Contacts of the strand formed by residues 234 - 238 (chain A) in PDB entry 1EKP
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 GLN 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A LEU* 3.3 5.5 - - - -
229A TYR* 2.9 69.6 + - + +
230A GLY* 5.3 0.4 - - - -
232A ASP* 3.1 28.3 + - - +
233A HIS* 1.3 75.2 - - - +
235A LEU* 1.3 64.9 + - - +
236A THR* 3.6 6.7 + - + +
262A ASN* 4.2 19.6 - - - +
264A VAL* 5.7 0.4 - - - +
290A THR* 4.1 28.7 + - + +
291A ILE 3.1 16.6 - - - +
292A THR* 4.0 5.6 - - + +
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Residues in contact with LEU 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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226A LEU* 4.3 25.4 - - + -
227A TRP 4.1 4.7 - - - -
228A LEU* 4.3 6.5 - - + -
233A HIS 3.8 2.0 - - - +
234A GLN* 1.3 75.0 - - - +
236A THR* 1.3 61.5 + - - +
243A ILE* 4.6 18.6 - - + -
245A VAL* 5.0 7.4 - - + -
259A PRO* 3.2 20.9 - - + +
291A ILE* 2.8 37.9 + - + +
292A THR 3.6 4.0 - - - +
293A MET* 3.5 35.4 - - + +
296A LEU* 4.3 22.2 - - + -
308A VAL* 6.3 1.8 - - + -
323A ILE* 5.7 0.9 - - + -
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Residues in contact with THR 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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192A ARG* 5.0 2.1 + - - +
226A LEU* 5.0 0.4 - - - +
227A TRP* 2.9 26.5 + - - +
229A TYR* 3.7 23.6 - - + -
234A GLN* 3.7 16.4 - - + +
235A LEU* 1.3 80.7 - - - +
237A GLU* 1.3 83.1 + - - +
242A ASN* 5.1 0.3 - - - -
243A ILE* 3.5 18.5 + - - +
259A PRO* 4.0 4.2 - - - +
264A VAL* 4.1 19.1 + - + -
265A ILE* 3.8 27.5 - - + +
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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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192A ARG* 3.4 22.4 + - - +
226A LEU* 3.5 8.5 - - - +
227A TRP* 2.9 37.3 + - + -
236A THR* 1.3 98.0 + - - +
238A VAL* 1.3 65.4 + - - +
239A GLY 4.8 2.2 - - - +
241A MET 3.3 14.5 + - - +
242A ASN* 4.0 8.7 - - - +
243A ILE* 4.4 3.6 - - - +
264A VAL 4.6 0.2 - - - +
265A ILE* 3.5 7.1 - - + -
266A LEU* 2.7 34.5 + - - +
370A PLP 2.7 31.6 + - - +
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Residues in contact with VAL 238 (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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182A VAL* 5.5 0.9 - - + -
184A LEU* 3.5 42.0 - - + -
224A GLN* 4.1 7.2 - - + -
225A VAL 3.3 5.6 - - - +
226A LEU* 4.1 4.5 - - + -
237A GLU* 1.3 77.6 - - - +
239A GLY* 1.3 59.4 + - - +
240A THR 2.8 0.5 + - - -
241A MET* 2.6 61.1 + - + +
242A ASN 5.0 0.4 - - - +
243A ILE* 3.4 38.4 - - + -
310A GLY* 5.1 4.5 - - - -
320A VAL* 5.2 4.3 - - + -
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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