Contacts of the strand formed by residues 90 - 96 (chain L) in PDB entry 4JZJ
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 90 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43L GLN* 3.6 30.7 - - + +
44L GLN 3.4 16.4 - - - +
45L LYS* 4.0 6.3 - - + +
46L PRO* 4.9 3.1 - - - -
88L ASP 3.2 8.2 + - - +
89L VAL* 1.3 77.6 - - - +
91L VAL* 1.3 64.7 + - - +
92L TYR* 3.8 5.3 - - + -
108L THR 3.8 0.5 - - - +
109L LYS* 3.8 2.8 - - - +
110L LEU* 3.0 32.7 + - - +
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Residues in contact with VAL 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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42L TYR 4.1 0.2 - - - +
43L GLN* 3.6 1.2 - - - -
44L GLN* 2.7 49.6 + - + +
90L ALA* 1.3 73.6 - - - +
92L TYR* 1.3 62.1 + - - +
93L TYR* 3.6 34.6 + - + +
106L GLN 5.2 0.2 - - - +
107L GLY* 4.1 4.0 - - - -
108L THR 3.4 21.8 - - - +
109L LYS* 3.5 29.8 - - + +
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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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6L GLN* 2.8 24.2 + - - +
21L ILE* 4.1 19.7 - - + -
41L TRP* 4.8 5.2 - - + -
42L TYR 3.3 15.3 - - - +
43L GLN* 3.1 35.8 + - + -
53L LEU* 4.2 3.6 - - + -
68L PHE* 3.7 24.9 - + - -
79L LEU* 3.6 23.8 - - + -
81L ILE* 3.9 6.9 - - + +
88L ASP* 2.5 30.7 + - - -
90L ALA* 3.8 16.2 - - + -
91L VAL* 1.3 75.8 - - - +
93L TYR* 1.3 62.6 + - - +
107L GLY* 3.2 2.6 - - - -
108L THR* 2.9 23.3 + - - +
110L LEU* 3.8 17.5 - - + -
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Residues in contact with TYR 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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39H GLN* 3.2 22.1 + - - -
43H LYS 3.3 10.2 + - - -
44H GLY* 3.6 16.6 - - - -
45H LEU* 4.2 16.2 - - + -
6L GLN* 3.2 3.6 - - - -
41L TRP* 3.3 8.9 - - - -
42L TYR* 2.6 51.2 + - + -
44L GLN* 3.4 27.3 + - + -
50L PRO* 4.9 0.4 - - + -
91L VAL* 3.6 28.8 - - + +
92L TYR* 1.3 75.2 - - - +
94L CYS* 1.3 65.1 + - - +
104L PHE* 4.3 12.8 - + + -
105L GLY 3.2 19.3 - - - -
106L GLN 3.5 20.6 + - - -
107L GLY* 3.6 5.6 - - - -
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Residues in contact with CYS 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 MET* 3.9 5.8 - - - -
6L GLN* 2.9 26.6 + - - -
23L CYS* 2.1 45.5 - - - -
39L LEU* 3.9 10.5 - - + -
40L THR 3.2 6.7 - - - +
41L TRP* 3.5 19.5 - - + -
93L TYR* 1.3 74.5 - - - +
95L GLN* 1.3 64.9 + - - +
104L PHE* 3.5 4.5 - - - -
105L GLY* 2.9 28.0 + - - -
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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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105H SER 4.4 5.9 + - - +
106H TRP* 5.7 0.5 - - - -
107H PHE* 4.0 12.5 - - - -
4L MET* 3.9 4.7 - - - -
39L LEU* 3.5 3.9 - - - -
40L THR* 2.7 38.9 + - - +
42L TYR* 3.0 32.8 + - + -
94L CYS* 1.3 78.9 - - - +
96L ASN* 1.3 68.0 + - - +
97L ASP* 3.1 6.8 + - - +
102L TYR* 2.7 49.9 + - - +
103L THR 3.4 5.8 - - - +
104L PHE* 3.7 29.7 - - + -
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Residues in contact with ASN 96 (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 ILE* 3.8 24.3 - - - +
4L MET* 3.5 24.0 - - - +
29L LEU* 3.7 8.3 - - + +
38L TYR 4.2 2.7 - - - -
95L GLN* 1.3 72.2 + - - +
97L ASP* 1.3 56.9 + - - +
98L TYR* 2.7 35.8 + - - +
99L SER* 3.2 24.7 + - - +
100L TYR 5.1 0.4 + - - -
101L PRO 4.0 1.0 + - - -
102L TYR* 3.3 25.3 - - - +
103L THR* 2.8 37.1 + - - +
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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