Contacts of the strand formed by residues 33 - 38 (chain E) in PDB entry 2OX4
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 TYR 33 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E LYS* 3.6 32.5 + - + -
26E VAL 3.1 14.1 - - - +
27E SER* 3.7 16.6 - - - +
31E GLY 4.0 12.1 - - - +
32E ILE* 1.3 75.2 - - - +
34E GLY* 1.3 60.6 + - - +
35E LEU* 3.8 13.2 - - + -
103E ILE* 3.5 9.0 - - - +
106E LYS* 2.9 50.5 + - - +
376E ASP* 2.5 37.6 + - - -
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Residues in contact with GLY 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E LYS* 3.4 4.9 - - - +
26E VAL 2.8 34.0 + - - -
33E TYR* 1.3 75.4 - - - +
35E LEU* 1.3 66.2 + - - +
99E ALA* 3.5 25.9 - - - +
102E ASP* 3.4 9.4 - - - -
103E ILE* 3.4 5.6 - - - +
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Residues in contact with LEU 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E PHE* 5.5 0.2 - - + -
23E LEU* 4.7 5.4 - - + -
24E VAL 3.4 19.5 - - - +
25E LYS* 3.9 14.8 - - + -
33E TYR* 3.8 18.2 - - + -
34E GLY* 1.3 81.7 - - - +
36E GLY* 1.3 60.3 + - - +
98E ILE* 3.6 12.8 - - - +
99E ALA* 3.5 11.8 - - - -
102E ASP* 2.8 16.0 + - - +
321E VAL* 4.2 18.6 - - + -
373E ILE* 3.7 13.6 - - + +
375E GLN 4.7 4.3 - - - +
376E ASP* 3.7 25.8 - - - +
377E ILE* 3.7 35.2 - - + +
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Residues in contact with GLY 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E LEU* 3.4 9.2 - - - +
24E VAL* 2.9 37.0 + - - +
35E LEU* 1.3 74.3 - - - +
37E GLU* 1.3 61.5 + - - +
95E ALA 3.4 20.2 - - - -
98E ILE* 3.8 10.1 - - - -
99E ALA* 3.7 2.6 - - - +
321E VAL* 3.9 3.6 - - - -
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Residues in contact with GLU 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E PRO* 4.2 7.7 - - - +
22E ILE 3.4 13.9 - - - +
23E LEU* 3.5 9.4 - - + +
36E GLY* 1.3 75.1 - - - +
38E ALA* 1.3 71.1 + - - +
39E GLY* 5.3 1.7 - - - -
41E ALA* 4.8 2.3 - - - +
95E ALA* 3.6 15.2 - - - +
98E ILE* 3.8 10.2 - - + +
290E GLY* 3.4 20.8 - - - -
318E GLY* 3.7 7.8 - - - -
319E THR* 2.6 49.7 + - - +
321E VAL* 3.5 8.9 - - + +
322E ALA* 2.9 33.0 + - + +
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Residues in contact with ALA 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ILE* 3.0 29.8 + - + +
37E GLU* 1.3 83.0 - - - +
39E GLY* 1.3 59.0 + - - +
40E ILE 2.9 10.7 + - - -
41E ALA* 4.2 2.8 + - - +
49E ALA* 4.2 25.6 - - + -
52E ILE* 6.5 0.2 - - + -
53E LEU* 4.6 5.6 - - + +
91E SER* 3.9 20.2 - - - +
95E ALA* 3.7 10.1 - - + +
290E GLY 3.6 4.3 - - - -
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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