Contacts of the strand formed by residues 233 - 237 (chain A) in PDB entry 1UKC
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 233 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ILE 3.8 1.4 + - - -
205A VAL* 3.5 17.1 - - - -
206A ILE* 3.2 24.6 + - - +
231A PHE* 3.6 5.2 - - - -
232A ILE* 1.3 79.9 - - - +
234A ALA* 1.3 62.0 + - - +
328A VAL* 3.9 7.8 - - - +
329A PRO 3.4 13.2 - - - -
480A PHE* 4.6 0.7 - - - -
484A LEU* 4.2 6.3 - - - -
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Residues in contact with ALA 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ILE* 3.2 11.7 - - + +
216A VAL* 3.8 25.8 - - + -
220A LEU* 4.3 22.4 - - + -
231A PHE* 5.2 0.2 - - + -
233A GLY* 1.3 75.5 - - - +
235A ILE* 1.3 63.1 + - - +
236A VAL* 4.6 2.2 - - + -
328A VAL* 4.8 0.4 - - + -
329A PRO 3.1 9.7 + - - +
330A VAL* 3.4 8.7 - - + +
331A LEU 3.0 24.6 + - - +
480A PHE* 3.6 4.7 - - - -
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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
----------------------------------------------------------
121A TRP* 4.7 0.9 - - - +
205A VAL* 4.0 5.6 - - + -
206A ILE 2.7 10.4 + - - +
207A HIS* 3.4 31.1 - - + +
208A GLY* 2.9 28.6 + - - -
216A VAL* 4.1 3.1 - - - +
234A ALA* 1.3 71.9 - - - +
236A VAL* 1.3 65.5 + - - +
237A GLU* 3.8 4.5 - - + +
331A LEU* 3.3 17.7 - - + +
477A PHE* 3.6 45.5 - - + +
480A PHE* 3.6 32.5 - - + -
481A VAL* 3.9 22.7 - - + -
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Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A GLY 4.0 1.8 - - - -
213A ALA* 3.9 22.4 - - + +
216A VAL* 3.8 21.5 - - + -
217A ALA* 5.6 2.5 - - + +
220A LEU* 4.8 4.7 - - + -
234A ALA* 4.6 3.8 - - + -
235A ILE* 1.3 76.5 - - - +
237A GLU* 1.3 58.8 + - - +
238A SER 3.5 1.0 + - - -
239A SER* 3.2 26.5 - - - +
330A VAL* 4.2 19.1 - - + -
331A LEU 2.7 9.4 + - - -
332A VAL* 3.3 15.1 - - + +
333A GLY 3.1 24.6 + - - +
407A VAL* 4.6 14.8 - - + -
422A TYR* 4.2 0.6 + - - -
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Residues in contact with GLU 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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207A HIS* 2.8 36.8 + - + +
208A GLY 2.9 17.0 + - - +
209A VAL* 3.2 22.3 - - + +
210A SER 3.0 25.1 + - - -
213A ALA* 3.4 1.4 - - - +
235A ILE* 4.7 4.3 - - + -
236A VAL* 1.3 71.1 - - - +
238A SER* 1.3 61.6 + - - +
422A TYR* 3.2 21.3 - - - +
441A THR* 4.3 0.2 - - - -
443A GLU* 2.5 29.9 - - - +
444A LEU* 3.5 19.2 - - - +
447A ILE* 3.4 20.8 - - + +
477A PHE* 5.1 0.2 - - + -
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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