + - - +
19A GLU* 4.2 16.6 + - - +
67A PHE* 1.3 72.8 + - - +
69A LEU* 1.3 70.9 + - - +
70A GLU* 2.9 26.1 + - - +
109A LEU* 3.5 6.7 - - - -
110A ARG* 2.7 39.5 + - - -
112A ALA* 4.9 6.4 - - - +
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Residues in contact with LEU 69 (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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14A LEU* 4.3 11.0 - - + -
15A ARG 3.6 22.7 - - - +
16A THR* 3.3 7.5 - - + -
17A ASP 2.6 27.1 + - - -
18A ASP* 3.0 17.9 + - + +
20A VAL* 3.8 24.9 - - + -
67A PHE 4.2 0.2 - - - -
68A THR* 1.3 70.4 - - - +
70A GLU* 1.3 62.1 + - - +
71A GLN 3.3 2.7 - - - +
101A LEU* 3.7 37.5 - - + -
107A ILE* 4.0 21.5 - - + -
108A LEU 4.0 2.2 - - - -
109A LEU* 3.8 20.4 - - + -
202A MET* 4.1 4.5 - - - -
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Residues in contact with GLU 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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16A THR* 4.2 6.9 - - - -
17A ASP* 4.9 10.3 - - - +
68A THR* 2.9 20.0 + - + +
69A LEU* 1.3 73.2 - - - +
71A GLN* 1.3 72.6 + - + +
108A LEU* 3.0 28.4 + - + +
110A ARG* 3.6 45.2 + - + +
117A TYR* 3.5 21.7 + - + -
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Residues in contact with GLN 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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16A THR* 3.9 5.6 - - - +
69A LEU* 3.3 3.6 - - - +
70A GLU* 1.3 89.8 + - + +
72A SER* 1.3 64.3 + - - +
73A LEU* 4.1 17.7 - - + +
81A MET* 4.7 16.1 - - - +
106A ALA 4.2 1.3 - - - -
107A ILE* 3.2 7.6 - - - +
108A LEU* 2.9 50.8 + - + +
147A TRP* 3.4 20.4 - - + -
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Residues in contact with SER 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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16A THR* 3.5 11.6 - - - +
71A GLN* 1.3 77.1 + - - +
73A LEU* 1.3 65.1 + - - +
99A ARG* 5.0 9.8 - - - +
100A THR 5.2 0.9 - - - -
101A LEU* 3.5 36.4 - - - +
105A HIS* 2.9 37.2 + - - +
106A ALA 3.3 4.9 - - - -
107A ILE* 3.9 6.7 - - - +
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Residues in contact with LEU 73 (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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71A GLN* 4.1 23.6 - - + +
72A SER* 1.3 81.0 + - - +
74A SER* 1.3 71.9 + - - +
77A ALA* 3.9 30.3 - - + +
78A LEU* 4.0 15.0 - - + +
81A MET* 4.5 14.8 - - + -
105A HIS* 3.2 7.3 - - - -
106A ALA* 2.7 42.4 + - + +
147A TRP* 3.8 23.1 - - + -
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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
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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