Contacts of the strand formed by residues 294 - 300 (chain A) in PDB entry 1XZQ
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 ILE 294 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A LEU* 4.7 7.2 - - + -
213A ARG 3.0 10.9 + - - +
214A MET* 3.4 50.3 - - + +
215A VAL 3.5 3.6 + - - -
261A PHE* 4.6 8.7 - - + -
292A ALA* 3.1 3.9 - - - +
293A ASP* 1.3 83.7 - - - +
295A VAL* 1.3 75.6 + - - +
296A LEU* 6.3 0.2 - - + -
320A ARG* 3.3 28.7 - - + +
321A TYR* 4.4 3.6 - - - -
322A LEU* 5.4 4.7 - - + -
367A ILE* 5.0 2.9 - - + +
370A GLU* 4.6 10.5 - - + -
371A THR* 3.7 28.9 - - + -
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Residues in contact with VAL 295 (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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215A VAL* 3.8 23.1 - - + +
217A VAL* 4.0 16.2 - - + -
289A ILE* 4.2 26.2 - - + +
292A ALA* 4.5 2.7 - - + +
294A ILE* 1.3 82.0 - - - +
296A LEU* 1.3 65.8 + - - +
297A PHE* 3.9 2.2 + - + +
312A ILE* 5.9 0.2 - - + -
316A ILE* 4.0 28.5 - - + -
319A LYS* 4.9 7.2 - - + -
320A ARG 2.9 12.5 + - - +
321A TYR* 3.2 11.4 - - + +
322A LEU* 2.9 27.4 + - - +
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Residues in contact with LEU 296 (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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214A MET* 4.1 25.6 - - + -
215A VAL 3.1 13.0 + - - +
216A ILE* 3.5 22.6 - - + +
217A VAL* 2.9 27.5 + - - +
228A LEU* 5.0 7.0 - - + -
231A LEU* 4.4 12.1 - - + -
294A ILE* 4.0 1.2 + - + -
295A VAL* 1.3 72.8 - - - +
297A PHE* 1.3 60.8 + - - +
298A VAL* 4.0 8.0 + - + -
322A LEU* 3.4 38.8 - - + +
324A VAL* 4.5 12.1 - - + -
363A LEU* 4.5 8.7 - - + -
367A ILE* 4.2 18.4 - - + -
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Residues in contact with PHE 297 (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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217A VAL* 3.5 40.8 - - + -
218A GLY* 4.4 4.0 - - - -
295A VAL* 3.9 4.4 + - + +
296A LEU* 1.3 72.7 - - - +
298A VAL* 1.3 57.4 + - - +
299A LEU* 3.4 39.7 + - + -
309A ASP* 4.1 22.7 - - + -
312A ILE* 4.3 13.9 - - + -
313A LEU* 3.5 34.8 - - + -
316A ILE* 4.3 13.7 - - + -
322A LEU 3.0 9.1 + - - +
323A VAL* 3.3 22.2 - - + +
324A VAL* 2.6 34.4 + - - +
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Residues in contact with VAL 298 (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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216A ILE* 4.9 2.0 - - + -
217A VAL 3.0 22.4 + - - +
218A GLY* 3.7 13.2 - - - -
219A LYS 4.8 0.3 + - - -
222A VAL* 4.2 25.6 - - + +
227A LEU* 5.4 4.7 - - + -
228A LEU* 3.9 31.2 - - + -
296A LEU* 4.4 12.6 - - + +
297A PHE* 1.3 73.9 - - - +
299A LEU* 1.3 68.4 + - - +
300A ASP 4.3 0.2 + - - -
324A VAL* 3.0 28.9 - - + +
326A ASN* 4.3 20.6 - - + +
363A LEU* 6.1 0.9 - - + -
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Residues in contact with LEU 299 (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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218A GLY* 5.9 0.2 - - - -
219A LYS* 5.5 6.5 - - + -
222A VAL* 4.7 0.4 - - - -
297A PHE* 3.4 45.3 + - + -
298A VAL* 1.3 79.4 - - - +
300A ASP* 1.3 62.1 + - - +
305A LEU* 4.1 22.0 - - + -
309A ASP* 4.0 19.1 - - - +
313A LEU* 5.1 0.7 - - + -
323A VAL* 4.8 10.1 - - + -
324A VAL 2.6 11.9 + - - +
325A ILE* 3.1 12.8 - - + -
326A ASN* 2.9 24.8 + - - -
334A ILE* 4.4 19.1 - - + -
339A ILE* 4.9 10.1 - - + -
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Residues in contact with ASP 300 (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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221A ASN* 4.2 12.9 - - - +
222A VAL* 3.9 23.1 - - + +
299A LEU* 1.3 75.3 - - - +
301A ALA* 1.3 62.9 + - - +
302A SER* 2.8 36.9 + - - -
303A SER* 3.3 24.1 + - - +
326A ASN* 3.8 12.8 - - - +
328A VAL* 4.9 11.8 - - - +
334A ILE* 3.2 20.3 - - - +
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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