Contacts of the strand formed by residues 25 - 31 (chain B) in PDB entry 2UX2
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 ALA 25 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B LEU* 3.5 11.0 - - - +
3B CYS* 3.6 6.8 - - - -
23B PHE* 3.7 2.6 - - - +
24B ASP* 1.3 87.4 - - - +
26B CYS* 1.3 59.9 + - - +
39B CYS* 3.8 0.7 - - - -
40B TRP 2.8 34.9 + - - +
41B LYS 4.2 1.6 - - - -
42B PHE* 3.6 31.9 - - + +
45B CYS* 4.7 4.9 - - - -
64B CYS 3.4 11.2 - - - +
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Residues in contact with CYS 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B LEU* 3.7 10.8 - - - -
2B GLN 3.4 13.2 - - - -
3B CYS* 2.0 46.2 - - - -
25B ALA* 1.3 74.4 - - - +
27B LEU* 1.3 60.3 + - - +
38B LYS 3.5 2.0 - - - -
40B TRP* 4.5 1.8 - - - -
62B TYR 3.8 0.5 - - - +
63B CYS* 3.2 7.6 - - - +
64B CYS* 2.8 29.9 + - - -
66B LYS 4.0 0.4 - - - -
68B LEU 4.7 0.4 - - - -
69B CYS* 3.7 22.2 - - - -
70B ASN* 3.5 23.1 - - + -
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B CYS* 1.3 75.0 - - - +
28B ILE* 1.3 67.2 + - - +
29B THR* 3.3 27.4 - - - +
36B TYR* 5.4 1.6 - - + +
37B ASN* 3.3 1.6 - - - -
38B LYS* 2.8 40.9 + - + +
40B TRP* 3.4 57.2 - - + -
50B VAL* 4.4 8.5 - - + -
54B LEU* 4.6 8.5 - - + -
61B TYR* 3.9 12.8 - - + -
62B TYR 3.4 5.8 - - - +
63B CYS* 3.6 20.2 - - - -
70B ASN* 3.0 11.4 + - - -
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Residues in contact with ILE 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LEU* 1.3 75.3 - - - +
29B THR* 1.3 67.2 + - - +
30B LYS* 5.1 1.1 - - + -
35B VAL* 4.2 6.7 - - + -
36B TYR 3.3 5.4 - - - +
37B ASN* 3.0 13.9 - - - +
61B TYR* 3.3 2.6 - - - +
62B TYR* 2.9 62.3 + - + +
70B ASN* 3.3 10.7 - - + +
71B PHE 3.3 11.2 - - - +
72B ASN* 2.6 60.6 - - - +
74B GLN* 4.4 3.1 - - + -
75B LEU* 3.9 10.3 - - + +
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Residues in contact with THR 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LEU* 3.3 25.5 - - - +
28B ILE* 1.3 79.2 + - - +
30B LYS* 1.3 66.3 + - - +
31B ALA* 4.0 3.9 + - + +
34B GLN 3.9 0.3 - - - +
35B VAL* 3.4 5.8 - - - +
36B TYR* 2.9 37.2 + - + +
50B VAL* 3.8 5.8 - - + +
54B LEU* 4.0 14.5 - - + +
59B LEU* 3.7 37.0 - - + -
60B THR 3.2 17.0 - - - +
61B TYR* 3.5 3.3 - - - +
75B LEU* 4.2 0.2 - - - -
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Residues in contact with LYS 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ILE* 5.1 0.9 - - + -
29B THR* 1.3 73.9 - - - +
31B ALA* 1.3 60.0 + - - +
32B GLY 3.8 7.0 + - - +
34B GLN 3.6 5.8 - - - +
35B VAL* 4.3 19.3 - - + -
59B LEU* 3.3 3.4 - - - -
60B THR* 3.0 35.4 + - - +
72B ASN* 3.0 39.1 + - - +
75B LEU* 3.5 26.2 - - + +
76B GLU* 2.9 44.6 + - + +
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Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B THR* 4.0 2.4 + - + -
30B LYS* 1.3 71.6 - - - +
32B GLY* 1.3 63.9 + - - +
33B LEU 3.3 0.7 + - - -
34B GLN* 2.9 27.6 + - - +
36B TYR* 4.4 5.8 - - + -
56B GLU* 3.3 39.2 - - + +
58B GLU 3.5 19.5 - - - +
59B LEU* 3.8 10.1 - - + -
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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