Contacts of the strand formed by residues 67 - 74 (chain B) in PDB entry 3LZR
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 67 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B TYR 3.8 0.8 + - - -
66B LEU* 1.3 70.9 - - - +
68B ILE* 1.3 64.0 + - - +
69B ALA* 5.2 2.7 - - + +
84B THR* 5.3 10.1 - - + -
120B TYR 3.4 6.2 - - - +
121B ILE* 3.5 2.3 - - - +
122B SER* 3.1 42.6 + - - -
123B ASN 5.0 0.2 + - - -
126B LYS* 4.3 24.4 - - + +
127B GLN* 3.1 26.3 + - - +
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Residues in contact with ILE 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ALA* 4.2 4.0 - - + -
47B ILE* 3.2 34.5 - - + -
66B LEU* 3.8 11.9 + - + +
67B THR* 1.3 76.9 - - - +
69B ALA* 1.3 61.1 + - - +
84B THR* 3.3 8.1 - - - +
85B LEU* 2.9 60.0 + - + +
96B TYR* 3.4 35.2 - - + -
119B PHE* 3.9 27.6 - - + -
120B TYR 3.8 2.0 - - - -
121B ILE* 4.5 8.3 - - + -
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Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B THR* 4.1 3.5 - - + +
68B ILE* 1.3 73.7 - - - +
70B TYR* 1.3 61.1 + - - +
83B GLY 3.3 11.7 - - - +
84B THR* 3.9 11.2 - - + -
118B THR 3.7 0.5 - - - +
119B PHE* 3.5 2.3 - - - -
120B TYR* 2.8 57.0 + - + +
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Residues in contact with TYR 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU* 4.2 9.0 - - + -
69B ALA* 1.3 75.2 - - - +
71B GLU* 1.3 63.3 + - - +
72B LEU* 4.0 15.0 - - + -
81B LYS* 4.2 16.0 - - + +
82B ARG* 3.4 14.4 + - - +
83B GLY* 2.9 65.4 + - - +
84B THR 3.6 6.7 - - - -
85B LEU* 3.8 30.3 - - + -
98B ALA* 4.4 7.5 - - + +
99B ASN 5.2 1.0 + - - -
100B ILE* 3.9 29.1 - - + +
117B LEU* 4.0 12.6 - - + -
118B THR 3.3 8.3 - - - +
119B PHE* 4.1 13.0 - - + -
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Residues in contact with GLU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B TYR* 1.3 74.4 - - - +
72B LEU* 1.3 58.7 + - - +
73B LYS* 3.6 13.1 + - - +
80B ILE* 3.7 28.6 - - + +
81B LYS 3.6 3.1 - - - -
82B ARG* 3.4 34.9 + - + +
116B GLU 3.4 7.6 - - - +
117B LEU* 4.4 1.6 - - - -
118B THR* 3.0 44.3 + - + +
147B LYS* 5.9 0.3 + - - -
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Residues in contact with LEU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ILE* 4.8 5.6 - - + -
43B LEU* 5.5 3.1 - - + -
70B TYR* 4.0 11.8 - - + -
71B GLU* 1.3 71.4 - - - +
73B LYS* 1.3 57.9 + - - +
79B ALA 3.8 1.7 - - - +
80B ILE* 3.7 1.8 - - - -
81B LYS* 3.0 46.3 + - + +
100B ILE* 4.4 20.0 - - + -
102B MET* 3.5 35.4 - - + -
110B PHE* 4.2 2.6 - - + -
115B TYR* 3.8 18.6 - - + -
116B GLU 3.9 7.6 - - - +
117B LEU* 4.2 13.2 - - + -
152B PHE* 3.8 31.0 - - + -
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Residues in contact with LYS 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B GLU* 3.6 15.2 + - - +
72B LEU* 1.3 76.0 - - - +
74B ASN* 1.3 68.3 + - - +
75B THR* 3.8 14.7 + - + +
78B GLY* 3.4 25.4 + - - -
79B ALA 3.5 8.1 - - - +
80B ILE* 4.1 25.1 - - + +
115B TYR* 3.2 7.7 - - - -
116B GLU* 2.7 58.6 + - + +
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Residues in contact with ASN 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B LYS* 1.3 68.7 - - - +
75B THR* 1.3 56.1 + - - +
76B ASP* 3.2 13.0 + - - +
77B THR* 3.0 35.9 + - - +
78B GLY* 2.6 37.8 + - - -
79B ALA* 3.2 12.8 + - + +
109B GLY 3.1 16.6 + - - +
110B PHE* 5.1 0.7 - - + -
111B GLY 3.8 7.3 + - - +
112B VAL 4.7 5.1 + - - -
113B GLY* 5.0 0.9 - - - -
114B ASN 3.6 10.0 + - - +
115B TYR* 3.0 39.8 + - + -
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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