Contacts of the strand formed by residues 77 - 83 (chain C) in PDB entry 3UYT
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 TYR 77 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C TYR* 6.0 1.3 - - - -
39C LEU* 4.3 34.5 - - + -
40C GLU 3.3 22.0 - - - +
41C CYS* 3.9 21.4 - - - -
42C VAL* 3.3 16.8 - - - +
73C ALA* 3.5 3.6 - - - -
74C GLU 2.8 37.6 + - - +
75C GLY 3.2 2.0 + - - -
76C ASP* 1.3 99.4 - - + +
78C ASN* 1.3 64.7 + - - +
79C VAL* 4.6 0.9 - - + -
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Residues in contact with ASN 78 (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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39C LEU* 3.3 6.6 - - - +
40C GLU* 2.6 65.9 + - + +
41C CYS 4.8 0.3 - - - +
42C VAL* 4.3 17.8 - - - +
47C PRO* 4.9 5.4 - - - +
49C LEU* 3.6 9.8 - - + +
72C GLY 3.7 2.8 + - - -
73C ALA* 4.0 15.2 - - - +
77C TYR* 1.3 76.9 + - - +
79C VAL* 1.3 64.0 + - - +
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Residues in contact with VAL 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C VAL* 3.6 24.2 - - + -
37C ILE* 3.5 28.5 - - + -
38C LYS 3.4 3.6 - - - +
39C LEU* 3.2 22.7 - - + -
49C LEU* 3.8 3.7 - - - +
70C TRP* 3.8 20.9 - - + -
71C CYS* 3.0 6.1 - - - -
72C GLY 2.4 56.5 + - - +
74C GLU* 4.1 10.8 - - + -
77C TYR* 4.6 1.8 - - + -
78C ASN* 1.3 75.1 - - - +
80C MET* 1.3 67.8 + - - +
81C VAL* 4.4 2.0 - - + -
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Residues in contact with MET 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ILE* 3.3 3.5 - - - +
38C LYS* 2.7 40.5 + - + +
49C LEU* 3.7 34.5 - - + +
52C GLU* 4.1 17.9 - - + +
53C SER* 3.6 22.9 - - - -
56C TYR* 4.3 0.7 - - + -
68C ILE* 3.0 35.4 - - + -
70C TRP 3.1 8.5 - - - +
71C CYS* 4.1 6.5 - - - -
79C VAL* 1.3 75.9 - - - +
81C VAL* 1.3 64.5 + - - +
295C 0CK 3.1 35.4 - - + -
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Residues in contact with VAL 81 (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 VAL* 6.4 0.2 - - + -
9C TYR* 4.1 19.5 - - + -
35C VAL* 3.4 40.2 - - + -
36C ALA 3.1 7.2 - - - +
37C ILE* 3.9 18.6 - - + -
68C ILE* 3.5 5.2 - - - +
69C ARG* 2.6 33.2 + - + -
70C TRP* 2.5 51.8 + - + +
79C VAL* 4.4 2.0 - - + -
80C MET* 1.3 79.4 - - - +
82C MET* 1.3 57.5 - - - +
295C 0CK 3.9 2.7 - - - -
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Residues in contact with MET 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C VAL* 3.6 5.2 - - - +
36C ALA* 2.9 28.3 + - + -
56C TYR* 3.7 27.4 - - + +
66C PRO* 3.9 24.9 - - + -
67C THR 3.4 13.5 - - - +
68C ILE* 3.8 15.0 - - + -
69C ARG* 3.9 6.7 - - - +
81C VAL* 1.3 74.9 - - - +
83C GLU* 1.3 74.4 + - - +
84C LEU 3.3 0.2 + - - -
85C LEU* 4.5 0.4 - - - -
148C ILE* 4.4 4.0 - - - -
295C 0CK 3.4 69.1 - - + -
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Residues in contact with GLU 83 (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 GLU 4.9 0.4 - - - -
65C ILE 4.6 0.2 - - - +
66C PRO* 3.5 12.6 - - + +
67C THR* 3.3 39.1 + - - +
69C ARG* 3.7 28.5 - - - +
82C MET* 1.3 86.3 - - - +
84C LEU* 1.3 66.3 + - - +
85C LEU* 3.4 21.1 + - + +
141C LYS* 6.1 0.2 - - - +
146C TYR* 3.7 20.1 + - - -
295C 0CK 3.7 2.8 - - - -
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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