Contacts of the strand formed by residues 70 - 78 (chain D) in PDB entry 3UYO
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 70 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41D GLU* 3.4 10.0 - - + +
42D THR* 3.0 35.8 + - - +
69D VAL* 1.3 77.6 - - - +
71D TYR* 1.3 60.6 + - - +
93D ASN* 6.3 1.3 - - + -
94D TYR 3.7 3.3 - - - +
95D ARG* 3.1 46.7 + - - +
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Residues in contact with TYR 71 (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 LEU* 5.2 3.1 - - + -
39D TYR* 5.0 3.8 - + + -
40D GLY* 3.4 24.2 - - - +
41D GLU* 3.8 12.3 - - + -
42D THR* 3.2 6.1 + - - -
65D LEU* 3.5 43.0 - - + +
66D SER* 2.9 37.2 + - - -
69D VAL* 3.6 35.9 - - + +
70D ASP* 1.3 72.7 - - - +
72D THR* 1.3 58.8 + - - +
73D ILE* 4.1 16.8 + - + +
92D ILE 3.9 0.3 - - - +
93D ASN* 3.2 6.8 - - - +
94D TYR* 2.9 37.1 + - - +
96D THR* 4.3 7.2 - - + -
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Residues in contact with THR 72 (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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38D THR* 3.8 1.0 + - - +
39D TYR* 3.3 4.2 - - - -
40D GLY 2.8 33.1 + - - -
42D THR* 2.8 27.6 + - - +
48D VAL* 5.8 0.7 - - - +
71D TYR* 1.3 70.7 - - - +
73D ILE* 1.3 63.8 + - - +
74D THR* 4.2 15.1 + - - +
91D SER* 4.8 6.5 - - - -
92D ILE 3.5 6.1 - - - +
93D ASN* 2.5 22.0 + - - +
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Residues in contact with ILE 73 (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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11D LEU* 4.0 10.8 - - + +
13D VAL* 5.0 0.4 - - + -
21D LEU* 3.6 31.0 - - + -
23D ILE* 4.2 21.3 - - + -
37D ILE* 4.2 9.2 - - + -
38D THR 3.3 7.6 - - - +
39D TYR* 4.1 7.9 - - + -
62D ILE* 3.9 30.3 - - + -
71D TYR* 4.7 8.5 - - + +
72D THR* 1.3 77.4 - - - +
74D THR* 1.3 66.5 + - - +
75D VAL* 4.7 0.4 - - + -
90D ILE 4.0 0.2 - - - +
91D SER* 3.1 4.6 - - - -
92D ILE* 2.9 50.1 + - + +
94D TYR* 4.9 6.7 - - + -
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Residues in contact with THR 74 (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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36D VAL 3.6 1.0 - - - +
37D ILE* 3.4 4.2 - - - +
38D THR* 2.8 47.3 + - - +
72D THR* 4.2 10.2 + - - +
73D ILE* 1.3 74.1 - - - +
75D VAL* 1.3 66.3 + - - +
76D TYR* 3.6 28.2 - - + +
89D PRO* 3.8 18.2 - - + -
90D ILE 3.3 10.3 - - - +
91D SER* 3.5 13.5 - - - -
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Residues in contact with VAL 75 (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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8D PRO* 3.8 26.9 - - + +
11D LEU* 3.9 30.5 - - + -
23D ILE* 4.4 7.4 - - + -
25D TRP* 4.6 8.1 - - + -
35D TYR* 3.9 20.9 - - + -
36D VAL 3.3 7.6 - - - +
37D ILE* 4.2 17.3 - - + -
73D ILE* 4.7 1.8 - - + -
74D THR* 1.3 78.6 - - - +
76D TYR* 1.3 63.8 + - - +
89D PRO* 3.3 4.4 - - - +
90D ILE* 2.9 42.0 + - + -
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Residues in contact with TYR 76 (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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154A ASN* 3.5 27.6 - - + -
157A GLU* 3.6 14.2 + - + +
158A TYR* 3.6 32.0 + + + -
161A SER* 4.6 5.9 - - - -
7D VAL 4.5 0.2 - - - -
35D TYR* 3.2 13.1 - - - -
36D VAL* 2.9 50.0 + - + +
38D THR* 4.1 20.9 + - + -
74D THR* 3.6 24.8 - - + +
75D VAL* 1.3 76.8 - - - +
77D ALA* 1.3 59.4 + - - +
85D TRP* 4.2 20.6 - + + -
87D TYR 5.8 1.1 - - - -
89D PRO* 3.6 27.4 - - + +
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Residues in contact with ALA 77 (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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7D VAL* 3.7 39.6 + - + +
32D VAL* 3.7 25.1 - - + -
35D TYR* 4.1 4.0 - - + -
76D TYR* 1.3 69.2 - - - +
78D GLY* 1.3 58.7 + - - +
79D TYR* 3.8 13.0 - - + -
85D TRP* 3.6 23.8 - - - +
86D PRO* 5.1 0.5 - - - +
87D TYR* 4.4 12.8 + - + +
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Residues in contact with GLY 78 (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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33D ASP 3.1 24.1 + - - -
34D PHE* 2.8 41.5 + - - -
36D VAL* 5.3 0.2 - - - -
76D TYR 3.8 1.6 + - - -
77D ALA* 1.3 73.0 - - - +
79D TYR* 1.3 66.1 + - - -
85D TRP* 3.7 15.3 - - - -
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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