Contacts of the strand formed by residues 227 - 237 (chain A) in PDB entry 6XYU
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 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A GLY* 4.2 2.2 - - - -
141A LEU 3.3 9.4 - - - -
143A ILE* 3.6 13.2 - - - -
174A ILE* 3.8 10.1 - - - -
222A ALA* 2.7 35.7 + - - +
223A HIS* 3.2 12.3 + - - -
225A PHE 3.3 2.2 - - - -
226A GLY* 1.3 73.4 - - - +
228A ASN* 1.3 61.6 + - - -
229A PRO* 3.5 2.6 - - - +
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Residues in contact with ASN 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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137A THR 4.5 8.1 - - - +
139A ASN* 3.3 45.9 + - - +
140A GLY 3.6 8.1 - - - +
141A LEU 2.7 17.5 + - - +
143A ILE* 3.1 12.0 - - - +
227A GLY* 1.3 70.5 - - - -
229A PRO* 1.3 66.0 - - - +
230A GLU* 2.9 24.0 + - - +
231A TRP* 2.9 40.2 + - + +
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Residues in contact with PRO 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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139A ASN* 5.6 0.2 - - - +
143A ILE* 4.1 2.7 - - + -
219A LYS* 3.3 48.1 - - + +
222A ALA* 3.6 17.7 - - + -
223A HIS* 3.4 37.7 - - + +
227A GLY 3.5 4.6 - - - +
228A ASN* 1.3 90.0 - - - +
230A GLU* 1.3 57.7 + - + +
231A TRP 3.1 0.7 - - - -
232A MET* 3.0 22.6 - - + +
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Residues in contact with GLU 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A LYS* 3.3 22.0 + - - +
228A ASN* 2.9 12.6 + - - +
229A PRO* 1.3 81.9 - - + +
231A TRP* 1.3 57.6 + - - +
232A MET 3.6 3.2 + - - -
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Residues in contact with TRP 231 (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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137A THR* 3.2 51.8 - - + -
140A GLY 3.6 20.2 - - - -
141A LEU 4.1 0.2 - - - -
142A PRO* 3.5 33.1 - - + +
143A ILE 2.9 23.2 + - - +
228A ASN* 2.9 27.3 + - + +
230A GLU* 1.3 78.8 - - - +
232A MET* 1.3 60.0 + - - +
233A THR* 4.2 1.5 + - - -
259A ARG* 3.6 10.8 - - - +
517A ALA 3.3 15.4 + - - -
518A LYS* 3.2 44.6 + - + -
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Residues in contact with MET 232 (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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143A ILE* 3.2 20.2 - - + +
145A ILE* 3.6 30.1 - - + -
215A ILE* 3.7 11.2 - - + +
218A LEU 4.6 3.1 - - - -
219A LYS* 3.5 39.5 - - + -
229A PRO* 3.0 25.1 - - + +
230A GLU 3.6 3.6 + - - -
231A TRP* 1.3 75.3 - - - +
233A THR* 1.3 65.1 + - - +
256A LEU 5.5 1.3 - - - +
257A VAL* 3.6 41.9 - - + +
258A LYS 5.0 0.9 + - - -
259A ARG* 3.8 11.1 + - - +
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Residues in contact with THR 233 (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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142A PRO* 6.1 0.2 - - - +
143A ILE 2.8 11.9 + - - -
144A LEU* 3.2 19.4 - - + +
145A ILE* 2.8 26.6 + - - +
231A TRP* 5.0 1.4 + - - -
232A MET* 1.3 77.2 - - - +
234A LEU* 1.3 73.3 + - - +
235A PHE* 4.2 3.3 - - + -
259A ARG* 3.2 33.0 - - + +
261A MET* 4.8 0.4 - - + +
513A VAL* 6.3 0.7 - - + -
516A PHE* 3.8 28.7 - - + -
517A ALA* 3.4 19.1 + - + +
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Residues in contact with LEU 234 (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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145A ILE* 3.5 34.3 - - + +
147A ILE* 4.8 3.4 - - + -
215A ILE* 3.7 22.7 - - + -
233A THR* 1.3 75.5 - - - +
235A PHE* 1.3 55.8 + - - +
244A VAL* 3.7 28.9 - - + +
247A GLN* 3.6 33.7 - - + -
248A LEU* 4.6 4.9 - - + -
257A VAL* 3.7 28.7 - - + +
259A ARG 3.1 8.8 + - - +
260A GLY* 3.1 3.9 - - - -
261A MET 2.7 30.0 + - - -
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Residues in contact with PHE 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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144A LEU* 3.6 24.2 - - + -
145A ILE 2.9 35.1 + - - +
146A TRP* 3.2 49.8 - + + -
147A ILE 3.0 23.0 + - - -
167A MET* 3.9 35.9 - - + -
175A VAL* 4.3 3.4 - - + -
233A THR* 4.2 5.2 - - + -
234A LEU* 1.3 77.7 - - - +
236A GLY* 1.3 57.1 + - - +
244A VAL* 3.5 6.0 - - - +
261A MET* 3.1 33.2 - - + -
263A GLN* 4.2 9.0 - - - -
487A PHE* 6.0 2.5 - - + -
488A PHE* 4.0 12.3 - + - -
513A VAL* 4.5 6.1 - - + -
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Residues in contact with GLY 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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146A TRP* 3.5 12.5 - - - -
147A ILE 3.2 15.7 - - - -
235A PHE* 1.3 75.5 - - - +
237A GLU* 1.3 59.6 + - - -
240A GLY 3.9 2.9 - - - -
241A SER* 3.3 13.0 - - - -
244A VAL* 3.6 2.0 - - - +
261A MET 3.2 5.7 + - - +
263A GLN* 3.0 30.7 + - - +
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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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146A TRP* 3.8 11.6 - - + -
147A ILE 3.7 3.8 + - - -
149A GLY* 3.3 10.8 + - - +
162A TYR* 5.2 0.2 + - - -
236A GLY* 1.3 74.7 - - - +
238A SER* 1.4 71.0 + - - +
239A ALA 3.1 1.0 + - - -
240A GLY 2.7 22.9 + - - -
241A SER 3.1 1.8 - - - +
263A GLN* 3.1 12.1 - - - +
264A SER* 4.4 1.2 - - - -
480A HIS* 3.1 30.4 + - - -
481A GLY* 3.5 11.8 + - - -
483A GLU* 3.4 22.3 - - - +
484A ILE* 3.5 29.9 - - + +
601A I40 3.4 25.3 - - - +
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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