Contacts of the strand formed by residues 66 - 73 (chain A) in PDB entry 2XB3
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 ASN 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A TRP* 3.6 11.1 - - - -
56A VAL* 4.5 9.8 - - + +
57A PHE 3.1 15.5 - - - +
58A HIS* 3.7 10.5 - - + -
63A THR 4.7 2.6 + - - +
64A THR 2.9 24.6 + - - +
65A GLU* 1.3 72.5 - - - +
67A VAL* 1.3 70.4 + - - +
68A SER* 4.3 8.8 + - - -
141A ARG* 4.0 10.5 - - - +
158A SER 4.8 1.4 - - - +
159A VAL* 3.3 4.0 - - - +
160A SER* 3.0 39.0 + - - -
173A PHE* 4.8 0.2 - - - -
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Residues in contact with VAL 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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38A PHE* 3.9 25.1 - - + -
40A TYR* 4.0 6.5 - - + -
44A TRP* 3.5 21.7 - - + -
55A VAL 4.7 0.2 - - - -
56A VAL* 3.5 0.9 - - - +
57A PHE* 3.0 37.2 + - + +
66A ASN* 1.3 76.9 - - - +
68A SER* 1.3 68.1 + - - +
157A LEU* 3.7 26.5 - - + -
158A SER 3.2 6.7 - - - +
159A VAL* 3.6 24.2 - - + -
176A ILE* 4.1 7.2 - - + -
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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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38A PHE* 5.8 0.9 - - - -
53A VAL* 4.6 5.0 - - - +
55A VAL* 3.1 13.5 - - - -
56A VAL* 3.9 14.6 - - - -
66A ASN* 4.3 8.3 - - - -
67A VAL* 1.3 78.5 - - - +
69A VAL* 1.3 66.2 + - - +
70A VAL* 4.8 8.0 - - - +
156A THR 3.5 1.4 - - - +
157A LEU* 3.3 2.9 - - - -
158A SER* 2.8 42.2 + - - -
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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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36A TYR* 3.7 38.6 - - + +
38A PHE* 3.4 37.5 - - + -
53A VAL* 3.7 2.2 - - - +
54A ASP* 2.7 34.7 + - - +
55A VAL* 2.9 11.0 + - + +
68A SER* 1.3 75.7 - - - +
70A VAL* 1.3 69.1 + - - +
71A VAL* 4.4 2.9 - - + -
155A TYR* 4.9 1.3 - - + -
156A THR 3.3 7.0 - - - +
157A LEU* 4.1 12.1 - - + -
180A PHE* 4.3 15.0 - - + -
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Residues in contact with VAL 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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52A PRO* 3.7 22.9 - - + +
53A VAL* 4.0 20.9 - - + -
68A SER* 4.8 8.7 - - - +
69A VAL* 1.3 74.9 - - - +
71A VAL* 1.3 69.7 + - - +
72A ASN* 3.7 24.0 - - - +
97A ILE* 6.0 9.2 - - + -
154A VAL 3.7 0.6 - - - +
155A TYR* 3.4 5.9 - - - -
156A THR* 2.8 48.5 + - + +
158A SER* 6.0 0.9 - - - +
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Residues in contact with VAL 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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34A ASP* 5.1 9.6 - - - +
36A TYR* 4.3 10.1 - - + -
52A PRO* 3.1 27.6 + - - +
54A ASP* 4.2 21.8 - - + +
69A VAL* 4.3 1.1 - - + -
70A VAL* 1.3 80.8 - - - +
72A ASN* 1.3 64.6 + - - +
153A LYS* 3.8 28.7 - - + -
154A VAL 3.5 6.3 - - - +
155A TYR* 3.7 31.4 - - + +
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Residues in contact with ASN 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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52A PRO* 3.4 23.8 - - - +
70A VAL* 3.7 19.4 - - - +
71A VAL* 1.3 73.5 - - - +
73A THR* 1.3 68.7 + - - +
97A ILE* 5.7 8.1 - - - +
153A LYS* 3.1 8.7 - - - +
154A VAL* 2.8 40.8 + - + +
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Residues in contact with THR 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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72A ASN* 1.3 75.8 - - - +
74A VAL* 1.3 72.6 + - - +
152A GLY 3.2 6.7 - - - +
153A LYS* 3.9 22.2 - - + -
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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