Contacts of the strand formed by residues 93 - 99 (chain B) in PDB entry 4I0A
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 CYS 93 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B HIS 3.8 0.2 - - - +
23B LYS* 3.2 6.6 - - - +
24B TYR* 2.6 49.2 + - + +
30B LEU* 5.4 0.9 - - + -
43B ILE* 5.2 1.1 - - - -
45B LYS* 3.3 9.3 + - - +
46B GLY 4.0 2.5 - - - -
47B SER 3.3 44.0 - - - -
48B VAL* 3.9 13.5 - - - -
89B ALA* 4.0 4.9 - - + -
91B THR 3.4 10.3 - - - -
92B ALA* 1.3 73.1 - - - +
94B GLU* 1.3 60.1 + - - +
95B VAL* 3.8 17.0 - - + -
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Residues in contact with GLU 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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21B ILE* 4.0 21.6 - - + +
22B HIS 3.5 2.2 - - - +
23B LYS* 4.2 23.8 - - + -
43B ILE 3.7 0.2 - - - -
44B VAL* 2.8 46.3 + - + +
45B LYS* 2.9 51.9 + - + +
93B CYS* 1.3 72.7 - - - +
95B VAL* 1.3 64.8 + - - +
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Residues in contact with VAL 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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20B HIS 3.9 0.7 - - - +
21B ILE* 3.5 3.6 - - - -
22B HIS* 2.8 36.0 + - - +
24B TYR* 4.0 16.5 - - + -
30B LEU* 3.9 22.4 - - + -
41B TYR* 3.7 28.7 - - + -
42B TYR 3.5 9.0 - - - +
43B ILE* 4.6 12.8 - - + -
71B ILE* 4.6 2.5 - - + -
93B CYS* 3.8 22.7 - - + -
94B GLU* 1.3 82.2 - - - +
96B ALA* 1.4 73.4 + - - +
97B GLU* 4.0 0.7 + - - +
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Residues in contact with ALA 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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16B LEU* 3.5 31.9 - - + -
19B CYS* 3.7 17.3 - - + -
20B HIS 3.5 4.7 - - - -
21B ILE* 3.8 11.0 - - + -
41B TYR* 3.1 8.8 - - - +
42B TYR* 2.7 41.0 + - + +
44B VAL* 4.3 4.6 - - + +
94B GLU 4.3 0.2 - - - -
95B VAL* 1.4 73.6 - - - +
97B GLU* 1.3 60.0 + - - +
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Residues in contact with GLU 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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19B CYS* 3.3 5.5 - - - +
20B HIS* 2.9 64.9 + - + +
22B HIS* 5.0 4.8 - - + -
24B TYR* 4.7 5.5 + - - -
39B THR* 2.8 37.2 + - + +
40B LEU 3.3 11.0 - - - +
41B TYR* 3.1 33.6 + - + -
95B VAL 4.0 1.3 + - - +
96B ALA* 1.3 75.9 - - - +
98B ILE* 1.3 67.1 + - - +
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Residues in contact with ILE 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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15B PHE* 4.0 20.6 - - + -
18B HIS* 3.7 26.7 - - + +
19B CYS* 3.8 9.9 - - - -
20B HIS* 4.9 4.5 - - - -
39B THR* 3.3 5.1 - - - -
40B LEU* 2.7 58.1 + - + +
97B GLU* 1.3 79.1 - - - +
99B SER* 1.3 67.5 + - - +
102B LYS* 3.7 27.4 - - + -
103B PHE* 4.0 8.1 - - + +
106B LEU* 3.7 29.2 - - + -
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Residues in contact with SER 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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20B HIS* 5.7 0.6 + - - -
38B GLU 3.6 9.6 - - - -
39B THR* 4.0 9.8 - - - +
98B ILE* 1.3 79.9 - - - +
100B TYR* 1.3 59.9 + - - +
101B LYS* 3.4 10.5 + - - +
102B LYS* 2.9 43.3 + - - +
103B PHE* 2.9 27.2 + - - +
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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