Contacts of the strand formed by residues 81 - 91 (chain D) in PDB entry 1UEA
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 GLU 81 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D ALA 4.3 2.9 - - - +
22D LYS* 4.4 4.4 - - - -
23D PHE 4.6 1.4 + - - -
76D SER* 2.7 27.6 + - - +
77D HIS* 2.9 46.3 + - + +
78D ALA* 2.9 16.9 + - + +
79D ARG 3.1 7.2 - - - +
80D SER* 1.3 77.4 - - - +
82D GLU* 1.3 65.9 + - - +
83D PHE* 3.3 27.7 - - + -
104D PRO* 3.8 21.2 - - + +
106D ASN* 5.9 3.8 - - - +
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Residues in contact with GLU 82 (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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20D ARG* 2.9 37.8 + - + +
21D ALA 3.5 7.6 - - - +
22D LYS* 4.2 24.9 - - + -
43D THR* 2.9 34.9 + - + +
80D SER 3.7 2.8 + - - +
81D GLU* 1.3 76.8 - - - +
83D PHE* 1.3 60.6 + - - +
104D PRO* 3.1 10.6 - - - +
105D TRP* 2.9 25.8 + - + -
106D ASN* 4.7 17.4 + - - +
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Residues in contact with PHE 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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20D ARG* 3.2 6.1 - - - -
21D ALA* 2.8 37.0 + - - +
23D PHE* 3.6 30.3 - + + -
72D TYR* 4.4 4.7 - - - -
74D HIS* 3.4 30.7 - + - -
75D ARG 4.0 7.2 - - - -
76D SER* 3.7 14.6 - - - -
81D GLU* 3.3 43.3 - - + -
82D GLU* 1.3 73.3 - - - +
84D LEU* 1.3 64.4 + - - +
85D ILE* 3.7 5.9 + - + +
102D VAL* 4.4 8.5 - - + -
103D ALA* 3.2 13.0 - - - +
104D PRO* 3.4 32.1 - - + -
105D TRP* 4.0 2.2 - - - +
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Residues in contact with LEU 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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18D VAL* 4.2 12.8 - - + -
19D ILE 3.0 19.1 - - - +
20D ARG* 4.4 0.9 - - - +
46D TYR* 4.2 11.9 - - + -
83D PHE* 1.3 74.8 - - - +
85D ILE* 1.3 74.7 + - - +
86D ALA* 4.0 4.3 - - + +
101D PHE* 3.5 11.9 - - + +
102D VAL* 3.1 8.1 - - - +
103D ALA 2.6 35.5 + - - +
105D TRP* 3.6 27.6 - - + +
108D LEU* 3.9 15.3 - - + -
116D PHE* 4.0 34.3 - - + -
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Residues in contact with ILE 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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17D LEU 3.5 2.4 - - - +
18D VAL* 3.4 2.8 - - - -
19D ILE* 2.9 46.5 + - + +
21D ALA* 4.5 18.2 - - + -
23D PHE* 4.0 28.0 - - + -
40D ILE* 4.7 9.2 - - + -
61D VAL* 5.0 6.5 - - + -
83D PHE* 4.1 9.9 - - + +
84D LEU* 1.3 80.8 - - - +
86D ALA* 1.3 61.5 + - - +
87D GLY 4.5 0.2 - - - +
94D LEU* 4.3 16.8 - - + -
96D ILE* 3.4 31.9 - - + -
101D PHE 3.7 2.7 - - - -
102D VAL* 4.2 11.9 - - + -
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Residues in contact with ALA 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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11D ALA* 4.1 26.5 - - + +
12D PHE* 4.8 0.7 - - - +
15D SER* 3.2 18.3 + - - +
17D LEU 3.5 5.6 - - - -
18D VAL* 4.4 9.2 - - + +
84D LEU* 4.0 7.2 - - + +
85D ILE* 1.3 75.0 - - - +
87D GLY* 1.3 57.4 + - - +
96D ILE* 3.2 11.2 - - - +
100D SER* 3.6 13.7 - - - -
101D PHE* 3.1 18.2 + - + +
116D PHE* 5.5 1.1 - - + -
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Residues in contact with GLY 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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15D SER* 3.1 7.5 + - - -
16D ASP 2.9 24.4 + - - -
17D LEU 3.1 13.7 + - - -
85D ILE* 4.0 2.0 - - - +
86D ALA* 1.3 75.3 - - - +
88D LYS* 1.3 62.7 + - - -
94D LEU* 4.1 9.1 - - - +
95D HIS 3.4 1.6 - - - -
96D ILE* 3.2 19.8 - - - +
100D SER* 5.1 1.8 - - - -
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Residues in contact with LYS 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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14D ASN* 2.8 33.0 + - - +
15D SER* 5.0 0.7 - - - -
16D ASP* 3.2 27.1 + - - +
87D GLY* 1.3 75.7 - - - +
89D LEU* 1.3 63.2 + - - +
90D GLN* 4.5 14.8 - - - +
93D LEU 3.5 0.7 - - - +
94D LEU* 3.6 1.7 - - - -
95D HIS* 2.7 44.3 + - + +
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Residues in contact with LEU 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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16D ASP* 2.9 25.9 + - + +
17D LEU* 3.5 41.3 - - + -
51D ALA* 4.3 21.1 - - + +
88D LYS* 1.3 73.1 - - - +
90D GLN* 1.3 65.3 + - - +
91D ASP 4.0 3.7 + - - +
92D GLY* 4.3 17.0 - - - +
93D LEU 3.4 21.3 - - - +
94D LEU* 3.9 9.9 - - + +
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Residues in contact with GLN 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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35D TYR* 3.9 16.8 + - - -
88D LYS* 3.9 13.9 + - - +
89D LEU* 1.3 71.5 + - - +
91D ASP* 1.3 69.3 + - - +
92D GLY 2.6 16.3 + - - -
93D LEU* 2.9 22.9 + - - +
95D HIS* 3.1 42.4 + - + +
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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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89D LEU* 4.0 4.9 + - - +
90D GLN* 1.3 77.7 - - - +
92D GLY* 1.3 60.6 + - - +
93D LEU* 4.8 8.1 - - + -
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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