Contacts of the strand formed by residues 53 - 57 (chain D) in PDB entry 1XWD
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 53 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ALA* 4.3 10.1 - - + -
37D TYR 3.7 8.3 - - - +
38D PRO* 4.8 0.2 - - - -
39D THR* 2.9 8.7 + - - -
51D LYS* 3.8 3.3 - - - +
52D ASN* 1.3 84.0 - - + +
54D THR* 1.3 63.5 + - - +
27E TRP* 3.4 35.2 - - + -
52E THR* 5.6 0.2 - - - +
53E PHE* 3.6 29.2 - - + -
56E LEU* 3.9 18.2 - - + -
77E PRO* 4.7 2.2 - - + -
91E SER* 3.4 14.0 + - - +
92E THR* 3.5 8.5 - - + +
93E ASP 3.0 21.9 + - - -
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Residues in contact with THR 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D ARG 4.1 0.2 - - - +
36D ALA* 3.5 1.6 - - - -
37D TYR* 2.8 71.5 + - + +
39D THR* 2.6 33.9 + - - +
40D PRO* 4.5 2.0 - - + +
43D SER* 5.3 1.2 - - - -
53D VAL* 1.3 73.3 + - - +
55D SER* 1.3 63.2 + - - +
56D GLU 4.0 0.5 + - - -
93E ASP* 3.8 17.2 + - - +
95E THR* 4.1 15.7 - - - +
98E GLY* 4.5 7.0 - - - +
99E LEU 5.4 0.2 - - - +
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Residues in contact with SER 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D ARG 3.5 8.6 + - - -
36D ALA* 4.4 8.3 - - - +
54D THR* 1.3 73.0 - - - +
56D GLU* 1.3 61.8 + - - +
57D SER* 4.5 2.8 + - - -
50E THR* 3.6 25.8 - - - +
51E CYS 4.5 0.3 + - - -
52E THR* 4.9 3.1 - - - -
87E CYS* 3.9 12.0 - - - +
92E THR* 3.4 25.9 - - - +
93E ASP 3.0 7.0 + - - -
94E CYS* 4.6 1.7 - - - -
95E THR* 2.8 31.3 + - - +
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Residues in contact with GLU 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D PHE* 5.8 1.2 - - - -
34D SER* 3.4 4.0 - - - -
35D ARG* 2.9 77.4 + - + +
37D TYR* 3.0 26.4 + - + +
54D THR 4.0 0.2 + - - -
55D SER* 1.3 74.6 + - - +
57D SER* 1.3 61.7 + - - +
95E THR* 3.1 5.8 - - - +
96E VAL 3.5 16.4 - - - +
97E ARG* 3.6 29.7 + - - -
98E GLY 3.0 19.9 + - - +
100E GLY 4.9 0.3 + - - -
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Residues in contact with SER 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D PHE 4.3 0.4 - - - -
34D SER* 3.6 9.2 - - - +
55D SER* 4.5 2.4 + - - -
56D GLU* 1.3 75.8 - - - +
58D THR* 1.3 63.3 + - - +
87D CYS* 3.8 13.7 + - - +
90D HIS* 3.0 30.8 + - - -
50E THR* 3.3 31.5 - - - +
95E THR 3.0 7.6 + - - +
96E VAL* 3.7 24.4 + - - +
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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