Contacts of the helix formed by residues 234 - 245 (chain A) in PDB entry 1ZRB
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 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A HIS* 4.2 20.2 - - + +
101A ARG* 4.0 20.2 - - + +
103A ILE* 3.6 33.2 - - + -
179A ASN* 3.8 24.7 - - + +
229A THR* 3.5 31.4 - - + -
230A HIS 3.5 7.4 + - - +
231A VAL 3.0 9.3 + - - +
233A ARG* 1.3 83.3 - - + +
235A LYS* 1.3 63.6 + - - +
236A LYS* 3.2 3.4 - - - -
237A TRP* 3.2 9.1 + - + +
238A ILE* 3.1 22.3 + - - +
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Residues in contact with LYS 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU* 3.8 40.5 + - + +
124A PRO 3.3 27.0 + - - +
125A ASP* 4.6 5.7 - - - +
231A VAL* 3.1 8.5 + - + +
232A PHE* 3.0 30.7 + - + +
234A LEU* 1.3 75.3 - - - +
236A LYS* 1.3 66.6 - - - +
238A ILE* 3.0 11.3 + - + +
239A GLN* 2.9 57.4 + - + +
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Residues in contact with LYS 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A PHE 4.7 0.4 + - - -
233A ARG 4.8 13.1 + - - +
234A LEU* 4.9 1.6 - - - -
235A LYS* 1.3 78.9 - - - +
237A TRP* 1.3 60.5 - - - +
239A GLN* 3.4 11.0 + - - +
240A LYS* 3.0 47.1 + - + +
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Residues in contact with TRP 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A TYR* 3.4 31.0 - - + -
90A ILE 3.8 3.1 - - - -
91A HIS* 3.4 54.5 - + + +
92A PRO* 3.4 22.4 - - + +
103A ILE* 3.9 26.7 - - + -
104A ALA* 4.0 1.3 - - - -
105A LEU* 3.8 31.2 - - + -
234A LEU* 3.2 9.4 + - - +
236A LYS* 1.3 80.4 - - + +
238A ILE* 1.3 81.8 + - + +
240A LYS* 3.3 12.3 + - + +
241A VAL* 3.1 46.4 + - + +
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Residues in contact with ILE 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ILE* 4.7 2.5 - - + -
53A LEU* 4.5 9.2 - - + -
103A ILE* 3.8 20.2 - - + -
105A LEU* 3.9 20.8 - - + +
123A LEU* 4.0 27.4 - - + -
231A VAL* 4.2 20.4 - - + -
234A LEU 3.1 15.8 + - - +
235A LYS* 3.0 18.3 + - + +
237A TRP* 1.3 95.0 - - + +
239A GLN* 1.3 63.0 + - + +
241A VAL* 3.4 2.4 + - - +
242A ILE* 3.0 36.8 + - + +
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Residues in contact with GLN 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A LYS* 2.9 56.9 + - - +
236A LYS* 3.8 9.8 - - - +
238A ILE* 1.3 71.9 - - + +
240A LYS* 1.3 65.8 + - + +
242A ILE* 3.2 8.6 + - + +
243A ASP* 2.8 35.5 + - - +
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Residues in contact with LYS 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A LYS* 3.0 37.1 + - + +
237A TRP* 3.6 14.1 - - + +
239A GLN* 1.3 76.1 - - + +
241A VAL* 1.3 64.6 + - + +
243A ASP* 2.9 21.9 - - - +
244A GLN* 3.1 29.5 + - + +
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Residues in contact with VAL 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A TRP* 3.9 12.0 - - + -
89A TYR* 3.9 27.6 - - + -
105A LEU* 3.7 17.9 - - + -
237A TRP* 3.1 50.9 + - + +
238A ILE 3.7 3.8 - - - +
240A LYS* 1.3 77.1 - - + +
242A ILE* 1.3 64.7 + - - +
244A GLN* 4.6 0.9 - - - -
245A PHE* 3.1 40.1 + - + +
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Residues in contact with ILE 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ILE* 4.6 6.7 - - + -
51A TRP* 3.5 54.5 - - + +
105A LEU* 4.3 11.4 - - + -
238A ILE* 3.0 26.3 + - + +
239A GLN* 3.2 9.4 + - + +
241A VAL* 1.3 78.6 - - - +
243A ASP* 1.3 64.7 + - + +
245A PHE 3.4 2.9 + - - -
246A GLY* 3.0 30.7 - - - +
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Residues in contact with ASP 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A GLN* 2.8 22.3 - - - +
240A LYS* 2.9 25.0 - - - +
242A ILE* 1.3 78.6 - - + +
244A GLN* 1.3 69.7 + - - +
245A PHE 3.4 0.2 - - - -
246A GLY* 4.1 9.7 + - - +
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Residues in contact with GLN 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A LYS* 3.1 36.9 + - + +
241A VAL* 3.9 2.9 - - - +
243A ASP* 1.3 83.3 + - - +
245A PHE* 1.3 92.4 + - + +
246A GLY 3.6 2.5 + - - -
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Residues in contact with PHE 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A TRP* 3.4 11.8 - - + -
89A TYR* 3.2 50.3 - + + +
107A LYS* 3.2 17.0 + - + +
241A VAL* 3.1 36.8 + - + +
242A ILE 3.6 1.8 - - - -
244A GLN* 1.3 107.0 - - + +
246A GLY* 1.3 64.3 + - - +
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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