Contacts of the strand formed by residues 224 - 229 (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 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A TYR* 4.4 12.3 + - - -
182A VAL* 4.4 14.4 - - + +
183A SER 3.1 4.3 + - - +
184A LEU* 3.3 25.7 - - + -
185A LEU* 2.9 27.9 + - - +
214A GLN* 3.4 18.9 + - - +
217A ALA* 4.1 2.0 - - - +
222A CYS* 3.5 2.3 - - - +
223A GLU* 1.3 88.7 - - + +
225A VAL* 1.3 64.1 + - - +
238A VAL* 4.1 5.8 - - + -
239A GLY* 3.8 19.6 - - - -
240A THR 5.1 0.4 - - - +
241A MET* 4.0 22.5 - - + +
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Residues in contact with VAL 225 (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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184A LEU* 4.9 0.4 - - - -
185A LEU* 3.7 12.1 - - + +
187A ASP 6.1 0.9 - - - +
190A PHE* 5.6 4.0 - - + -
210A THR 5.7 0.2 - - - +
213A VAL* 3.7 42.4 - - + +
214A GLN* 4.0 13.7 - - + +
217A ALA* 4.0 10.5 - - + -
224A GLN* 1.3 84.6 - - - +
226A LEU* 1.3 66.2 + - - +
227A TRP* 3.6 36.7 + - + +
238A VAL* 3.3 5.3 - - - -
239A GLY* 2.8 30.9 + - - +
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Residues in contact with LEU 226 (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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184A LEU* 4.1 15.9 - - + +
185A LEU 2.9 20.8 + - - +
186A ALA* 3.8 25.5 - - + -
187A ASP 4.4 3.5 + - - +
224A GLN 4.1 0.8 + - - -
225A VAL* 1.3 76.5 - - - +
227A TRP* 1.3 64.8 + - - +
228A LEU* 3.5 19.4 + - + +
235A LEU* 4.3 30.7 - - + -
236A THR 5.0 0.2 - - - +
237A GLU 3.5 17.3 - - - +
238A VAL* 4.1 15.0 - - + +
243A ILE* 5.1 4.7 - - + -
293A MET* 4.6 4.5 - - - -
323A ILE* 4.1 28.5 - - + -
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Residues in contact with TRP 227 (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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190A PHE* 3.8 32.5 - - + -
191A ILE 4.2 1.6 - - - -
192A ARG* 3.4 52.5 - - + +
210A THR* 3.6 35.9 - - + -
213A VAL* 3.9 25.4 - - + -
225A VAL* 3.7 25.6 + - + -
226A LEU* 1.3 70.1 - - - +
228A LEU* 1.3 63.1 + - - +
235A LEU* 4.0 1.7 - - - -
236A THR* 2.9 45.8 + - - +
237A GLU* 2.9 22.4 + - + +
239A GLY* 3.4 31.8 + - - +
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Residues in contact with LEU 228 (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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186A ALA* 4.0 18.8 - - + -
187A ASP 4.9 1.4 + - - +
188A PRO* 3.9 39.8 - - + +
190A PHE 3.9 9.0 + - - +
191A ILE* 3.8 21.1 - - - +
192A ARG 5.5 0.7 + - - -
226A LEU* 3.5 27.5 + - + +
227A TRP* 1.3 76.3 - - - +
229A TYR* 1.3 62.3 + - - +
233A HIS* 4.1 15.7 - - + +
234A GLN 3.3 11.0 - - - +
235A LEU* 4.3 6.3 - - - -
236A THR* 4.7 0.4 - - - -
293A MET* 4.0 24.7 - - + -
325A TYR* 4.0 13.7 - - + -
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Residues in contact with TYR 229 (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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191A ILE* 4.4 12.3 - - + -
193A ALA 3.5 26.0 - - - +
194A TRP* 3.8 10.1 - - + -
195A VAL* 3.3 39.2 + - + +
228A LEU* 1.3 75.5 - - - +
230A GLY* 1.3 74.1 + - - +
232A ASP* 3.6 0.3 - - - +
234A GLN* 2.9 54.7 + - + +
236A THR* 3.7 21.1 - - + -
264A VAL* 4.3 12.3 - - + -
194B TRP* 3.4 35.3 - + - -
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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