Contacts of the helix formed by residues 248 - 256 (chain B) in PDB entry 2ZA5
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 248 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B HIS* 3.5 40.4 - + - -
105B ALA* 3.0 20.7 + - - +
107B ILE* 3.8 26.2 - - + -
193B ASP* 2.4 36.3 + - + +
243B THR* 3.7 30.3 - - + -
244B ARG 3.9 7.0 - - - -
245B VAL 3.1 7.2 + - - +
247B TYR* 1.3 107.0 - + + +
249B LEU* 1.3 64.9 + - - +
250B ASP* 3.3 3.3 + - - -
251B TRP* 3.3 9.6 + - + +
252B ILE* 2.9 25.6 + - + +
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Residues in contact with LEU 249 (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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127B LEU* 4.1 24.9 - - + -
128B PRO* 3.4 30.5 - - + +
129B PRO* 3.9 0.9 - - + -
130B ALA* 3.5 35.2 - - + +
245B VAL* 3.5 11.8 + - + +
246B THR* 3.4 20.6 + - - +
247B TYR 3.6 1.0 - - - -
248B TYR* 1.3 76.4 - - - +
250B ASP* 1.3 60.2 + - - +
252B ILE* 3.4 5.1 + - + +
253B HIS* 2.8 56.9 + - + +
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Residues in contact with ASP 250 (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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247B TYR 5.3 1.5 + - - +
248B TYR* 3.3 1.0 - - - -
249B LEU* 1.3 77.0 - - - +
251B TRP* 1.3 66.3 + - - +
253B HIS* 3.1 9.4 + - - +
254B HIS* 3.1 35.9 + - + -
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Residues in contact with TRP 251 (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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93B ILE* 3.5 37.7 - - + -
94B VAL 3.8 0.7 - - - -
95B HIS* 3.5 56.5 - + + +
96B PRO* 3.7 17.8 - - + +
107B ILE* 4.2 23.3 - - + -
108B ALA* 4.0 4.5 - - - -
109B LEU* 3.7 26.9 - - + -
248B TYR* 3.3 13.1 + - + +
250B ASP* 1.3 77.6 - - - +
252B ILE* 1.3 85.2 + - + +
254B HIS* 2.9 30.1 + - - +
255B TYR* 3.5 28.2 + + - -
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Residues in contact with ILE 252 (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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49B ILE* 4.1 13.2 - - + -
55B LEU* 4.4 10.3 - - + -
107B ILE* 4.2 18.8 - - + -
109B LEU* 4.2 9.6 - - + -
127B LEU* 4.2 20.0 - - + -
245B VAL* 4.3 20.4 - - + -
248B TYR 2.9 27.2 + - - +
249B LEU* 3.6 7.2 - - + +
251B TRP* 1.3 93.9 - - + +
253B HIS* 1.3 62.0 + - + +
255B TYR* 3.0 5.7 + - - +
256B VAL* 2.9 48.0 + - + +
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Residues in contact with HIS 253 (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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127B LEU* 4.5 13.8 - - + +
249B LEU* 2.8 44.8 + - + +
250B ASP* 3.1 9.1 + - - +
252B ILE* 1.3 80.9 - - + +
254B HIS* 1.3 66.4 + - - +
255B TYR 3.1 1.7 + - - -
256B VAL* 3.7 24.8 - - + +
257B PRO 5.3 5.4 - - - -
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Residues in contact with HIS 254 (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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250B ASP* 3.1 29.7 + - + +
251B TRP* 2.9 24.0 + - - +
253B HIS* 1.3 80.0 - - - +
255B TYR* 1.3 75.1 + - + +
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Residues in contact with TYR 255 (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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53B TRP* 3.6 28.1 - + + -
91B ARG* 4.3 28.6 + - - +
93B ILE* 3.6 27.5 - - + +
96B PRO* 6.0 0.3 - - - +
109B LEU* 4.0 20.0 - - + -
251B TRP* 3.5 41.5 + + - -
252B ILE 3.0 4.2 + - - +
253B HIS 4.7 0.2 - - - -
254B HIS* 1.3 92.9 - - + +
256B VAL* 1.3 61.9 + - - +
257B PRO* 3.4 10.7 - - - +
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Residues in contact with VAL 256 (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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49B ILE* 4.1 11.7 - - + +
50B HIS* 3.5 33.2 - - + -
53B TRP* 3.9 24.2 - - + +
109B LEU* 4.0 17.5 - - + -
127B LEU* 6.1 1.8 - - + -
252B ILE* 2.9 31.5 + - + +
253B HIS* 3.7 28.2 - - + +
255B TYR* 1.3 78.7 - - - +
257B PRO* 1.3 74.5 - - + +
258B LYS 3.7 1.0 + - - -
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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