Contacts of the strand formed by residues 62 - 70 (chain A) in PDB entry 2X10
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 MSE 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A ILE* 4.2 6.4 - - - +
59A MSE 2.9 32.0 + - - +
60A ASN* 3.5 14.1 - - + +
61A ASP* 1.3 91.1 - - - +
63A PRO* 1.3 85.4 - - + +
64A ILE* 3.8 5.3 + - + +
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Residues in contact with PRO 63 (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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56A GLN* 6.1 2.0 - - + +
57A ASN 4.2 6.1 - - - +
58A ILE* 5.5 3.1 - - + -
62A MSE 1.3 101.7 - - + +
64A ILE* 1.3 65.6 + - - +
65A TYR* 4.2 30.3 - - + +
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Residues in contact with ILE 64 (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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55A MSE 4.4 0.2 - - - -
56A GLN* 3.3 7.9 - - - +
57A ASN* 3.2 41.8 + - + +
58A ILE 5.5 0.4 - - - -
59A MSE 4.0 28.5 - - + +
62A MSE 4.1 9.2 - - + +
63A PRO* 1.3 78.8 - - - +
65A TYR* 1.3 74.1 + - - +
66A MSE 4.8 6.9 - - - +
192A LEU* 5.1 15.7 - - + -
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Residues in contact with TYR 65 (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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34A PHE* 3.8 27.2 - - + -
35A ALA 5.2 5.4 - - - -
37A ALA* 4.6 22.4 - - + -
54A LEU* 4.1 16.8 - - + -
55A MSE 3.4 3.4 - - - -
56A GLN* 3.4 42.3 + - + -
63A PRO* 4.2 28.0 - - + +
64A ILE* 1.3 84.2 - - - +
66A MSE 1.3 66.0 + - - +
192A LEU* 4.0 7.8 - - - +
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Residues in contact with MSE 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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34A PHE* 3.8 4.6 - - - -
53A ASP 3.6 0.7 - - - +
54A LEU* 3.3 3.4 - - - +
55A MSE 2.7 56.6 + - + +
56A GLN 5.2 0.2 - - - -
57A ASN* 4.4 24.2 - - - +
64A ILE* 4.8 7.2 - - - +
65A TYR* 1.3 82.5 - - - +
67A TYR* 1.3 63.6 + - - +
68A SER* 2.9 29.6 - - - +
190A ALA* 3.4 26.0 - - + -
191A LEU 3.3 18.2 - - - +
192A LEU* 4.4 14.6 - - + -
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Residues in contact with TYR 67 (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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34A PHE* 3.3 37.2 - + - -
41A LEU 3.4 11.6 + - - -
42A GLY* 3.6 3.6 - - - -
43A TRP* 3.0 48.7 + + + -
45A THR* 4.9 5.4 - - + -
52A TRP* 3.2 14.8 - - + -
53A ASP 3.6 7.2 - - - -
54A LEU* 3.8 34.6 - - + +
66A MSE 1.3 72.8 - - - +
68A SER* 1.3 61.4 + - - +
81A LEU* 3.5 47.3 - - + -
191A LEU* 3.0 35.3 + - + +
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Residues in contact with SER 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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51A GLY 3.6 1.2 - - - +
52A TRP* 3.3 2.4 - - - -
53A ASP* 2.9 37.3 + - - +
55A MSE 4.4 14.8 - - - +
66A MSE 2.9 36.7 - - - +
67A TYR* 1.3 76.2 + - - +
69A VAL* 1.3 66.0 + - - +
70A CYS* 6.4 0.2 - - - -
189A VAL 3.3 12.8 + - - -
190A ALA* 3.9 1.2 - - - +
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Residues in contact with VAL 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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51A GLY* 3.6 25.1 - - - +
52A TRP* 3.9 22.0 - - + +
68A SER* 1.3 79.6 - - - +
70A CYS* 1.3 64.3 + - - +
71A ASN* 4.2 12.1 - - - +
79A ASN* 3.4 14.4 - - - +
184A ASP* 3.3 43.3 - - + +
187A ALA 2.9 14.8 - - - +
188A CYS* 3.4 0.4 - - - -
189A VAL* 3.1 19.7 + - + +
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Residues in contact with CYS 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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68A SER* 6.4 0.4 - - - -
69A VAL* 1.3 73.8 - - - +
71A ASN* 1.3 67.1 + - - +
72A VAL* 3.5 9.0 + - - +
73A MSE 5.8 1.0 - - - +
108A PHE* 3.8 18.8 - - - -
187A ALA 3.6 4.3 - - - -
188A CYS* 2.0 44.4 - - - -
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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