Contacts of the strand formed by residues 87 - 92 (chain L) in PDB entry 2UZI
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 THR 87 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38L TYR 3.9 0.2 - - - +
39L GLN* 3.5 2.1 - - - -
40L GLN* 2.8 43.7 + - - +
42L PRO* 5.8 3.9 - - - +
86L ALA* 1.3 74.5 - - - +
88L TYR* 1.3 64.8 + - - +
89L TYR* 3.6 35.0 - - + +
103L GLY* 4.0 2.7 - - - -
104L THR 3.4 25.4 - - - +
105L LYS* 3.9 22.0 - - + +
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Residues in contact with TYR 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8L GLN* 2.9 8.2 - - - +
23L ILE* 4.0 17.0 - - + -
37L TRP* 4.8 2.9 - - + -
38L TYR 3.2 9.4 - - - +
39L GLN* 2.9 33.0 + - + -
49L LEU* 3.6 26.5 - - + -
64L PHE* 3.6 14.3 - + - -
75L LEU* 3.6 23.6 - - + -
77L ILE* 4.0 9.6 - - + -
84L ASP* 2.8 34.9 + - - +
86L ALA* 3.8 15.5 - - + -
87L THR* 1.3 75.9 - - - +
89L TYR* 1.3 61.3 + - - +
103L GLY* 3.2 1.9 - - - -
104L THR* 2.8 32.3 + - - +
106L VAL* 3.9 21.5 - - + -
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Residues in contact with TYR 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H GLN* 3.3 18.9 + - - -
43H LYS 3.6 8.1 + - - -
44H GLY* 3.7 2.4 - - - -
45H LEU* 3.5 41.7 - - + -
8L GLN* 3.5 4.3 - - - +
36L ASN 3.8 0.2 - - - +
37L TRP* 3.4 6.7 - - - -
38L TYR* 2.8 47.4 + - + +
40L GLN* 3.7 24.2 + - + -
87L THR* 3.6 31.1 + - + +
88L TYR* 1.3 75.3 - - - +
90L CYS* 1.3 68.1 + - - +
100L PHE* 4.2 11.7 - - + -
101L GLY 3.5 13.5 - - - -
102L GLN 3.7 8.7 + - - -
103L GLY* 3.4 25.6 - - - -
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Residues in contact with CYS 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L MET* 4.1 2.0 - - - -
8L GLN* 3.2 26.9 - - - +
25L CYS* 2.1 53.6 - - + -
35L LEU* 4.0 6.3 - - + -
36L ASN 3.1 9.9 - - - +
37L TRP* 3.7 16.3 - - + -
89L TYR* 1.3 77.3 - - - +
91L GLN* 1.3 61.6 + - - +
100L PHE* 3.4 2.3 - - - -
101L GLY* 2.8 33.4 + - - -
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Residues in contact with GLN 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102H PHE* 3.4 30.6 - - - -
6L MET* 3.7 8.3 - - - +
35L LEU* 3.3 4.7 - - - +
36L ASN* 2.7 58.7 + - - +
38L TYR* 3.7 18.2 + - + -
90L CYS* 1.3 78.3 - - - +
92L GLN* 1.3 77.7 + - - +
93L SER* 3.6 7.1 - - - -
98L MET* 3.3 19.4 + - - +
99L THR 3.3 15.7 - - - +
100L PHE* 3.5 28.7 - - + -
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Residues in contact with GLN 92 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4L ILE 4.6 8.7 - - - +
6L MET* 3.5 20.7 - - + +
31L ILE* 4.1 11.8 - - + +
34L TYR 3.7 11.4 - - - +
91L GLN* 1.3 85.7 + - - +
93L SER* 1.3 63.1 + - - +
94L VAL* 3.4 18.2 - - + +
95L MET* 2.5 55.2 + - - +
97L PRO 2.9 19.6 + - - +
98L MET* 3.3 7.8 - - - -
99L THR* 3.2 18.4 + - - +
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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