Contacts of the strand formed by residues 89 - 98 (chain C) in PDB entry 5SWW
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 ILE 89 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39C ARG* 3.8 4.7 - - - +
40C LEU* 3.0 53.6 + - + +
87C ALA 5.3 3.1 - - - +
88C GLN* 1.3 86.6 + - - +
90C TYR* 1.3 68.0 + - - +
118C THR 4.8 3.4 - - - +
119C HIS* 3.4 22.2 - - + +
121C ARG* 4.3 16.8 - - + +
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Residues in contact with TYR 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C VAL* 3.9 19.5 - - + -
38C GLU 3.4 4.0 - - - +
39C ARG* 3.6 43.5 - - + -
40C LEU* 4.7 0.7 - - - -
49C ASP 5.6 2.0 - - - -
83C GLN 4.6 2.3 + - - -
84C LEU* 3.7 32.9 - - + -
85C ASP* 3.4 47.5 + - - +
88C GLN* 3.9 14.8 - - + -
89C ILE* 1.3 77.9 - - - +
91C ARG* 1.3 61.1 + - - +
92C VAL* 4.1 2.0 + - + -
119C HIS* 2.9 13.7 + + - +
120C VAL* 3.5 10.9 - - + +
121C ARG* 2.9 29.6 + - - +
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Residues in contact with ARG 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C GLU 3.6 1.9 - - - +
37C VAL* 3.5 2.3 - - - -
38C GLU* 2.5 72.2 + - + +
40C LEU* 3.9 32.7 - - + +
90C TYR* 1.3 72.9 - - - +
92C VAL* 1.3 64.4 + - - +
93C THR* 4.1 6.9 + - - +
121C ARG* 3.4 13.5 - - + +
122C LEU 6.1 0.2 - - - -
123C ARG* 3.5 48.0 - - + +
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Residues in contact with VAL 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C TYR* 5.0 0.2 - - + -
36C GLU 3.2 8.7 - - - +
37C VAL* 4.0 21.3 - - + -
75C PHE* 3.6 22.0 - - + -
82C LEU* 5.7 0.4 - - + -
84C LEU* 5.5 3.8 - - + -
90C TYR* 5.0 2.7 - - + +
91C ARG* 1.3 75.1 - - - +
93C THR* 1.3 61.7 + - - +
94C TRP* 3.4 31.2 - - + +
113C PHE* 6.3 0.2 - - + -
120C VAL* 3.7 26.5 - - + -
121C ARG 2.9 10.0 + - - +
122C LEU* 3.5 14.1 - - + +
123C ARG* 2.9 29.4 + - - +
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Residues in contact with THR 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C CYS 3.4 1.9 - - - +
35C TYR* 3.2 6.2 - - - -
36C GLU* 2.9 48.7 + - - +
38C GLU* 4.7 7.3 + - - -
91C ARG* 4.5 8.0 + - - +
92C VAL* 1.3 72.2 - - - +
94C TRP* 1.3 64.0 - - - +
95C PHE* 3.5 32.3 - - + -
123C ARG* 3.4 36.6 + - + +
125C PHE* 4.0 8.5 - - + -
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Residues in contact with TRP 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C LEU* 3.7 30.9 - - + +
34C CYS 3.7 1.6 - - - -
35C TYR* 4.1 2.5 - - + -
72C ALA* 4.1 33.2 - - + -
75C PHE* 3.3 40.3 - + + -
76C LEU* 4.9 4.9 - - + -
92C VAL* 3.4 28.2 - - + +
93C THR* 1.3 76.6 - - - +
95C PHE* 1.3 61.6 + - - +
96C ILE* 3.9 7.9 - - + +
100C PRO* 4.6 5.8 - - + -
110C VAL* 4.1 18.6 - - + -
122C LEU* 3.9 17.7 - - + -
123C ARG 2.9 12.5 + - - +
124C ILE* 3.9 38.6 - - + -
125C PHE* 2.9 33.5 + - - +
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Residues in contact with PHE 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C PHE* 3.2 15.7 - - + -
33C LEU* 4.3 0.2 - - - -
34C CYS* 2.9 49.6 + - + +
36C GLU* 3.3 22.9 - - + -
93C THR* 3.5 22.4 - - + -
94C TRP* 1.3 73.7 - - - +
96C ILE* 1.3 60.0 + - - +
125C PHE* 3.4 33.0 - + + -
153C MET* 4.0 13.5 - - + -
157C GLU* 4.2 15.3 - - + -
160C HIS* 3.5 24.9 - + - -
161C CYS* 3.3 31.2 - - - -
165C PHE* 3.8 8.3 - + - -
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Residues in contact with ILE 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C PHE* 4.1 2.6 - - - -
31C THR* 3.7 14.1 - - + -
32C TYR 3.3 10.8 - - - +
33C LEU* 3.8 28.9 - - + +
71C ALA* 4.5 5.4 - - + -
72C ALA* 4.8 5.6 - - + +
94C TRP* 4.8 5.8 - - + -
95C PHE* 1.3 74.8 - - - +
97C SER* 1.3 62.5 + - - +
98C TRP 3.2 25.6 - - - +
100C PRO* 4.4 14.1 - - + -
124C ILE* 4.0 19.1 - - + -
125C PHE 2.9 15.7 + - - +
126C ALA* 4.0 9.4 - - + -
127C ALA* 3.0 26.0 + - - +
153C MET* 4.4 0.2 - - - +
0G C 4.4 9.2 - - - +
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Residues in contact with SER 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ASN* 3.0 20.7 + - - +
22C PHE* 4.1 6.6 - - - -
30C LYS 4.3 0.9 + - - -
31C THR* 4.0 5.4 - - - -
32C TYR* 2.8 37.2 + - - -
96C ILE* 1.3 71.6 - - - +
98C TRP* 1.3 57.8 + - - +
127C ALA* 3.7 8.9 - - - +
128C ARG* 2.5 64.3 + - - +
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Residues in contact with TRP 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C GLY* 3.4 22.2 - - - -
28C ARG 3.2 21.0 + - - -
30C LYS 3.4 8.3 + - - -
31C THR* 3.0 26.8 - - - +
96C ILE* 3.2 28.6 - - - +
97C SER* 1.3 78.6 - - - +
99C SER* 1.3 65.5 + - - +
126C ALA* 4.6 0.2 - - - -
128C ARG* 3.0 55.5 - - + +
129C ILE 3.4 13.9 - - - -
130C TYR* 3.5 33.0 - + + -
-1G T 3.1 39.7 - + - -
0G C 3.7 24.1 + + + -
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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