Contacts of the helix formed by residues 93 - 100 (chain B) in PDB entry 2ZUB
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 SER 93 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B THR* 3.2 8.0 + - - -
92B GLY* 1.3 78.5 - - - +
94B GLN* 1.3 59.8 + - - +
95B ALA* 3.3 0.3 + - - +
96B LEU* 3.2 26.3 + - - -
97B ASP* 2.9 28.1 + - - +
312B PHE* 3.4 17.0 - - - +
319B ILE* 3.7 8.2 + - - -
320B ARG 3.9 15.7 - - - -
321B ASP* 2.5 23.9 + - - -
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Residues in contact with GLN 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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150A GLU* 3.4 35.9 - - + +
151A GLY 3.9 9.6 - - - +
154A ARG* 4.8 6.8 + - - -
180A ARG* 3.1 24.4 + - - +
90B SER* 4.8 2.0 + - - -
92B GLY 4.0 3.0 + - - +
93B SER* 1.3 69.5 - - - +
95B ALA* 1.3 65.7 + - - +
97B ASP* 3.2 25.0 + - - +
98B GLY* 3.1 9.9 + - - -
321B ASP* 3.2 18.6 + - - +
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Residues in contact with ALA 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ILE* 4.7 5.9 - - - +
215A HIS* 5.4 8.5 - - + +
93B SER* 3.6 1.1 - - - +
94B GLN* 1.3 77.9 - - - +
96B LEU* 1.3 59.9 + - - +
98B GLY* 3.3 4.3 + - - -
99B LEU 3.2 15.6 + - - -
310B VAL* 3.2 36.7 - - + +
311B VAL 3.4 15.9 - - - +
321B ASP* 3.1 17.6 + - - +
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Residues in contact with LEU 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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91B THR* 3.6 33.4 - - + +
93B SER* 3.2 9.9 + - - +
95B ALA* 1.3 74.3 - - - +
97B ASP* 1.3 67.6 + - - +
98B GLY 3.0 1.6 - - - -
99B LEU* 3.1 14.5 + - + +
100B LEU* 2.9 34.2 + - + +
112B PHE* 5.0 7.2 - - + -
123B LEU* 4.3 17.7 - - + -
285B ILE* 5.3 1.6 - - + -
287B LEU* 5.3 0.4 - - + -
297B ALA* 3.4 31.2 - - + -
310B VAL* 4.1 5.4 - - + -
312B PHE* 4.0 32.8 - - + -
319B ILE* 4.5 2.5 - - + -
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Residues in contact with ASP 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ARG* 4.0 7.6 - - - +
90B SER* 2.9 23.1 + - - -
91B THR* 3.0 32.6 + - - +
93B SER 2.9 14.4 + - - +
94B GLN* 3.2 27.2 + - - +
96B LEU* 1.3 74.2 - - - +
98B GLY* 1.3 58.3 + - - +
100B LEU* 3.1 8.3 + - - -
102B GLY* 2.7 50.2 + - - +
103B GLY* 4.2 3.4 - - - +
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Residues in contact with GLY 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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180A ARG* 3.5 29.9 - - - +
182A ILE* 3.9 19.5 - - - +
94B GLN 3.1 6.9 + - - -
95B ALA 3.6 4.3 - - - -
96B LEU 3.0 0.8 - - - -
97B ASP* 1.3 76.0 - - - +
99B LEU* 1.3 66.6 + - - +
100B LEU 2.9 1.6 - - - -
101B ALA* 2.8 15.6 + - - -
102B GLY 4.7 0.4 - - - -
306B PRO* 5.6 2.3 - - - +
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Residues in contact with LEU 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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182A ILE* 4.0 25.8 - - + +
95B ALA 3.2 5.5 + - - -
96B LEU* 3.1 15.0 + - + +
98B GLY* 1.3 75.0 - - - +
100B LEU* 1.3 59.4 + - + +
101B ALA 3.5 1.9 + - - -
285B ILE* 4.8 6.3 - - + -
297B ALA* 3.6 43.1 - - + +
298B ARG* 3.9 5.4 - - - +
299B VAL* 3.6 24.0 - - + +
305B LEU* 3.7 18.5 - - - +
306B PRO* 4.1 9.2 - - - +
308B GLY 3.2 23.6 - - - +
309B GLU* 4.5 2.5 - - - -
310B VAL* 4.0 15.7 - - + -
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Residues in contact with LEU 100 (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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88B LYS* 3.1 12.5 + - - -
91B THR* 4.4 9.0 - - + -
96B LEU* 2.9 25.5 + - + +
97B ASP 3.6 0.2 - - - +
98B GLY 2.9 1.2 - - - -
99B LEU* 1.3 81.2 - - + +
101B ALA* 1.3 69.2 + - - +
102B GLY 2.9 2.6 + - - -
103B GLY* 3.0 25.3 + - - +
104B ILE* 3.8 29.6 - - + -
110B THR* 5.0 7.4 - - + +
112B PHE* 4.3 14.8 - - + -
283B ILE* 4.4 5.6 - - + -
285B ILE* 4.2 22.0 - - + -
305B LEU* 3.5 26.7 - - + -
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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