Contacts of the strand formed by residues 283 - 289 (chain A) in PDB entry 2ZUC
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 ILE 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A LEU* 5.0 1.6 - - + -
108A THR* 4.3 16.2 - - + +
109A MET 3.2 5.7 + - - +
110A THR* 3.5 19.3 - - + +
111A GLU* 2.7 30.2 + - - +
281A PRO* 4.4 1.4 - - - +
282A GLY* 1.3 75.0 - - - +
284A ARG* 1.3 63.1 + - - +
285A ILE* 3.8 26.9 - - + -
301A ASP 3.3 6.1 - - - +
302A ALA* 3.3 26.2 - - + -
303A PRO* 3.4 23.8 - - + -
304A HIS 5.4 0.7 - - - +
305A LEU* 4.0 17.7 - - + -
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Residues in contact with ARG 284 (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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111A GLU* 3.2 32.7 + - - +
113A PHE* 4.0 25.5 - - + -
255A ASN* 5.2 3.2 + - - -
279A HIS* 4.3 39.1 + - - -
281A PRO* 3.7 27.4 - - + +
283A ILE* 1.3 79.3 - - - +
285A ILE* 1.3 62.3 + - - +
300A VAL* 2.9 42.3 + - + +
301A ASP* 2.9 47.0 + - + +
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Residues in contact with ILE 285 (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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96A LEU* 5.2 0.9 - - + -
99A LEU* 4.4 5.4 - - + -
100A LEU* 4.0 20.0 - - + -
110A THR* 4.5 2.7 - - + -
111A GLU 2.7 10.5 + - - +
112A PHE* 3.2 39.5 - - + -
113A PHE* 3.1 25.0 + - - -
283A ILE* 3.8 22.9 - - + -
284A ARG* 1.3 72.6 - - - +
286A GLN* 1.3 62.3 + - - +
287A LEU* 4.4 0.4 - - + -
297A ALA* 4.0 24.7 - - + -
298A ARG 3.5 9.0 - - - +
299A VAL* 3.6 32.8 - - + -
305A LEU* 4.8 0.7 - - + -
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Residues in contact with GLN 286 (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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113A PHE* 3.4 39.5 + - + +
114A GLY* 5.2 3.8 - - - -
257A VAL* 5.2 4.6 - - - +
285A ILE* 1.3 73.4 - - - +
287A LEU* 1.3 74.8 + - - +
288A LYS* 4.0 22.8 - - + +
296A ILE 3.7 0.5 - - - +
297A ALA* 3.3 4.3 - - - -
298A ARG* 2.8 58.3 + - + +
300A VAL* 3.4 12.3 - - + +
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Residues in contact with LEU 287 (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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96A LEU* 5.4 0.2 - - + -
112A PHE* 4.2 30.5 - - + -
113A PHE 2.8 15.9 + - - +
114A GLY* 3.5 19.2 - - - -
115A GLU 4.2 1.7 + - - -
118A SER* 3.6 23.3 - - - +
119A GLY 3.6 33.4 - - - +
120A LYS* 3.7 17.3 - - + +
123A LEU* 4.7 3.6 - - + -
285A ILE* 4.4 0.7 - - + -
286A GLN* 1.3 81.3 + - - +
288A LYS* 1.3 63.0 + - - +
296A ILE 3.3 3.8 - - - +
297A ALA* 3.6 29.2 - - + -
312A PHE* 4.0 12.3 - - + -
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Residues in contact with LYS 288 (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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115A GLU* 6.4 1.3 - - - -
118A SER* 4.6 2.5 - - - -
286A GLN* 4.0 27.5 + - + +
287A LEU* 1.3 79.6 - - - +
289A LYS* 1.3 66.7 + - - +
295A ARG* 3.4 10.8 - - - +
296A ILE* 2.9 62.9 + - + +
298A ARG* 5.4 8.1 - - + +
309A GLU* 4.5 10.3 - - - +
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Residues in contact with LYS 289 (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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115A GLU* 3.1 30.8 + - + +
116A PHE* 3.5 22.4 + - - +
117A GLY* 3.9 11.1 - - - +
118A SER* 3.9 21.1 - - - -
288A LYS* 1.3 78.0 - - - +
290A SER* 1.3 62.3 + - - +
295A ARG* 3.9 18.4 - - - +
296A ILE* 5.9 0.8 - - - +
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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