Contacts of the strand formed by residues 86 - 93 (chain C) in PDB entry 3ARE
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 86 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C LYS* 5.1 2.5 - - + -
37C GLN 3.3 25.6 - - - +
38C ASP* 4.0 13.0 - - - +
39C THR* 5.3 6.3 - - - +
84C ASP 3.1 12.1 + - - +
85C THR* 1.3 75.7 - - - +
87C THR* 1.3 64.7 - - - +
88C TYR* 3.4 17.3 - - + +
111C GLN* 4.8 2.7 - - - -
112C LEU 3.0 27.4 + - - -
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Residues in contact with THR 87 (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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35C PHE 4.0 0.3 - - - +
36C LYS* 3.7 2.4 - - - -
37C GLN* 2.8 51.7 + - - +
39C THR* 5.5 5.8 - - - +
86C ALA* 1.3 75.1 - - - +
88C TYR* 1.3 63.7 + - - +
89C ILE* 4.1 12.7 + - + +
108C ALA 4.6 4.5 - - - +
109C GLY* 4.2 10.8 - - - -
110C THR 3.3 23.6 - - - +
111C GLN* 4.3 14.7 - - + +
37D GLN* 6.0 0.2 - - - +
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Residues in contact with TYR 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C GLN* 3.1 9.9 + - - -
20C LEU* 3.6 25.8 - - + -
34C TRP* 4.4 7.2 - - + -
35C PHE 3.5 5.4 - - - +
36C LYS* 4.1 11.1 - - + +
46C LEU* 3.7 31.2 - - + -
62C TYR* 4.3 16.5 + + - -
75C LEU* 4.1 9.6 - - + -
77C ILE* 5.2 5.2 - - + +
84C ASP* 2.7 44.8 + - - +
86C ALA* 3.4 23.8 - - + +
87C THR* 1.3 72.0 - - - +
89C ILE* 1.3 62.5 + - - +
110C THR 2.8 36.5 + - - +
112C LEU* 3.6 25.4 - - + +
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Residues in contact with ILE 89 (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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5C GLN* 3.5 2.2 - - - -
33C ARG 3.8 0.5 - - - +
34C TRP* 3.5 7.7 - - - -
35C PHE* 2.9 41.3 + - + +
37C GLN* 3.8 15.0 - - + +
43C LEU* 3.8 20.9 - - + -
87C THR* 4.2 9.6 - - + +
88C TYR* 1.3 76.9 - - - +
90C CYS* 1.3 65.2 + - - +
91C VAL* 3.9 19.9 + - + +
106C PHE* 4.5 7.6 - - + -
107C GLY 3.4 24.7 - - - +
108C ALA 5.0 1.6 - - - +
109C GLY* 4.0 11.4 - - - -
37D GLN* 3.8 25.4 - - - +
43D LEU* 4.8 3.6 - - + -
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Residues in contact with CYS 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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3C VAL* 3.8 7.6 - - + +
5C GLN* 2.7 21.1 + - + +
22C CYS* 2.0 53.4 - - + -
32C LEU* 3.7 27.1 - - - -
33C ARG 3.7 3.4 - - - -
34C TRP* 4.1 9.6 - - + -
89C ILE* 1.3 72.0 - - - +
91C VAL* 1.3 62.6 + - - +
92C VAL* 4.7 1.8 - - - -
106C PHE 3.9 0.2 - - - -
107C GLY 3.2 23.9 + - - -
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Residues in contact with VAL 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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31C HIS* 4.2 1.4 + - + +
32C LEU* 3.3 3.1 - - - +
33C ARG* 2.7 48.2 + - + +
35C PHE* 3.6 30.5 - - + -
89C ILE* 3.9 8.1 - - + +
90C CYS* 1.3 77.7 - - - +
92C VAL* 1.3 64.8 + - - +
93C GLY 4.3 0.2 + - - -
104C LEU* 3.8 39.3 - - + -
105C HIS 3.3 10.3 - - - +
106C PHE* 3.5 29.4 - - + -
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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
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3C VAL* 4.0 19.7 - - + -
24C TYR* 4.0 15.7 - - + -
26C VAL* 3.9 33.9 - - + -
29C ASP* 4.4 15.9 - - + -
31C HIS 3.5 11.9 - - - +
32C LEU* 3.8 24.7 - - + -
90C CYS* 4.7 3.4 - - - -
91C VAL* 1.3 79.8 - - - +
93C GLY* 1.3 65.4 + - - +
104C LEU* 3.5 0.9 - - - -
105C HIS* 2.8 40.5 + - - -
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Residues in contact with GLY 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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28C PRO 4.1 0.2 - - - +
30C ASN* 3.2 25.5 + - - +
31C HIS* 3.0 28.2 + - - +
91C VAL 4.3 0.6 - - - -
92C VAL* 1.3 73.9 - - - +
94C ASP* 1.3 63.5 + - - -
95C ARG 3.4 3.6 - - - -
103C ARG 4.0 2.2 - - - -
104C LEU* 3.7 22.3 - - - +
97D ALA 5.0 1.6 - - - -
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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