Contacts of the strand formed by residues 82 - 87 (chain D) in PDB entry 2PI8
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 82 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25D ASN 5.1 2.1 - - - +
63D ALA* 3.9 24.0 - - + +
64D VAL* 3.9 18.6 - - + -
67D TRP* 3.8 34.3 - - + -
77D MSE 3.4 31.2 + - + +
78D ARG* 3.5 26.2 + - - +
80D PHE* 4.0 11.4 - - + +
81D GLY* 1.3 79.6 - - - +
83D ASP* 1.3 63.6 + - - +
84D ALA 4.2 0.9 + - - -
333D LEU* 4.1 31.0 - - + -
334D LYS 3.8 7.9 - - - +
335D THR* 4.6 3.4 - - + +
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Residues in contact with ASP 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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23D LEU* 3.7 20.0 - - + +
25D ASN 5.7 0.7 - - - -
78D ARG* 3.5 25.5 + - - +
81D GLY 3.6 2.1 - - - +
82D ILE* 1.3 77.8 - - - +
84D ALA* 1.3 60.1 + - - +
85D TRP* 3.4 24.1 - - - +
332D VAL 3.4 1.6 - - - +
333D LEU* 3.5 2.4 - - - -
334D LYS* 2.7 38.4 + - + +
335D THR 3.7 1.6 - - - +
336D ALA* 3.3 34.7 + - - +
337D PRO* 5.2 0.5 - - - +
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Residues in contact with ALA 84 (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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22D SER 3.6 0.9 - - - +
23D LEU* 3.5 5.5 - - - +
24D VAL* 3.1 34.3 + - + +
25D ASN 5.0 2.7 + - - +
27D PRO* 3.7 31.0 - - + -
77D MSE 4.7 4.0 - - + +
82D ILE 4.2 1.2 + - - -
83D ASP* 1.3 71.7 - - - +
85D TRP* 1.3 60.8 + - - +
86D GLN 3.7 0.4 - - - -
331D TRP* 3.9 18.8 - - + -
333D LEU* 4.0 14.6 - - + -
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Residues in contact with TRP 85 (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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21D PHE* 3.2 54.5 - + + -
22D SER 3.5 4.5 - - - -
23D LEU* 3.7 37.9 - - + -
83D ASP* 3.4 27.2 - - + +
84D ALA* 1.3 72.1 - - - +
86D GLN* 1.3 67.2 + - - +
87D MSE 3.7 0.9 + - - +
331D TRP* 3.6 0.6 - - - -
332D VAL* 2.9 60.2 + - + +
334D LYS* 3.6 35.7 - - + +
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Residues in contact with GLN 86 (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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14D ASP* 3.3 35.0 + - - +
17D PHE* 3.6 25.5 + - + +
20D PRO 3.1 4.2 - - - +
21D PHE* 3.4 0.2 - - - -
22D SER* 2.6 52.1 + - - +
24D VAL* 3.7 7.1 - - + +
85D TRP* 1.3 73.5 - - - +
87D MSE 1.3 73.8 + - - +
93D TYR 4.8 0.2 + - - -
94D GLY* 4.4 11.3 - - - -
329D ARG* 4.5 5.9 - - + +
330D VAL 3.4 13.7 - - - +
331D TRP* 3.1 40.6 + - + +
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Residues in contact with MSE 87 (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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17D PHE 4.9 1.1 - - - +
19D GLN 4.6 0.9 - - - -
20D PRO 3.3 9.4 - - - +
21D PHE* 4.6 6.5 - - + -
22D SER* 5.1 1.3 - - - -
85D TRP 4.2 0.2 - - - +
86D GLN* 1.3 86.8 + - - +
88D GLU* 1.3 65.2 + - - +
89D GLY 3.5 0.2 + - - -
94D GLY* 4.3 9.0 - - - -
96D VAL* 3.9 8.9 - - + +
264D ILE* 4.8 1.8 - - + -
265D ILE* 3.6 27.8 - - + -
305D GLN* 3.3 44.4 - - + +
307D PHE* 3.7 18.8 - - + -
329D ARG* 6.0 0.9 - - - -
330D VAL* 3.1 43.4 + - + +
332D VAL* 4.1 24.2 - - + -
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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