Contacts of the strand formed by residues 86 - 94 (chain D) in PDB entry 5J0Z
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 ASP 86 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83D ASN* 5.6 5.8 - - - +
84D ALA 4.0 6.1 - - - +
85D ARG* 1.3 73.4 - - - +
87D ALA* 1.3 58.2 + - - +
105D ARG 4.2 0.2 - - - +
106D PHE* 3.3 2.2 - - - -
107D SER* 3.1 43.6 + - - +
84E ALA* 6.2 4.7 - - + -
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Residues in contact with ALA 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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85D ARG* 3.7 14.5 + - - +
86D ASP* 1.3 73.5 - - - +
88D ASP* 1.3 64.0 + - - +
89D VAL* 4.3 2.2 + - + +
104D GLU* 3.4 35.7 - - + +
105D ARG 3.4 7.2 - - - +
106D PHE* 4.1 2.5 - - + -
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Residues in contact with ASP 88 (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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87D ALA* 1.3 76.6 - - - +
89D VAL* 1.3 67.4 + - - +
90D VAL* 3.9 2.2 - - + +
104D GLU* 3.2 6.5 - - - +
105D ARG* 3.0 38.6 + - + +
77E ARG* 3.9 25.5 - - - +
84E ALA* 5.0 14.5 - - - +
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Residues in contact with VAL 89 (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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68D PRO* 4.0 28.7 - - + -
87D ALA* 5.6 1.8 - - + +
88D ASP* 1.3 77.6 - - - +
90D VAL* 1.3 62.4 + - - +
91D ASP 4.4 2.9 - - - +
92D ILE* 4.1 22.7 - - + -
102D TYR* 3.9 32.1 - - + +
103D LEU 3.9 9.2 - - - +
104D GLU* 4.3 2.2 - - - +
75E GLU* 3.6 11.8 - - - +
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Residues in contact with VAL 90 (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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42D PHE* 4.5 4.0 - - + -
88D ASP* 3.9 4.3 - - + +
89D VAL* 1.3 75.8 - - - +
91D ASP* 1.3 64.3 + - + +
103D LEU* 2.7 28.7 + - + +
104D GLU 3.7 2.0 - - - -
105D ARG* 3.4 37.0 - - + +
75E GLU* 3.2 37.0 - - - +
77E ARG* 3.9 17.7 - - - +
133E ARG* 3.7 29.8 - - + -
135E VAL* 5.9 2.1 - - - +
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Residues in contact with ASP 91 (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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65D THR* 3.4 21.1 - - - +
89D VAL* 4.0 1.7 - - - -
90D VAL* 1.3 87.5 - - + +
92D ILE* 1.3 70.0 + - - +
93D SER* 3.1 11.4 + - - -
101D GLN 3.5 3.0 - - - +
103D LEU* 2.9 36.4 + - + +
133E ARG* 5.5 4.3 - - - +
135E VAL* 4.7 12.3 - - + +
136E ASP* 2.7 26.9 - - - +
179E ARG* 3.0 16.6 + - - +
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Residues in contact with ILE 92 (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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65D THR* 3.2 31.7 - - - +
66D TYR* 3.4 24.7 + - + +
67D GLU 4.3 1.3 - - - +
68D PRO* 3.5 35.9 - - + -
71D ILE* 3.8 15.0 - - + -
73D ILE* 3.7 17.0 - - + -
89D VAL* 4.1 9.9 - - + -
91D ASP* 1.3 79.5 + - - +
93D SER* 1.3 59.0 + - - +
94D VAL* 4.2 3.8 + - + -
100D VAL* 3.7 28.5 - - + -
101D GLN 3.3 4.3 - - - +
102D TYR* 3.9 17.0 - - + -
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Residues in contact with SER 93 (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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63D VAL* 3.9 13.2 - - - +
64D LYS 3.6 3.8 - - - -
91D ASP* 3.1 9.0 + - - -
92D ILE* 1.3 69.9 - - - +
94D VAL* 1.3 61.5 + - - +
95D SER 4.0 0.2 - - - -
99D THR 4.0 0.5 - - - +
100D VAL* 3.5 1.2 - - - +
101D GLN* 2.7 53.8 + - - +
136E ASP* 2.7 37.2 + - - -
179E ARG* 3.3 11.8 + - - -
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Residues in contact with VAL 94 (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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52D LEU* 3.9 40.4 - - + +
54D PHE* 3.5 8.4 - - + -
63D VAL* 3.1 15.6 - - - +
64D LYS* 2.7 24.9 + - + +
66D TYR* 3.5 33.9 - - + -
71D ILE* 4.9 0.4 - - + -
92D ILE* 4.8 3.4 - - + -
93D SER* 1.3 75.6 - - - +
95D SER* 1.3 73.5 + - - +
98D GLY* 4.4 6.5 - - - -
99D THR 3.5 8.7 - - - +
100D VAL* 4.2 15.9 - - + -
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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