Contacts of the strand formed by residues 89 - 95 (chain L) in PDB entry 1UB6
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 GLY 89 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42L LEU* 4.2 5.2 - - - -
43L GLN 3.6 10.3 - - - -
44L LYS* 4.4 4.0 - - - -
45L PRO* 4.4 7.4 - - - +
87L ASP 3.5 1.0 + - - -
88L VAL* 1.3 77.4 - - - +
90L VAL* 1.3 66.1 + - - -
91L TYR* 3.8 7.6 - - - -
108L LYS* 3.5 9.7 - - - +
109L LEU 3.0 27.4 + - - -
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Residues in contact with VAL 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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45H LYS* 6.3 1.8 - - + -
42L LEU* 3.6 1.8 - - - +
43L GLN* 2.9 40.1 + - + +
89L GLY* 1.3 76.9 - - - +
91L TYR* 1.3 64.3 + - - +
92L TYR* 3.5 39.9 - - + +
105L ALA 5.0 0.9 - - - +
106L GLY* 3.8 4.9 - - - -
107L THR 3.4 24.0 - - - +
108L LYS* 4.1 28.9 - - + +
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Residues in contact with TYR 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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6L GLN* 2.8 24.8 - - - +
21L ILE* 3.6 31.2 - - + -
40L TRP* 4.9 2.0 - - + -
41L TYR 3.7 3.4 - - - +
42L LEU* 3.4 29.6 - - + +
52L LEU* 3.5 25.4 - - + -
67L PHE* 3.7 16.0 - + - -
78L LEU* 3.5 24.7 - - + -
80L ILE* 3.8 9.9 - - + +
87L ASP* 2.4 40.4 + - - +
89L GLY 3.8 8.3 - - - -
90L VAL* 1.3 73.6 - - - +
92L TYR* 1.3 54.9 - - - +
107L THR* 2.8 25.2 + - - -
109L LEU* 3.8 17.3 - - + -
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Residues in contact with TYR 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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41H GLN* 6.4 0.4 - - - -
45H LYS* 3.4 31.0 - - - +
46H ARG* 4.2 19.1 - - - -
6L GLN* 3.4 4.3 - - - +
39L TYR 3.9 0.2 - - - +
40L TRP* 3.2 9.7 - - - -
41L TYR* 2.9 80.8 + + + -
43L GLN* 3.7 19.0 - - + +
90L VAL* 3.5 39.0 - - + +
91L TYR* 1.3 73.2 - - - +
93L CYS* 1.3 63.1 + - - +
104L GLY 3.7 9.9 - - - -
105L ALA 3.5 21.1 + - - -
106L GLY* 3.4 15.7 - - - -
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Residues in contact with CYS 93 (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 LEU* 3.4 11.4 - - + -
6L GLN* 3.1 35.2 + - - +
23L CYS* 2.0 54.3 - - + -
38L LEU* 4.1 6.1 - - + -
39L TYR 3.4 5.2 - - - -
40L TRP* 3.7 17.0 - - + -
92L TYR* 1.3 78.4 - - - +
94L ALA* 1.3 63.7 + - - +
103L PHE* 4.0 0.5 - - - +
104L GLY* 2.9 23.2 + - - -
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Residues in contact with ALA 94 (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 LEU* 3.4 10.5 - - - +
38L LEU* 3.5 7.4 - - - +
39L TYR* 2.9 62.5 + - + +
41L TYR* 4.3 4.9 - - + -
93L CYS* 1.3 79.6 - - - +
95L GLN* 1.3 61.9 + - - +
102L THR 3.6 12.8 - - - +
103L PHE* 3.8 11.2 - - + +
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Residues in contact with GLN 95 (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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2L ALA* 4.1 16.8 - - + +
4L LEU* 3.8 20.6 - - + +
29L LEU* 3.9 16.1 - - + +
37L TYR 3.5 10.3 - - - +
39L TYR* 3.9 6.3 + - - -
94L ALA* 1.3 77.8 - - - +
96L ASN* 1.3 61.1 + - - +
97L LEU* 2.8 32.9 - - - +
98L GLU* 3.3 16.4 + - - +
100L PRO 3.2 20.4 - - - +
101L PRO* 4.3 7.4 - - - +
102L THR* 2.8 41.8 + - - +
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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