Contacts of the strand formed by residues 46 - 49 (chain A) in PDB entry 1PRH
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 ILE 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A CYS* 4.0 2.0 - - - -
44A GLN 4.8 3.6 - - - +
45A GLY* 1.3 75.1 - - - -
47A CYS* 1.3 76.9 + - - +
48A VAL* 3.2 9.9 + - + +
58A ASP* 2.8 47.8 + - + +
130A TYR* 3.7 31.6 - - + +
135A ASP 5.0 7.4 - - - +
136A TYR* 5.9 1.8 - - - -
137A ILE* 6.0 5.4 - - + -
153A PRO* 5.9 5.4 - - + -
546B LYS* 4.7 13.9 - - + +
548B SER* 3.7 29.6 - - - +
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Residues in contact with CYS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A CYS* 2.0 63.8 - - + +
40A PRO* 4.0 9.9 - - + -
41A CYS* 3.5 16.3 - - + -
45A GLY 4.0 0.8 + - - -
46A ILE* 1.3 81.8 - - + +
48A VAL* 1.3 61.8 + - - +
49A ARG* 3.7 0.9 + - - +
55A TYR* 3.5 25.6 - - - -
56A GLN 3.5 4.3 - - - -
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Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE* 3.2 8.8 + - + +
47A CYS* 1.3 73.6 - - - +
49A ARG* 1.3 67.4 + - - +
50A PHE* 3.4 30.2 - - + -
55A TYR* 3.4 1.6 - - - +
56A GLN* 2.7 53.3 + - + +
57A CYS 5.3 0.2 - - - -
58A ASP* 5.0 4.0 - - + +
320B HIS* 4.0 7.6 - - + +
323B TRP* 3.7 26.2 - - + -
548B SER* 4.7 23.6 - - - +
551B GLY* 5.3 6.1 - - - -
552B GLY* 5.7 2.7 - - - +
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Residues in contact with ARG 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL* 5.1 5.7 - - - +
34A ASN* 2.8 54.2 - - - +
35A PRO* 3.8 17.9 - - + +
36A CYS* 4.2 8.5 - - - -
47A CYS 3.7 3.8 + - - -
48A VAL* 1.3 72.6 - - - +
50A PHE* 1.3 78.3 + - - +
52A LEU* 3.0 26.5 + - - +
54A ARG 3.5 6.5 - - - -
55A TYR* 4.1 4.5 - - - +
158A ASP* 4.3 5.3 + - - -
320B HIS* 3.1 20.4 - - - +
322B THR* 3.5 34.2 + - - +
323B TRP* 3.7 21.6 - - + -
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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