Contacts of the strand formed by residues 243 - 248 (chain A) in PDB entry 1OZ2
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 LYS 243 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A GLY 3.8 5.8 - - - +
242A MET* 1.3 78.5 - - - +
244A LEU* 1.3 63.9 + - - +
257A ILE* 4.8 0.7 - - + -
258A LEU 3.3 4.7 - - - +
259A THR* 2.8 26.5 + - - +
273A ASP* 2.8 24.5 + - - +
293A ALA* 5.0 0.9 + - - +
316A TRP* 3.8 18.4 - - + -
319A TYR* 3.6 25.0 + - + -
320A LEU* 4.4 4.5 - - + -
323A THR* 3.4 31.0 - - - +
325A ALA* 3.6 15.3 - - + -
326A GLN 3.0 14.0 + - - +
327A ALA* 3.4 6.5 - - - +
328A ALA* 2.9 22.7 + - - +
600A SO4 5.2 3.4 + - - -
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Residues in contact with LEU 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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238A PHE* 4.7 4.0 - - + -
242A MET 3.8 12.1 - - - +
243A LYS* 1.3 80.4 - - - +
245A GLU* 1.3 80.0 + - - +
257A ILE* 3.5 5.7 - - - -
258A LEU* 2.9 40.1 + - + +
260A VAL* 3.8 20.0 - - + -
268A LEU* 5.5 0.2 - - + -
270A LEU* 4.0 16.6 - - + -
290A ILE* 3.7 29.8 - - + -
291A HIS 3.5 10.1 - - - +
292A PRO* 4.9 0.7 - - + -
293A ALA 4.5 5.8 - - - +
316A TRP* 3.8 10.8 - - - -
328A ALA* 4.5 7.0 - - + -
333A PHE* 3.8 19.1 - - + -
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Residues in contact with GLU 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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244A LEU* 1.3 84.1 - - - +
246A GLY* 1.3 59.1 + - - +
255A TYR* 5.8 4.0 - - + -
256A PHE 3.4 9.4 - - - +
257A ILE* 4.3 4.7 - - + -
258A LEU* 4.2 4.3 - - - -
290A ILE* 3.4 3.1 - - - -
291A HIS* 2.8 36.9 + - + +
292A PRO 3.5 13.5 - - - +
293A ALA* 4.2 0.2 - - - -
294A GLY* 2.8 11.8 + - - -
295A TRP* 3.4 13.2 + - + +
296A PHE* 2.8 49.5 + - + +
303A LEU* 5.9 0.2 - - + -
316A TRP* 2.8 36.8 + - + +
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Residues in contact with GLY 246 (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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245A GLU* 1.3 77.3 - - - +
247A ILE* 1.3 67.6 + - - -
255A TYR* 3.3 10.4 - - - -
256A PHE* 2.9 35.0 + - - +
258A LEU* 3.7 15.6 - - - +
289A ASP 3.4 11.9 - - - -
290A ILE* 4.1 1.6 - - - -
291A HIS* 4.7 2.5 - - - -
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Residues in contact with ILE 247 (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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246A GLY* 1.3 75.0 - - - -
248A ASP* 1.3 65.2 - - - +
249A PRO* 3.3 18.2 - - + +
252A PRO* 4.0 24.5 - - + +
254A MET 3.3 8.3 - - - +
255A TYR* 3.4 28.0 - - + +
258A LEU* 4.8 0.9 - - - +
272A PHE* 4.8 1.4 - - - -
281A PHE* 4.0 12.0 - - - -
289A ASP* 3.1 49.5 + - + +
291A HIS* 5.3 2.2 - - - +
374A ARG* 5.7 0.9 - - - +
389A TRP* 3.7 29.8 - - + +
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Residues in contact with ASP 248 (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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246A GLY 3.8 0.6 + - - -
247A ILE* 1.3 71.6 - - - +
249A PRO* 1.3 71.3 - - - +
250A GLN* 3.0 18.9 + - - +
251A HIS* 2.9 47.3 + - + +
252A PRO* 3.2 5.9 - - - +
254A MET 3.0 8.8 + - - +
256A PHE* 3.9 31.0 - - + -
272A PHE* 3.9 18.0 - - + -
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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