Contacts of the strand formed by residues 84 - 91 (chain D) in PDB entry 5U72
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 ALA 84 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D GLN* 4.1 6.3 - - + -
37D GLN 3.5 15.3 - - - +
38D HIS* 3.7 20.9 - - + +
39D ALA 5.1 2.5 - - - +
82D ASP 3.1 9.3 + - - +
83D SER* 1.3 76.5 - - - +
85D SER* 1.3 60.8 + - - +
86D TYR* 3.7 12.5 - - + +
104D LYS* 3.7 3.8 - - - +
105D LEU* 2.7 38.1 + - - +
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Residues in contact with SER 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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35D TYR 3.9 0.2 - - - +
36D GLN* 3.6 0.5 - - - -
37D GLN* 2.8 46.9 + - - +
39D ALA 5.5 0.4 - - - +
84D ALA* 1.3 75.4 - - - +
86D TYR* 1.3 66.6 + - - +
87D LEU* 4.1 15.0 + - - -
102D GLY* 5.4 1.4 - - - -
103D THR 3.2 7.4 - - - -
104D LYS* 3.6 22.5 + - - +
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Residues in contact with TYR 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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6D GLN* 2.8 28.7 + - - -
20D ILE* 3.9 23.8 - - + -
34D TRP* 4.0 17.3 - - + -
35D TYR 3.3 4.9 - - - +
36D GLN* 3.1 31.9 + - + -
46D LEU* 3.6 19.7 - - + -
60D PHE* 3.9 9.9 - + - -
73D LEU* 3.5 19.3 - - + -
75D LEU* 3.7 12.3 - - + +
82D ASP* 2.7 34.9 + - - +
84D ALA* 3.7 20.0 - - + -
85D SER* 1.3 73.9 - - - +
87D LEU* 1.3 58.2 + - - +
103D THR* 2.8 22.4 + - - +
105D LEU* 3.8 13.0 - - + -
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Residues in contact with LEU 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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6D GLN* 3.8 2.2 - - - -
33D PHE 3.6 1.2 - - - +
34D TRP* 3.3 7.8 - - - -
35D TYR* 2.8 45.2 + - + +
37D GLN* 3.8 29.6 - - + +
43D PRO* 4.0 24.2 - - + -
85D SER* 4.5 11.4 - - - -
86D TYR* 1.3 74.7 - - - +
88D CYS* 1.3 60.3 + - - +
89D ALA 4.0 0.3 + - - -
99D TRP* 4.1 29.8 - - + -
100D GLY 5.2 3.8 - - - +
101D ALA 4.9 3.1 - - - +
102D GLY* 3.9 20.9 - - - +
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Residues in contact with CYS 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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4D ILE* 4.0 4.6 - - + +
6D GLN* 2.9 21.6 + - - +
22D CYS* 2.0 55.4 - - + -
32D LEU* 3.9 23.8 - - - -
33D PHE 3.5 3.1 - - - -
34D TRP* 3.9 7.6 - - + -
87D LEU* 1.3 73.1 - - - +
89D ALA* 1.3 63.6 + - - +
90D VAL* 4.9 0.4 - - - -
99D TRP* 3.6 2.5 - - - -
100D GLY* 2.7 32.1 + - - +
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Residues in contact with ALA 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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4D ILE* 5.5 0.2 - - - -
32D LEU* 3.4 1.8 - - - -
33D PHE* 2.6 53.1 + - + +
35D TYR* 4.7 0.2 - - + -
88D CYS* 1.3 77.5 - - - +
90D VAL* 1.3 63.5 + - - +
97D LEU* 4.0 16.8 - - + -
98D ILE 3.3 9.6 - - - +
99D TRP* 3.6 33.4 - - + -
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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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4D ILE* 4.3 13.9 - - + -
24D TYR* 3.8 20.4 - - + -
26D THR* 4.2 20.0 - - + +
29D PHE* 3.7 17.0 - - + -
31D GLY 3.4 7.4 - - - +
32D LEU* 3.7 30.3 - - + -
88D CYS* 4.9 2.2 - - - -
89D ALA* 1.3 77.5 - - - +
91D LYS* 1.3 75.9 + - - +
92D ASP 3.8 0.5 + - - -
96D GLN 3.3 3.1 - - - +
97D LEU* 3.4 4.5 - - - -
98D ILE* 2.8 36.6 + - + +
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Residues in contact with LYS 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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152C TYR* 6.2 1.3 - - + -
29D PHE* 3.6 0.7 - - - -
30D ASN* 2.8 53.0 + - + +
31D GLY 2.9 12.0 + - - +
33D PHE* 4.2 25.5 - - + -
48D TYR* 5.7 0.7 - - + -
90D VAL* 1.3 78.0 - - - +
92D ASP* 1.3 56.8 + - - +
95D TYR* 3.7 44.0 + - + +
96D GLN 3.3 2.9 - - - +
97D LEU* 4.4 17.8 - - + +
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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