Contacts of the strand formed by residues 89 - 96 (chain C) in PDB entry 2Y1T
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 PHE 89 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C LYS* 3.9 26.2 - - + -
7C TYR 4.1 0.2 - - - -
8C LEU* 3.7 52.7 - - + -
45C GLY* 3.9 5.2 - - - +
46C VAL 3.2 24.5 - - - +
47C ALA* 3.6 13.5 - - + -
83C TYR* 2.8 20.0 + - - -
86C ASP 3.8 15.3 - - - -
87C ASN* 3.1 28.1 + - - +
88C ASP* 1.3 76.2 - - - +
90C TRP* 1.3 62.9 + - - +
91C PHE* 3.2 27.5 - - + -
143C DUD 4.2 0.2 - - - +
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Residues in contact with TRP 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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26C LEU* 3.6 31.0 - - + -
43C PRO* 3.9 1.0 - - - +
44C LEU* 3.0 32.3 + - + +
45C GLY 4.1 1.6 + - - -
46C VAL* 2.8 25.2 + - + +
47C ALA* 4.3 0.9 - - - -
48C MET* 3.7 56.1 + - + +
50C LEU* 4.5 6.3 - - + -
56C ALA* 3.5 23.6 - - + -
58C VAL* 3.9 17.3 - - + -
79C ILE* 3.7 34.9 - - + +
83C TYR* 3.8 12.0 - + - -
88C ASP 3.6 15.0 - - - -
89C PHE* 1.3 76.8 - - - +
91C PHE* 1.4 65.3 + - - +
111C PHE* 3.8 17.3 - + - -
143C DUD 3.5 5.6 - - - +
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Residues in contact with PHE 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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41C LEU* 4.2 41.1 - - + -
42C VAL 3.3 6.7 - - - +
43C PRO* 3.6 36.6 - - + -
44C LEU* 3.8 9.2 - - - +
58C VAL* 5.3 3.5 - - - +
83C TYR* 4.6 4.9 - - - -
89C PHE* 3.2 37.9 - - + -
90C TRP* 1.4 70.6 - - - +
92C PHE* 1.3 59.5 + - - +
93C PRO* 4.0 0.4 - - - -
143C DUD 2.8 40.8 + + + +
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Residues in contact with PHE 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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41C LEU* 4.6 1.3 - - - -
42C VAL* 2.7 45.9 + - + +
44C LEU* 4.0 16.4 - - + +
58C VAL* 4.8 1.3 - - + -
60C PRO* 4.2 10.5 - - + -
64C THR* 4.5 2.2 - - + -
70C VAL* 3.9 20.0 - - + -
71C ILE* 5.6 0.2 - - - -
72C GLN* 3.1 48.9 - - + -
91C PHE* 1.3 73.6 - - - +
93C PRO* 1.3 59.7 - - - +
94C ALA* 3.3 32.2 + - + -
108C ILE* 4.0 25.4 - - + -
109C CYS* 3.5 32.3 - - + -
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Residues in contact with PRO 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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62B SER 5.7 4.9 - - - +
39C PHE* 3.9 7.0 - - + -
40C LYS 4.1 0.9 - - - +
41C LEU* 3.8 24.7 - - + -
72C GLN* 3.3 17.7 - - + +
73C THR* 3.0 39.8 + - - +
74C ASN* 3.4 33.2 - - + +
91C PHE 3.8 2.7 - - - +
92C PHE* 1.3 82.1 - - + +
94C ALA* 1.3 59.2 + - - +
143C DUD 3.7 18.4 - - + +
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Residues in contact with ALA 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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34C ILE* 3.9 19.9 - - + +
38C GLU 4.1 0.3 - - - +
39C PHE* 3.2 8.7 - - - -
40C LYS 2.8 43.5 + - - +
42C VAL* 3.9 5.4 - - + -
70C VAL* 4.2 11.0 - - + -
71C ILE 3.5 4.5 - - - -
92C PHE* 3.3 25.8 + - + -
93C PRO* 1.3 73.4 - - - +
95C TYR* 1.3 57.6 + - - +
102C ILE* 5.2 0.4 - - + -
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Residues in contact with TYR 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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65B TYR* 2.4 37.0 - + - +
97B LEU* 3.6 46.2 + - + +
37C ASP* 3.2 49.0 + - - +
38C GLU 3.7 6.3 - - - -
70C VAL* 3.2 5.6 - - - -
71C ILE* 3.0 45.3 + - + +
73C THR* 3.5 19.2 - - + +
93C PRO 4.0 0.6 + - - -
94C ALA* 1.3 71.8 - - - +
96C ALA* 1.3 75.4 + - - +
97C LEU* 3.7 19.1 + - + -
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Residues in contact with ALA 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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34C ILE* 3.6 23.1 - - + +
35C LYS 3.5 18.8 - - - +
37C ASP* 2.9 30.3 + - - -
38C GLU 3.1 7.7 + - - -
69C GLY 3.7 4.3 - - - -
70C VAL* 3.9 3.6 - - + -
94C ALA 4.2 0.6 + - - -
95C TYR* 1.3 77.1 - - - +
97C LEU* 1.3 61.4 + - - +
98C ARG 3.4 18.4 - - - +
100C THR* 3.9 8.3 - - + -
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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