Contacts of the strand formed by residues 84 - 91 (chain D) in PDB entry 3W58
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 VAL 84 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A ASP* 3.6 30.9 + - + +
95A ASN* 5.7 0.2 - - - +
107A LYS* 5.5 6.6 - - - -
20D ARG* 4.2 21.1 - - + -
21D GLY* 3.2 22.9 - - - +
22D GLU* 3.8 25.4 - - + +
82D GLY 5.5 0.4 - - - +
83D SER* 1.3 78.2 - - - +
85D ALA* 1.3 65.3 + - - +
129D LYS* 4.6 13.2 - - + -
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Residues in contact with ALA 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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19D VAL 3.7 1.2 - - - +
20D ARG* 3.4 2.7 - - - -
21D GLY 2.9 32.1 + - - +
23D VAL* 5.1 1.3 - - + -
77D PHE* 5.4 1.6 - - + -
79D PHE* 3.7 36.1 - - + -
83D SER 4.0 2.2 + - - +
84D VAL* 1.3 79.1 - - - +
86D GLU* 1.3 60.3 - - - +
87D VAL* 5.2 0.2 - - - -
101D PRO* 4.8 12.1 - - + -
126D PHE* 3.8 8.8 - - + -
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Residues in contact with GLU 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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18D ARG* 2.9 42.6 + - - +
19D VAL 3.3 10.5 - - - +
20D ARG* 3.2 48.1 + - + +
85D ALA* 1.3 74.6 - - - +
87D VAL* 1.3 68.0 + - - +
88D CYS* 3.8 9.4 - - - -
100D LEU* 4.0 1.6 - - - +
101D PRO* 3.5 16.3 - - + +
202D BME 2.9 43.6 + - - +
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Residues in contact with VAL 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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17D LEU 3.7 1.6 - - - +
18D ARG* 3.6 1.4 - - - -
19D VAL* 2.8 34.5 + - + +
30D PHE* 5.0 1.1 - - + -
32D LEU* 4.7 15.0 - - + -
43D LEU* 6.5 0.4 - - + -
45D PHE* 4.4 16.6 - - + -
79D PHE* 4.9 7.0 - - + -
85D ALA 5.0 0.7 - - - +
86D GLU* 1.3 76.2 - - - +
88D CYS* 1.3 65.5 + - - +
89D ILE* 3.7 21.4 - - + +
98D VAL* 4.1 14.6 - - + -
99D LYS 3.6 4.5 - - - +
100D LEU* 3.5 27.4 - - + -
126D PHE* 4.4 20.4 - - + -
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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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16D CYS* 4.1 11.4 - - - -
17D LEU 3.3 4.0 - - - -
18D ARG* 3.5 30.5 - - - -
86D GLU* 3.8 8.5 - - - -
87D VAL* 1.3 76.0 - - - +
89D ILE* 1.3 64.2 + - - +
97D THR 3.6 1.0 - - - +
98D VAL* 3.5 4.7 - - - +
99D LYS* 2.8 38.9 + - + +
202D BME 2.4 42.4 - - - -
203D BME 4.0 6.1 - - - -
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Residues in contact with ILE 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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11D LEU* 4.3 3.1 - - + +
15D GLU 3.8 0.7 - - - +
16D CYS* 3.6 4.2 - - - -
17D LEU* 2.8 62.7 + - + +
19D VAL* 4.8 5.2 - - + -
32D LEU* 4.9 4.9 - - + -
34D LEU* 3.9 33.0 - - + -
43D LEU* 4.9 1.8 - - + -
87D VAL* 3.7 27.8 - - + +
88D CYS* 1.3 81.7 - - - +
90D THR* 1.3 73.8 + - - +
96D LEU* 4.2 17.3 - - + -
97D THR 3.4 8.7 - - - +
98D VAL* 4.6 12.3 - - + -
117D ILE* 4.8 9.0 - - + -
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Residues in contact with THR 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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11D LEU* 5.3 0.4 - - - -
14D GLY* 3.5 19.9 + - - -
15D GLU 3.3 18.3 + - - -
16D CYS* 4.7 6.5 - - - -
89D ILE* 1.3 79.1 - - - +
91D PHE* 1.3 70.8 + - - +
96D LEU* 3.4 1.6 - - - -
97D THR* 2.8 54.1 + - + +
99D LYS* 6.0 1.3 - - - -
203D BME 5.5 7.0 - - - +
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Residues in contact with PHE 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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11D LEU* 3.5 29.6 - - + -
12D LYS 3.6 12.8 - - - -
13D PRO* 3.2 36.9 - - + +
14D GLY* 3.0 24.9 + - - +
15D GLU 5.4 0.2 - - - -
90D THR* 1.3 83.5 + - - +
92D ASP* 1.3 72.2 + - - +
95D ASN 3.4 11.4 - - - +
96D LEU* 3.8 18.8 - - + -
110D ASN* 4.0 4.9 - - - -
114D LEU* 3.3 28.7 - - + -
115D GLU 3.5 16.6 - - - -
116D ALA* 3.7 4.3 - - - -
117D ILE* 3.8 26.5 - - + -
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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