Contacts of the strand formed by residues 79 - 83 (chain D) in PDB entry 4PRH
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 LEU 79 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43D ARG* 6.1 0.7 - - - +
53D LEU* 3.8 37.7 - - + -
54D PHE* 3.8 16.1 - - + -
68D GLU* 3.2 8.3 - - - +
69D LYS* 2.9 40.4 + - + +
70D GLU 3.3 0.2 - - - -
78D ARG* 1.4 83.7 - - + +
80D LYS* 1.3 61.0 + - - +
89D LEU* 4.2 13.7 - - + -
90D HIS 3.5 1.8 - - - +
91D ILE* 3.7 35.2 - - + -
98D ASP* 5.6 2.7 - - - -
102D TYR* 4.1 18.4 - - + +
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Residues in contact with LYS 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D GLU* 3.4 37.1 + - + +
67D LYS 3.4 8.3 - - - +
68D GLU* 4.3 15.0 - - + -
78D ARG 5.6 0.4 - - - +
79D LEU* 1.3 74.4 - - - +
81D ALA* 1.3 61.6 + - - +
82D THR* 3.9 9.0 - - - +
88D PHE 3.5 1.0 - - - +
89D LEU* 3.5 3.6 - - - +
90D HIS* 2.6 78.3 + - + +
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Residues in contact with ALA 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D TRP* 4.0 10.1 - - + -
54D PHE* 3.5 32.9 - - + -
56D LEU* 3.4 22.0 - - + +
66D GLU* 3.4 8.5 - - - +
67D LYS 2.8 31.5 + - - +
80D LYS* 1.3 73.4 - - - +
82D THR* 1.3 61.3 + - - +
88D PHE 3.2 8.1 - - - +
89D LEU* 4.1 2.2 - - + -
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Residues in contact with THR 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D LEU* 3.4 3.5 - - - +
61D GLU 4.0 4.9 - - - +
66D GLU* 3.4 28.0 - - + +
80D LYS* 3.9 13.2 - - - +
81D ALA* 1.3 76.1 - - - +
83D LEU* 1.3 60.2 + - - +
84D THR* 5.9 1.8 - - - -
87D SER* 2.7 28.5 + - - -
88D PHE* 2.9 25.8 + - - +
90D HIS* 3.1 23.2 + - - +
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Residues in contact with LEU 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D TYR* 3.9 9.6 - - + +
30D LEU* 3.9 20.6 - - + -
39D LEU* 3.8 17.0 - - + -
56D LEU* 3.9 27.8 - - + +
58D SER* 3.4 35.4 - - - +
59D ALA* 3.8 4.2 - - + +
60D GLY* 3.1 25.5 + - - -
61D GLU 3.8 8.0 + - - +
82D THR* 1.3 76.7 - - - +
84D THR* 1.4 80.6 + - - +
86D GLU 3.7 9.9 - - - +
87D SER* 3.8 17.0 - - - +
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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