Contacts of the strand formed by residues 42 - 48 (chain B) in PDB entry 2UUY
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 PHE 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A TYR* 3.6 10.8 - - - +
44A PHE* 3.8 28.5 - + - -
60A HIS 3.5 24.0 - - - -
61A CYS* 4.1 11.0 - - - -
62A TYR 4.6 6.1 - - - -
63A LYS* 4.4 14.8 - - + -
38B CYS* 5.0 5.6 - - - -
40B ALA* 3.5 24.0 - - + -
41B ARG* 1.3 74.6 - - - +
43B THR* 1.3 60.0 + - - +
44B ARG* 3.9 10.2 + - - +
55B TYR 3.4 1.9 - - - +
56B GLU* 3.2 7.1 - - - -
57B GLY 2.9 35.6 + - - +
58B CYS* 5.5 0.7 - - - -
59B TYR 3.7 28.3 - - - +
60B THR* 5.5 7.6 - - + -
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Residues in contact with THR 43 (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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42A TYR* 3.0 42.7 + - + -
41B ARG* 4.4 2.6 - - - -
42B PHE* 1.3 71.5 - - - +
44B ARG* 1.3 68.7 + - - +
45B TYR* 3.9 18.8 - - + +
54B VAL* 3.4 29.2 - - + -
55B TYR 3.5 2.9 - - - -
56B GLU* 4.3 11.8 + - + +
64B SER* 4.4 14.4 - - - +
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Residues in contact with ARG 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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42B PHE* 4.3 11.7 - - + -
43B THR* 1.3 81.9 + - - +
45B TYR* 1.3 64.6 + - - +
46B TYR* 3.7 20.0 - - + -
54B VAL* 3.4 4.0 - - - +
55B TYR* 2.8 36.3 + - - +
59B TYR* 3.4 35.9 + - + +
60B THR* 3.7 13.6 + - - -
61B GLY 2.8 16.6 + - - +
62B GLY 3.2 24.2 + - - -
63B TYR* 3.5 4.1 + - - -
64B SER* 3.5 34.2 - - - +
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Residues in contact with TYR 45 (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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43B THR* 3.9 19.2 - - + +
44B ARG* 1.3 72.7 - - - +
46B TYR* 1.3 60.6 + - - +
52B CYS* 4.7 0.4 - - + -
53B LYS 3.5 2.9 - - - +
54B VAL* 3.5 31.4 - - + +
62B GLY* 3.3 2.4 - - - -
63B TYR* 2.8 43.1 + - - +
64B SER 3.4 17.3 - - - -
65B ARG* 4.3 0.4 - - - +
66B MET* 3.4 63.5 - - + -
69B CYS* 3.5 26.5 - - + -
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Residues in contact with TYR 46 (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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33B PRO* 3.5 30.2 - - + +
34B VAL 5.4 0.2 + - - -
44B ARG* 3.7 24.0 - - + -
45B TYR* 1.3 77.3 - - - +
47B CYS* 1.3 62.5 + - - +
48B MET* 3.3 20.4 + - - +
52B CYS* 3.2 0.3 - - - -
53B LYS 2.9 30.2 + - - +
55B TYR* 3.7 20.4 - + + -
59B TYR* 3.5 24.5 - + + +
60B THR 4.0 0.5 + - - -
61B GLY* 3.0 31.3 + - - -
62B GLY* 3.3 18.6 - - - -
69B CYS* 3.5 5.2 - - - -
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Residues in contact with CYS 47 (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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46B TYR* 1.3 72.7 - - - +
48B MET* 1.3 66.6 + - - +
49B GLY 3.5 15.3 + - - -
51B CYS 3.7 1.3 - - - -
52B CYS* 3.9 4.0 - - - -
63B TYR* 6.0 1.5 - - + -
69B CYS* 3.4 6.8 - - - -
72B ASN 4.3 5.6 - - - +
73B CYS* 2.0 61.0 - - + -
74B PRO* 3.7 5.6 - - - -
75B ALA* 4.0 8.1 - - + -
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Residues in contact with MET 48 (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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24B CYS* 4.7 1.1 - - - -
26B VAL* 3.7 25.3 - - + -
30B TRP* 3.2 38.8 + - + +
31B SER 3.2 15.3 - - - -
32B GLU* 3.9 11.2 - - + -
33B PRO* 4.0 7.0 - - + -
46B TYR* 3.7 18.8 - - - +
47B CYS* 1.3 81.1 - - - +
49B GLY* 1.3 58.8 + - - +
50B ASN 3.1 8.1 - - - -
51B CYS* 2.8 24.6 + - - +
53B LYS* 4.0 4.5 - - + -
55B TYR* 3.6 34.8 - - + +
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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