Contacts of the strand formed by residues 39 - 44 (chain B) in PDB entry 5YXK
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 39 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B PHE* 4.0 28.7 - - + -
32B TRP 3.5 6.3 - - - +
33B GLN* 4.8 7.4 - - + +
37B ASN 4.4 7.2 - - - +
38B LEU* 1.3 76.6 - - - +
40B LEU* 1.3 63.9 + - - +
41B ASN* 3.5 29.6 - - - +
42B GLU* 4.4 1.8 - - + +
52B SER* 3.4 32.1 + - - +
53B VAL* 3.4 6.5 - - + +
54B HIS* 3.1 24.8 + - - +
57B TYR* 3.7 6.5 - - - -
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Residues in contact with LEU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 3.8 28.9 - - + -
32B TRP* 2.8 17.1 + - + +
33B GLN 3.8 3.6 - - - -
34B ASP 3.8 23.1 - - - +
38B LEU 4.0 0.2 - - - +
39B VAL* 1.3 73.9 - - - +
41B ASN* 1.3 62.6 - - - +
50B PHE* 5.6 0.2 - - - -
53B VAL* 3.4 18.6 - - - +
57B TYR* 3.7 43.7 - - + +
61B THR* 3.7 21.3 + - + +
70B LEU* 3.8 19.1 - - + -
72B LEU* 4.6 8.1 - - + -
83B TYR* 3.8 17.7 - - + -
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Residues in contact with ASN 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PHE* 3.7 0.7 - - - -
32B TRP* 3.1 30.2 + - + +
39B VAL* 3.5 9.0 - - - +
40B LEU* 1.3 80.7 - - - +
42B GLU* 1.3 76.4 + - - +
43B VAL* 5.5 2.0 - - - -
48B GLU* 3.2 26.6 + - - +
49B LYS 3.8 1.4 + - - +
50B PHE* 3.5 24.1 - - - -
53B VAL* 3.7 6.3 - - - -
61B THR* 3.0 22.6 + - - +
63B PHE* 4.7 1.6 - - - +
70B LEU* 3.7 31.2 - - + +
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Residues in contact with GLU 42 (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 VAL* 3.9 3.6 - - + +
30B VAL 3.2 9.0 - - - +
31B PHE* 3.7 39.0 - - + -
39B VAL* 4.7 3.8 - - + -
41B ASN* 1.3 81.3 + - - +
43B VAL* 1.3 72.3 + - - +
44B TYR* 3.3 17.1 - - + +
47B LYS 3.7 0.2 - - - +
48B GLU* 3.4 3.8 - - - -
49B LYS* 2.8 79.9 + - + +
52B SER* 4.0 16.0 + - - -
53B VAL* 5.5 0.2 - - + -
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Residues in contact with VAL 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 4.7 8.2 - - + +
28B LEU 3.8 1.4 - - - +
29B VAL* 3.3 4.3 - - - +
30B VAL* 2.8 45.1 + - + +
32B TRP* 3.8 20.9 - - + -
41B ASN* 5.4 1.8 - - - +
42B GLU* 1.3 76.0 - - - +
44B TYR* 1.3 58.7 + - - +
45B LEU 3.7 1.1 + - - -
46B GLY* 3.5 35.4 - - - +
47B LYS 3.5 5.8 - - - +
48B GLU* 4.5 6.3 - - + +
63B PHE* 3.7 45.3 - - + -
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Residues in contact with TYR 44 (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 LEU 4.3 0.4 - - - -
29B VAL* 3.7 25.8 - - + -
42B GLU* 3.3 26.8 - - - +
43B VAL* 1.3 71.8 - - - +
45B LEU* 1.3 94.1 + - + +
46B GLY 3.1 0.7 + - - -
47B LYS* 2.8 24.4 + - + +
49B LYS* 3.7 32.5 - - + -
90B LYS* 3.4 26.3 - - + -
95B MET* 5.8 1.8 - - - -
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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