Contacts of the strand formed by residues 82 - 87 (chain X) in PDB entry 2AE0
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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60X VAL* 6.4 1.1 - - + -
63X ALA* 3.7 35.9 - - + +
64X VAL* 4.0 10.8 - - + +
67X TRP* 3.8 28.7 - - + -
77X MET* 3.4 51.9 + - + +
78X ARG* 4.2 12.0 - - - +
80X PHE* 3.2 12.3 - - + +
81X GLY* 1.3 76.7 - - - +
83X ASP* 1.3 71.4 + - - +
84X ALA* 4.0 1.0 + - - +
333X LEU* 4.0 18.2 - - + -
334X LYS 3.6 5.2 - - - +
335X THR* 4.7 2.7 - - + -
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Residues in contact with ASP 83 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23X LEU* 4.0 18.6 - - + +
78X ARG* 4.8 11.0 - - - +
81X GLY 4.6 4.5 - - - +
82X ILE* 1.3 76.7 - - - +
84X ALA* 1.3 60.4 + - - +
85X TRP* 3.8 23.0 + - - +
332X VAL 3.4 5.2 - - - +
333X LEU* 3.4 4.9 - - - +
334X LYS* 2.7 36.0 + - - +
335X THR 4.4 0.7 - - - -
336X ALA* 3.4 31.7 + - - +
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Residues in contact with ALA 84 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23X LEU* 3.4 5.7 - - - +
24X VAL* 3.1 47.4 + - + +
27X PRO* 4.1 17.9 - - + -
77X MET* 4.4 6.7 - - + -
82X ILE 4.0 1.8 + - - +
83X ASP* 1.3 72.0 - - - +
85X TRP* 1.3 63.4 + - - +
86X GLN 3.8 0.2 - - - -
331X TRP* 4.1 10.5 - - + -
332X VAL 3.6 3.6 - - - -
333X LEU* 4.0 16.2 - - + -
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Residues in contact with TRP 85 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19X GLN* 4.9 5.2 - - - -
21X PHE* 4.1 24.5 - - + -
22X SER* 3.6 5.6 - - - -
23X LEU* 3.4 45.3 - - + -
83X ASP* 3.8 25.2 + - + +
84X ALA* 1.3 72.1 - - - +
86X GLN* 1.3 65.0 + - - +
87X MET* 3.5 3.5 + - - +
331X TRP* 3.3 1.9 - - - -
332X VAL* 2.8 49.8 + - + +
334X LYS* 4.4 17.8 - - + +
1439X EDO 4.0 32.1 + - - -
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Residues in contact with GLN 86 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14X ASP* 3.0 35.1 + - - +
17X PHE* 3.6 32.1 - - + -
21X PHE* 3.4 3.9 - - - -
22X SER* 2.9 36.6 + - - +
24X VAL* 4.0 13.3 - - + +
28X ASP* 5.3 1.4 + - - +
84X ALA 3.7 0.2 + - - -
85X TRP* 1.3 71.8 - - - +
87X MET* 1.3 68.3 + - - +
88X GLU 3.8 0.3 + - - -
94X GLY* 4.5 4.6 - - - -
329X ARG* 3.7 20.4 - - - +
330X VAL 3.5 10.1 - - - +
331X TRP* 3.3 34.7 + - + +
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Residues in contact with MET 87 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17X PHE* 4.7 0.4 - - - -
20X PRO 3.5 5.4 - - - -
21X PHE* 3.6 17.5 - - + -
85X TRP 4.2 0.4 - - - +
86X GLN* 1.3 79.2 - - - +
88X GLU* 1.3 62.5 + - - +
89X GLY 3.2 1.3 + - - -
94X GLY* 3.4 18.5 - - - +
96X VAL* 3.9 11.0 - - + +
265X ILE* 3.9 20.2 - - + -
305X GLN* 3.3 43.7 - - + +
307X PHE* 3.5 29.6 - - + -
330X VAL* 2.9 41.1 + - - +
332X VAL* 4.2 9.6 - - + -
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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