Contacts of the strand formed by residues 234 - 238 (chain A) in PDB entry 1UPX
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 GLY 234 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A ASN 3.5 1.4 + - - -
233A PRO* 1.3 76.4 - - - +
235A ILE* 1.3 65.5 + - - +
257A VAL* 4.1 2.5 - - - -
258A ASP 3.1 11.9 - - - -
260A TYR* 4.3 7.9 - - - -
298A PHE* 3.4 21.2 - - - -
300A GLY* 3.5 3.3 - - - -
301A PRO* 3.3 22.5 - - - +
351A ALA* 3.8 1.7 - - - +
354A CYS* 6.2 0.2 - - - +
355A PRO 5.0 2.2 + - - -
357A PRO* 4.6 5.1 - - - +
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Residues in contact with ILE 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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234A GLY* 1.3 77.8 - - - +
236A LEU* 1.3 69.1 + - - +
237A ILE 3.9 0.2 + - - -
248A LEU* 4.0 35.7 - - + -
252A THR* 4.3 2.2 - - + -
257A VAL* 3.9 15.9 - - + -
258A ASP 2.9 8.4 + - - +
259A VAL* 3.5 5.1 - - + +
260A TYR 2.9 26.0 + - - +
298A PHE* 3.6 3.1 - - - -
301A PRO* 3.4 11.2 - - + +
303A LEU* 4.6 2.0 - - + -
347A ILE* 3.9 37.9 - - + +
348A ILE* 4.0 24.2 - - + -
351A ALA* 3.7 13.5 - - + -
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Residues in contact with LEU 236 (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 ILE* 1.3 73.3 - - - +
237A ILE* 1.3 58.3 + - - +
260A TYR* 3.5 15.5 - - + -
261A THR 3.4 33.0 - - - +
262A HIS* 3.6 16.4 - - + -
284A TYR* 3.8 16.2 - - + -
295A PHE* 3.7 36.3 - - + -
298A PHE* 3.4 35.1 - - + -
301A PRO 2.9 9.3 + - - +
302A VAL* 3.2 8.6 - - + +
303A LEU* 2.8 27.0 + - - +
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Residues in contact with ILE 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ILE 3.9 0.8 + - - -
236A LEU* 1.3 73.9 - - - +
238A SER* 1.3 63.3 + - - +
244A ASP 4.1 1.3 - - - -
245A LEU* 3.7 54.1 - - + +
248A LEU* 4.2 14.6 - - + -
259A VAL* 4.2 4.9 - - + -
260A TYR 2.9 18.5 + - - +
261A THR* 4.2 10.1 - - + -
262A HIS* 2.9 23.0 + - - -
265A MET* 3.4 13.4 - - + +
303A LEU* 3.5 22.2 - - + +
305A THR* 3.7 26.9 - - + -
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Residues in contact with SER 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ILE* 1.3 73.7 - - - +
239A GLY* 1.3 67.5 + - - +
262A HIS* 2.7 40.0 + - - -
263A SER* 4.3 2.8 - - - -
265A MET* 3.5 6.3 - - - +
288A TRP* 6.0 0.2 - - - +
295A PHE* 4.4 7.2 - - - -
302A VAL* 4.8 1.8 - - - -
303A LEU 2.8 11.8 + - - -
304A LEU* 3.9 22.0 - - - +
305A THR* 2.9 31.8 + - - +
308A CYS 4.9 2.9 + - - -
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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