Contacts of the strand formed by residues 269 - 275 (chain A) in PDB entry 4AY1
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 TYR 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A PHE* 3.2 17.1 - + - -
213A ASP* 2.8 36.1 + - - -
227A ASN* 3.3 33.6 + - - -
267A PRO* 3.4 22.8 - - + +
268A THR* 1.3 81.0 - - - +
270A GLY* 1.3 69.2 + - - +
271A HIS* 3.7 12.8 - + - -
301A PHE* 4.2 12.6 - + + -
302A LEU 3.2 19.3 - - - +
303A ALA* 4.3 0.2 - - - -
304A TYR 4.5 0.7 - - - +
307A ILE* 4.3 4.5 - - - -
336A TYR* 4.6 5.9 - - - -
337A ASP 4.7 2.6 + - - -
360A TRP* 3.6 31.8 - + - -
364A MET* 3.6 25.6 - - + -
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Residues in contact with GLY 270 (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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227A ASN* 4.3 2.7 - - - -
269A TYR* 1.3 81.9 - - - +
271A HIS* 1.3 61.6 + - - -
301A PHE* 3.2 9.2 - - - +
302A LEU 3.0 30.0 + - - -
307A ILE* 3.8 6.1 - - - +
334A VAL* 4.8 3.8 - - - -
335A GLY 3.1 17.3 - - - -
336A TYR* 4.2 8.5 - - - -
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Residues in contact with HIS 271 (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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213A ASP* 2.6 25.7 + - - -
215A HIS 3.3 24.2 - - - +
216A GLY* 4.4 10.0 - - - -
217A SER 5.6 1.0 + - - +
218A TRP* 3.6 20.5 - + - -
225A GLY 5.2 0.2 - - - +
227A ASN* 3.1 32.8 - - + +
269A TYR* 3.7 11.6 - + - -
270A GLY* 1.3 73.0 - - - -
272A SER* 1.3 59.5 + - - +
273A PHE* 4.1 11.8 - - + -
300A GLY 2.9 20.9 + - - +
301A PHE* 3.8 12.4 - + + +
333A TRP 4.0 0.5 - - - +
334A VAL* 3.6 2.3 - - - -
335A GLY* 3.0 29.9 + - - +
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Residues in contact with SER 272 (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 SER* 4.6 3.1 + - - -
271A HIS* 1.3 75.0 - - - +
273A PHE* 1.3 69.6 + - - +
289A PRO* 3.7 5.7 - - - +
290A GLY* 3.1 31.2 + - - -
291A ALA 4.4 3.4 + - - -
300A GLY* 2.9 26.5 + - - +
301A PHE* 3.8 2.1 + - - -
302A LEU* 4.8 13.0 - - - +
332A GLN* 4.9 3.1 - - - -
333A TRP 3.3 9.0 - - - -
334A VAL* 3.9 16.4 - - - +
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Residues in contact with PHE 273 (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 GLY* 3.6 42.4 - - - -
217A SER* 3.8 6.1 - - - -
219A GLU* 4.7 0.2 - - - -
222A LEU* 4.1 8.3 - - + -
223A ILE 3.6 15.9 - - - -
224A THR* 4.1 13.0 - - + -
225A GLY 3.3 37.0 - - - -
271A HIS* 4.1 12.6 - - + -
272A SER* 1.3 78.5 - - - +
274A THR* 1.3 61.4 + - - +
275A LEU 3.9 0.2 + - - -
286A ALA* 4.0 25.8 - - + -
288A GLY 3.5 4.5 - - - -
290A GLY* 3.4 12.0 - - - +
332A GLN* 3.7 4.0 - - - -
333A TRP* 2.9 52.6 + + + +
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Residues in contact with THR 274 (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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273A PHE* 1.3 72.2 - - - +
275A LEU* 1.3 62.2 + - - +
286A ALA* 3.2 6.7 - - - +
287A SER* 2.8 44.2 + - - +
288A GLY* 2.8 9.4 + - - -
289A PRO 2.7 23.3 + - - -
290A GLY* 3.5 3.6 - - - -
291A ALA 4.1 0.7 + - - -
331A ASN* 3.5 32.1 - - - +
332A GLN* 3.1 15.4 + - - +
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Residues in contact with LEU 275 (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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224A THR* 3.5 32.1 - - + -
274A THR* 1.3 83.3 - - - +
276A ALA* 1.3 60.6 + - - +
277A SER 3.4 13.6 - - - +
279A GLU 3.6 22.7 - - - +
280A THR* 4.0 18.6 - - + -
284A ALA* 4.1 3.1 - - + -
285A PRO 3.8 9.4 - - - +
286A ALA* 4.2 0.2 - - - +
287A SER* 4.2 2.1 + - - -
328A VAL* 4.2 13.9 - - + -
330A GLY 4.6 1.1 - - - +
331A ASN* 2.8 41.4 + - + +
333A TRP* 4.0 17.5 - - + -
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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