Contacts of the strand formed by residues 93 - 100 (chain B) in PDB entry 3LZP
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 93 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLY 3.1 19.1 + - - -
58A PRO* 4.3 5.4 - - - -
89B VAL* 3.6 5.4 - - - -
90B ALA* 2.9 23.8 + - - -
92B ASP* 1.3 80.7 - - - +
94B PRO* 1.3 77.9 - - - +
95B HIS* 3.6 8.5 + - - -
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Residues in contact with PRO 94 (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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57A PHE* 3.6 40.4 - - + -
58A PRO* 4.2 1.3 - - + -
61A PHE* 4.0 16.8 - - + -
129A PHE* 4.3 1.3 - - + -
46B ASP* 4.9 2.4 - - - +
48B HIS* 4.6 6.8 + - - -
62B TRP* 3.6 55.1 - - + -
88B MET 3.2 12.3 - - - +
89B VAL* 3.8 2.4 - - + -
92B ASP 5.1 0.3 - - - +
93B GLY* 1.3 86.2 - - - +
95B HIS* 1.3 62.5 + - - +
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Residues in contact with HIS 95 (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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132A HIS* 3.3 13.5 - + - -
42B HIS* 3.6 0.2 + - - -
44B GLU* 3.3 33.9 + - + +
45B ALA 3.7 12.3 - - - +
46B ASP* 4.1 12.6 - - - +
62B TRP* 3.6 12.2 - - - +
87B PRO* 3.4 3.8 - - - +
88B MET* 2.9 40.0 + - + +
90B ALA* 3.9 14.7 - - + +
92B ASP* 4.7 2.8 + - - -
93B GLY 3.6 10.5 + - - -
94B PRO* 1.3 75.9 - - - +
96B TYR* 1.3 81.8 + - - +
97B GLY 3.7 1.3 - - - -
200B CU 2.1 31.3 - - - -
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Residues in contact with TYR 96 (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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65A TYR* 4.4 1.8 - - - -
43B LEU 3.9 0.2 - - - +
44B GLU* 3.2 3.5 - - - -
45B ALA* 2.8 38.2 + - + +
47B ILE* 4.2 9.4 - - + -
62B TRP* 3.4 24.0 - + - -
63B MET 2.6 29.1 + - - -
64B PRO* 3.2 8.0 - - - +
65B TYR 3.2 1.0 + - - -
66B LEU* 3.0 56.8 + - + +
68B ILE* 3.6 24.5 - - + -
85B LEU* 3.9 21.5 - - + +
86B MET 3.3 5.2 - - - -
87B PRO* 3.9 27.1 - - + -
95B HIS* 1.3 75.3 - - - +
97B GLY* 1.3 57.1 + - - +
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Residues in contact with GLY 97 (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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33B ASP* 4.6 0.3 - - - +
42B HIS* 3.9 6.1 - - - -
43B LEU 3.0 11.0 - - - -
84B THR 4.5 0.2 - - - +
85B LEU* 3.8 4.7 - - - -
86B MET* 2.9 32.3 + - - +
88B MET* 3.5 14.6 - - - +
95B HIS* 3.7 12.9 - - - -
96B TYR* 1.3 75.6 - - - +
98B ALA* 1.3 62.4 + - - +
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Residues in contact with ALA 98 (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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33B ASP* 3.4 9.6 - - - +
42B HIS* 3.4 7.6 - - - -
43B LEU* 2.9 29.2 + - - +
70B TYR* 4.4 4.9 - - + +
84B THR 3.7 13.5 - - - +
85B LEU* 3.5 18.2 - - + -
86B MET* 6.2 0.2 - - + -
97B GLY* 1.3 77.4 - - - +
99B ASN* 1.3 69.8 + - - +
100B ILE* 3.6 12.4 - - + +
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Residues in contact with ASN 99 (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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24B PRO* 3.6 2.5 - - - +
25B ILE 2.8 39.3 + - - +
33B ASP* 2.8 22.2 + - - +
34B LEU* 2.8 45.9 + - + +
36B ALA* 3.6 14.8 - - - +
39B ALA* 3.7 13.7 - - + -
41B ILE 3.4 2.6 - - - +
42B HIS* 2.8 28.5 + - - +
70B TYR* 5.2 0.2 + - - -
98B ALA* 1.3 74.2 - - - +
100B ILE* 1.3 63.7 + - - +
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Residues in contact with ILE 100 (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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34B LEU* 4.1 0.9 - - - -
39B ALA* 3.9 2.4 - - - +
40B ASP 2.8 26.7 + - - -
41B ILE* 2.8 32.1 + - + +
43B LEU* 3.5 41.5 - - + -
70B TYR* 3.7 31.2 - - + +
72B LEU* 4.5 6.5 - - + -
81B LYS* 3.7 20.0 - - + +
98B ALA* 3.6 9.0 - - + +
99B ASN* 1.3 81.4 - - - +
101B ALA* 1.3 69.9 + - - +
102B MET* 3.6 16.3 + - - -
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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