Contacts of the strand formed by residues 28 - 33 (chain B) in PDB entry 1WBB
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 LEU 28 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B LYS* 3.8 2.5 - - - +
27B ILE* 1.3 80.2 - - - +
29B LEU* 1.3 58.6 + - - +
30B PHE* 4.1 0.7 - - + -
39B LEU* 4.5 13.2 - - + -
43B ASP* 3.5 34.8 - - + +
46B ARG* 4.4 14.1 - - + -
47B ALA* 5.3 4.7 - - + -
50B LEU* 5.4 2.9 - - + -
83B LEU* 4.2 25.8 - - + -
88B GLU* 3.5 40.7 + - + +
89B SER 3.7 9.4 + - - +
90B VAL* 4.5 6.5 - - + -
91B ALA* 2.9 26.8 + - - +
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Residues in contact with LEU 29 (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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17B TYR* 3.9 20.1 - - + +
20B LEU* 3.8 13.0 - - + +
21B LYS* 3.5 46.9 - - + +
24B HIS* 5.4 4.3 - - + +
27B ILE 4.5 0.9 - - - +
28B LEU* 1.3 75.6 - - - +
30B PHE* 1.3 74.4 + - - +
31B TYR* 3.7 2.2 + - + -
38B ALA 3.3 12.1 - - - +
39B LEU* 3.9 8.9 - - - +
43B ASP* 3.1 20.0 + - - +
91B ALA* 3.5 22.7 - - + +
93B CYS* 3.9 16.4 - - + -
110B VAL* 4.1 10.1 - - + -
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Residues in contact with PHE 30 (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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28B LEU* 5.1 1.1 - - + -
29B LEU* 1.3 73.8 - - - +
31B TYR* 1.3 58.9 + - - +
37B TYR* 3.8 31.9 - + + -
38B ALA 3.9 3.6 - - - -
39B LEU* 3.6 32.8 - - + -
51B LEU* 5.4 1.3 - - + -
71B ILE* 3.5 33.7 - - + -
76B VAL* 4.2 3.6 - - + -
79B TYR* 5.0 4.0 - - + -
80B LEU* 3.6 18.6 - - + -
83B LEU* 3.7 28.0 - - + -
90B VAL* 3.5 16.2 - - + -
91B ALA 2.8 13.6 + - - +
92B ILE* 3.9 18.4 - - + -
93B CYS* 3.0 30.0 + - - +
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Residues in contact with TYR 31 (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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14B MET* 5.3 7.2 - - + +
16B GLN* 3.7 19.4 - - - +
17B TYR* 3.6 49.3 + + + +
20B LEU* 4.0 11.7 - - + -
29B LEU* 4.4 5.6 - - + +
30B PHE* 1.3 75.1 - - - +
32B ARG* 1.3 69.7 + - - +
33B MET* 3.3 25.8 + - - +
37B TYR* 3.8 2.3 - - - -
38B ALA* 2.9 41.4 + - + +
40B PHE* 4.6 7.6 - + - -
93B CYS* 3.6 16.4 - - + -
108B ARG* 3.3 46.0 + - - -
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Residues in contact with ARG 32 (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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31B TYR* 1.3 74.0 - - - +
33B MET* 1.3 62.0 + - - +
34B GLY 3.2 28.8 + - - +
36B PHE 3.5 16.1 + - - -
37B TYR* 3.7 15.8 - - + -
73B TYR* 3.7 42.6 - - - +
93B CYS 3.0 20.6 + - - +
94B GLU* 3.3 34.4 + - - +
108B ARG* 2.7 37.2 + - - +
2E G 5.8 1.6 - - - +
3E C 3.8 22.1 + - - -
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Residues in contact with MET 33 (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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14B MET* 6.2 2.0 - - + -
31B TYR* 3.3 33.4 - - - +
32B ARG* 1.3 79.1 - - - +
34B GLY* 1.3 58.9 - - - +
35B ASP 3.0 9.2 + - - -
36B PHE* 3.0 31.1 + - + +
38B ALA* 3.8 19.5 - - + +
40B PHE* 4.3 13.0 - - + -
68B MET* 5.5 7.6 - - - -
108B ARG* 4.5 1.8 - - - +
2E G 4.2 6.7 - - - -
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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