Contacts of the strand formed by residues 83 - 90 (chain C) in PDB entry 3T0E
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ARG* 4.4 17.0 - - - -
37C GLN 3.1 22.9 - - - +
38C LEU* 4.4 7.2 - - + +
39C PRO* 5.4 4.3 - - - -
80C ARG 5.0 0.2 - - - +
81C ASP 3.0 10.7 + - - +
82C ALA* 1.3 77.7 - - - +
84C VAL* 1.3 67.5 + - - +
85C TYR* 3.9 3.4 + - + -
104C LEU* 3.6 6.9 - - - +
105C LEU* 2.9 32.7 + - - +
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Residues in contact with VAL 84 (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 ARG* 3.0 5.4 - - - +
37C GLN* 2.8 38.6 + - + +
39C PRO* 6.5 0.9 - - + -
83C ALA* 1.3 75.4 - - - +
85C TYR* 1.3 62.8 + - - +
86C TYR* 3.2 44.1 + - + +
102C GLY* 4.3 2.0 - - - -
103C THR 3.4 17.0 - - - +
104C LEU* 3.6 26.0 - - + +
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Residues in contact with TYR 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C GLN* 3.0 20.0 + - - -
19C LEU* 3.6 25.8 - - + -
34C TRP* 4.2 12.1 - + + -
35C TYR 3.6 3.1 - - - -
36C ARG* 2.9 51.0 + - + -
46C VAL* 4.7 5.8 - - + -
72C LEU* 3.9 20.6 - - + -
74C LEU* 3.7 13.7 - - + +
81C ASP* 2.9 38.4 + - - +
83C ALA* 4.0 9.4 - - + -
84C VAL* 1.3 71.6 - - - +
86C TYR* 1.3 63.5 + - - +
103C THR* 2.7 23.6 + - - +
105C LEU* 3.7 26.0 - - + -
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Residues in contact with TYR 86 (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* 3.8 2.2 - - - +
33C HIS 4.1 0.2 - - - +
34C TRP* 3.4 9.0 - - - -
35C TYR* 2.5 43.5 + - + +
37C GLN* 3.1 37.3 + - + -
43C PRO* 5.2 0.9 - - + -
84C VAL* 3.2 32.4 - - + +
85C TYR* 1.3 72.8 - - - +
87C CYS* 1.3 60.0 + - - +
88C THR* 4.1 7.2 - - + -
99C PHE* 3.4 39.7 - + + -
100C GLY 4.2 12.6 - - - +
101C THR 4.3 6.3 - - - -
102C GLY* 3.5 23.6 - - - -
36D GLN* 3.4 12.0 + - - -
40D GLN 5.3 0.6 + - - -
41D SER* 4.2 12.6 - - - -
42D LEU* 4.1 9.4 - - + -
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Residues in contact with CYS 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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3C THR* 2.6 24.7 + - - -
5C GLN* 2.8 30.2 + - + +
21C CYS* 2.0 47.1 - - - -
23C HIS* 4.5 2.9 - - - -
32C ILE* 4.2 13.2 - - - -
33C HIS 3.9 2.2 - - - -
34C TRP* 3.7 22.0 - - + -
86C TYR* 1.3 71.6 - - - +
88C THR* 1.3 65.5 + - - +
100C GLY* 4.6 7.5 - - - +
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Residues in contact with THR 88 (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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2C LYS* 5.8 1.1 - - - -
3C THR* 4.4 3.4 - - - -
32C ILE* 3.8 8.1 - - - +
33C HIS* 3.1 38.4 + - - +
35C TYR* 4.0 4.7 - - + -
86C TYR* 4.3 10.8 - - + +
87C CYS* 1.3 86.6 - - - +
89C VAL* 1.3 70.8 + - - +
97C LEU* 3.4 27.7 - - + +
98C ILE 3.6 22.0 - - - +
99C PHE* 4.2 10.3 - - + -
100C GLY 4.1 10.5 - - - +
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Residues in contact with VAL 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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2C LYS* 4.0 22.9 - - + -
3C THR* 3.6 18.4 - - + -
23C HIS* 5.0 6.7 - - + -
26C ILE* 3.8 33.4 - - + -
30C ASP* 4.9 3.6 - - + -
31C TYR 3.7 5.6 - - - +
32C ILE* 5.2 1.6 - - + -
88C THR* 1.3 83.2 - - - +
90C TYR* 1.3 61.4 - - - +
94C THR* 4.1 21.2 - - + +
96C LYS 4.1 12.1 - - - +
97C LEU* 4.7 3.6 - - - +
98C ILE* 4.8 7.5 + - + +
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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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30C ASP* 3.9 2.7 - - - -
31C TYR* 2.9 35.0 + - - +
33C HIS* 4.1 32.2 + + + +
35C TYR* 4.8 1.1 - - - -
89C VAL* 1.3 75.9 - - - +
91C GLY* 1.3 73.1 + - - +
94C THR 3.7 9.4 - - - -
95C ASN 3.9 16.6 - - - -
96C LYS 5.1 1.6 - - - -
97C LEU* 4.2 31.4 - - + -
95D ARG* 3.3 26.0 + - - -
99D TYR* 4.4 2.5 - - - -
100D ASN* 3.4 27.0 + - - +
101D SER 3.1 29.8 + - - -
103D LEU* 4.5 19.1 - - + -
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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