Contacts of the strand formed by residues 77 - 81 (chain B) in PDB entry 2EZ9
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 77 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B ALA* 3.4 31.7 + - - -
69B ASP* 4.2 9.9 - - - -
75B LYS 3.3 2.8 + - - -
76B ILE* 1.3 73.9 - - - +
78B VAL* 1.3 63.4 + - - +
103B PRO 3.0 11.3 + - - -
104B VAL* 3.2 2.9 - - - +
105B LEU 2.8 26.3 + - - +
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Residues in contact with VAL 78 (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 LEU* 4.7 9.2 - - + -
26B VAL* 3.8 34.3 - - + +
28B HIS 4.8 4.2 + - - -
29B LEU* 3.3 35.1 - - + -
30B TYR* 3.2 26.5 + - - -
66B ALA* 3.6 4.5 - - - +
69B ASP* 5.0 1.0 + - - -
76B ILE* 4.3 6.5 - - + +
77B GLY* 1.3 79.7 - - - +
79B CYS* 1.3 68.7 + - - +
105B LEU* 3.4 34.8 - - + +
107B LEU* 5.1 5.2 - - + -
154B ILE* 6.2 0.2 - - + -
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Residues in contact with CYS 79 (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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30B TYR 3.2 13.0 - - - +
62B GLY* 3.7 23.8 - - - +
63B ALA* 3.8 20.6 - - - +
66B ALA* 4.0 1.6 - - + -
78B VAL* 1.3 79.2 - - - +
80B PHE* 1.3 65.5 + - - +
90B LEU* 4.0 14.8 - - + -
94B LEU* 4.1 8.1 - - - -
104B VAL* 4.3 6.5 - - - -
105B LEU 3.0 8.8 + - - +
106B ALA* 3.4 22.1 - - - -
107B LEU* 3.0 21.5 + - - +
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Residues in contact with PHE 80 (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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29B LEU* 4.0 23.6 - - + -
30B TYR 2.9 24.6 + - - +
31B GLY* 3.5 16.9 - - - -
32B ILE 3.5 28.2 + - - -
37B ILE* 3.7 22.2 - - + -
40B ILE* 5.5 4.5 - - + -
41B MET* 3.4 32.1 - - - -
44B LEU* 4.2 7.0 - - + -
53B TYR* 3.4 35.2 - + - -
59B GLU* 4.3 3.1 - - - +
79B CYS* 1.3 76.6 - - - +
81B GLY* 1.3 59.9 + - - +
90B LEU* 3.7 17.2 - - - +
107B LEU* 3.1 28.5 - - + +
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Residues in contact with GLY 81 (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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32B ILE 4.8 0.9 - - - -
37B ILE* 4.0 5.4 - - - +
59B GLU* 4.4 4.9 - - - -
80B PHE* 1.3 77.4 - - - +
82B SER* 1.3 66.1 + - - +
86B GLY* 3.7 20.6 - - - -
87B GLY* 3.9 3.8 - - - -
90B LEU* 4.0 3.9 - - - +
107B LEU 3.0 7.1 + - - +
108B ILE* 3.4 5.4 - - - +
109B GLY 2.9 23.4 + - - -
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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