Contacts of the strand formed by residues 224 - 228 (chain A) in PDB entry 2WLS
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 ARG 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A MET 5.4 0.2 + - - -
196A SER* 3.2 25.5 + - - +
197A VAL 3.4 3.0 + - - +
198A THR* 3.3 17.3 + - - +
199A LEU 2.9 22.2 + - - -
222A PHE* 3.6 8.4 - - - -
223A HIS* 1.3 95.0 + - - +
225A ALA* 1.3 63.6 + - - +
324A LEU* 5.0 1.1 - - - -
325A GLN* 3.3 35.7 + - + +
483A PHE* 3.3 14.8 + - + -
484A ALA 2.9 29.0 + - - -
485A ARG 4.2 6.9 + - - -
486A THR 4.8 1.8 - - - -
487A GLY* 3.2 33.6 - - - +
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Residues in contact with ALA 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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199A LEU* 3.3 6.1 - - + +
209A VAL* 3.6 25.6 - - + -
213A ILE* 3.8 22.0 - - + -
222A PHE* 4.3 7.6 - - + -
224A ARG* 1.3 80.1 - - - +
226A VAL* 1.3 63.1 + - - +
227A LEU* 4.3 2.7 - - + -
324A LEU* 5.4 0.9 - - + -
325A GLN 3.2 6.1 + - - -
326A VAL* 3.1 12.4 - - + +
327A LEU 2.9 22.5 + - - -
483A PHE* 3.5 3.7 - - - -
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Residues in contact with VAL 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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115A LEU* 6.2 0.7 - - + -
198A THR* 4.2 5.6 - - + -
199A LEU 2.7 10.6 + - - +
200A PHE* 3.3 36.9 - - + -
201A GLY 3.4 5.9 + - - -
209A VAL* 4.1 5.4 - - - +
225A ALA* 1.3 78.1 - - - +
227A LEU* 1.3 67.2 + - - +
228A GLN* 3.9 15.0 - - + -
327A LEU* 3.1 26.5 - - + +
328A VAL* 5.3 0.2 - - - -
428A TYR* 5.3 0.7 - - - +
480A TRP* 3.8 31.6 - - + +
483A PHE* 3.9 23.3 - - + -
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Residues in contact with LEU 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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206A ALA* 3.6 27.8 - - + +
209A VAL* 3.9 16.2 - - + -
210A GLY* 4.0 15.7 - - - -
213A ILE* 4.6 6.3 - - + -
225A ALA* 4.3 4.9 - - + -
226A VAL* 1.3 76.6 - - - +
228A GLN* 1.3 65.2 + - - +
229A SER 3.9 0.7 + - - -
230A GLY 3.6 17.8 - - - +
231A THR* 5.7 0.2 - - + -
232A PRO* 4.0 3.1 - - + -
326A VAL* 3.7 25.8 - - + -
327A LEU 2.9 9.6 + - - -
328A VAL* 3.3 11.3 - - + +
329A GLY 3.2 22.7 + - - +
411A VAL* 5.9 1.3 - - + +
414A LEU* 3.6 28.3 - - + -
418A LEU* 6.2 0.7 - - + -
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Residues in contact with GLN 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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117A TRP* 4.1 8.5 - - - -
200A PHE* 3.8 16.1 - - - +
201A GLY 3.0 17.4 + - - +
202A GLU* 3.1 14.0 - - + +
203A SER 3.0 20.3 + - - -
206A ALA* 3.4 1.1 - - - +
226A VAL* 3.9 12.3 - - + +
227A LEU* 1.3 72.8 - - - +
229A SER* 1.3 67.8 + - - +
230A GLY 3.3 1.9 + - - -
428A TYR* 3.4 20.2 - - - +
450A GLU* 3.2 33.5 + - - +
451A ILE* 4.4 4.2 - - - +
454A ILE* 4.4 7.7 - - - +
480A TRP* 3.0 30.3 + - + -
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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