Contacts of the strand formed by residues 83 - 89 (chain D) in PDB entry 4LOU
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 83 (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* 3.7 27.1 - - + -
37D GLN 3.2 14.6 - - - +
38D LYS* 3.8 12.8 - - + +
81D ASP 3.3 8.3 + - - +
82D ALA* 1.3 76.8 - - - +
84D THR* 1.3 63.9 + - - +
85D TYR* 4.0 4.6 - - + +
101D THR 3.6 1.4 - - - +
102D LYS* 3.8 2.0 - - - -
103D LEU* 2.8 34.2 + - - +
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Residues in contact with THR 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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35D TYR 3.3 2.4 - - - +
36D GLN* 3.6 2.1 - - - -
37D GLN* 2.7 47.6 + - - +
83D ALA* 1.3 76.1 + - - +
85D TYR* 1.3 63.3 + - - +
86D TYR* 3.4 37.5 + - + +
100D GLY* 4.1 2.9 - - - -
101D THR 3.3 24.5 - - - +
102D LYS* 4.1 18.5 + - + +
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Residues in contact with TYR 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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6D GLN* 2.7 29.0 + - - -
21D MET* 3.5 36.6 - - + -
34D TRP* 4.3 11.0 - - + -
35D TYR 3.3 3.1 - - - +
36D GLN* 2.8 53.8 + - + -
46D TRP* 4.2 12.8 - + - -
61D PHE* 3.8 13.6 - + - -
72D LEU* 4.2 13.2 - - + -
74D ILE* 4.7 2.2 - - + -
81D ASP* 2.4 33.7 + - - +
83D ALA* 4.0 14.4 - - + -
84D THR* 1.3 71.9 - - - +
86D TYR* 1.3 56.6 + - - +
100D GLY* 3.7 0.2 - - - -
101D THR 3.0 19.7 + - - +
103D LEU* 4.1 14.1 - - + -
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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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39C GLN* 3.0 22.7 + - - -
43C LYS 3.9 4.7 + - - -
44C GLY* 4.3 7.6 - - - -
45C LEU* 3.4 36.3 - - + -
6D GLN* 3.4 1.3 - - - -
34D TRP* 3.1 6.1 - - - -
35D TYR* 2.6 50.5 + - + +
37D GLN* 3.0 30.4 + - + -
43D PRO* 5.8 0.4 - - + -
84D THR* 3.4 32.7 - - + +
85D TYR* 1.3 71.0 - - - +
87D CYS* 1.3 64.7 + - - +
97D PHE* 4.5 4.3 - - + -
98D GLY 3.7 18.2 - - - -
99D GLY 3.6 20.2 + - - -
100D GLY* 3.9 6.1 - - - -
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Residues in contact with CYS 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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4D LEU* 3.6 14.6 - - - -
6D GLN* 2.8 24.3 + - - +
23D CYS* 2.1 44.9 - - + -
32D ILE* 4.3 2.5 - - + -
33D HIS 3.3 7.4 - - - +
34D TRP* 3.8 27.4 - - + -
86D TYR* 1.3 74.7 - - - +
88D GLN* 1.3 58.6 + - - +
97D PHE* 3.3 4.9 - - - +
98D GLY 2.7 26.4 + - - -
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Residues in contact with GLN 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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106C TRP 3.8 14.6 + - - -
107C TYR* 4.1 0.7 - - - -
108C PHE* 3.5 21.3 - - + -
4D LEU* 3.8 3.1 - - - -
32D ILE* 3.7 3.4 - - - +
33D HIS* 2.8 49.3 + - - +
35D TYR* 2.3 40.5 + - + -
87D CYS* 1.3 78.2 - - - +
89D GLN* 1.3 84.9 + - - +
90D TRP* 4.0 3.0 - - - +
95D GLN* 4.0 1.2 - - - +
96D THR 3.5 11.9 - - - +
97D PHE* 3.5 33.2 - - + -
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Residues in contact with GLN 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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2D ILE* 4.1 16.1 - - + +
4D LEU* 3.5 15.8 - - + +
29D VAL* 3.5 24.9 - - + +
31D TYR 5.1 0.2 - - - -
32D ILE* 4.2 8.5 - - + +
33D HIS* 5.1 0.2 - - - -
88D GLN* 1.3 81.7 + - - +
90D TRP* 1.3 58.9 + - - +
91D SER* 3.0 26.7 + - - -
92D SER* 3.0 17.8 + - - -
94D PRO 3.3 25.1 + - - -
95D GLN* 2.9 38.5 - - - +
96D THR* 3.0 28.4 + - - +
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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