Contacts of the strand formed by residues 42 - 46 (chain W) in PDB entry 5A0Q
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 TYR 42 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14W LEU* 3.7 20.0 - - + +
34W ILE* 4.0 10.5 - - + -
35W HIS 3.4 5.2 - - - +
36W PHE* 3.3 47.6 - + + +
37W ILE* 4.3 1.3 - - - +
38W SER 4.0 0.4 - - - -
39W PRO* 4.2 3.7 + - - +
41W ILE* 1.3 78.0 - - - +
43W CYS* 1.3 62.1 + - - +
100W LEU* 3.7 0.9 - - - -
101W GLY 3.0 30.7 + - - +
176W CYS* 3.3 30.0 - - - -
177W VAL 4.8 0.7 - - - -
178W ILE* 3.3 33.0 - - + -
183W LEU* 3.8 21.7 - - + +
184W ASP 5.2 1.0 - - - -
185W PHE* 4.6 16.3 + + - +
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Residues in contact with CYS 43 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33W LYS 3.4 1.0 - - - +
34W ILE* 4.6 1.8 - - - -
35W HIS* 3.0 36.6 + - - +
37W ILE* 3.6 28.5 - - + -
42W TYR* 1.3 75.8 - - - +
44W CYS* 1.4 63.3 + - - +
56W THR* 4.5 5.0 - - + +
83W LEU* 4.5 2.0 - - - -
98W LEU* 3.1 54.1 - - - -
99W VAL 3.4 11.7 - - - -
100W LEU* 4.2 9.4 - - + -
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Residues in contact with CYS 44 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3W ILE* 3.7 23.1 - - + -
4W ALA 4.3 5.2 - - - -
14W LEU* 4.2 14.6 - - - +
15W GLY 3.7 23.3 - - - -
16W ALA* 4.2 4.3 - - - -
33W LYS 3.2 7.9 - - - +
34W ILE* 3.7 30.7 - - - -
43W CYS* 1.4 74.2 - - - +
45W GLY* 1.4 58.5 + - - +
98W LEU* 3.3 7.7 - - - +
99W VAL* 3.0 36.0 + - + +
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Residues in contact with GLY 45 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3W ILE* 3.5 9.3 - - - +
33W LYS* 3.4 34.0 + - - +
35W HIS* 4.5 2.6 - - - -
43W CYS 4.0 0.2 + - - -
44W CYS* 1.4 74.1 - - - +
46W ALA* 1.3 62.0 + - - +
52W THR* 3.0 25.4 - - - -
97W ALA 3.5 5.8 - - - -
98W LEU* 3.8 0.9 - - - -
300W KNM 4.2 5.4 - - - -
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Residues in contact with ALA 46 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1W THR* 4.1 2.7 - - - +
3W ILE* 3.6 17.9 - - + -
45W GLY* 1.3 73.3 - - - +
47W GLY* 1.3 65.1 + - - +
48W THR 4.1 0.7 - - - +
52W THR* 3.8 1.4 + - - -
96W ALA* 3.3 7.8 - - - +
97W ALA* 2.9 25.9 + - - +
127W MET* 3.9 13.2 - - - -
128W GLY* 3.8 17.7 - - - -
300W KNM 3.5 20.8 - - + +
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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