Contacts of the strand formed by residues 287 - 292 (chain A) in PDB entry 2POD
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 ALA 287 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A LEU* 4.7 1.0 - - - +
266A VAL* 3.7 12.6 - - - +
268A ALA* 4.8 4.0 - - + -
281A LEU* 3.8 35.1 + - + +
282A LEU* 5.8 0.9 - - + -
284A THR* 4.3 2.4 + - - -
285A ASN 5.0 1.6 - - - -
286A ALA* 1.3 81.7 + - - +
288A GLY* 1.3 59.3 + - - +
289A ILE 4.2 11.0 - - - +
290A VAL* 5.0 0.4 - - + -
315A LEU* 3.7 29.0 - - + +
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Residues in contact with GLY 288 (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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265A PRO* 3.9 17.5 - - - +
266A VAL 2.8 11.5 + - - +
286A ALA 3.8 2.0 + - - -
287A ALA* 1.3 74.5 - - - +
289A ILE* 1.3 67.7 + - - +
315A LEU* 3.6 15.4 - - - +
316A PRO* 3.3 22.9 - - - +
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Residues in contact with ILE 289 (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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241A PHE* 5.1 4.7 - - + -
242A TRP* 3.8 38.4 - - + -
265A PRO* 4.6 13.0 - - + -
266A VAL 3.0 7.5 + - - +
267A CYS* 3.8 21.3 - - - -
268A ALA 3.0 25.6 + - - +
287A ALA* 4.2 4.4 - - - +
288A GLY* 1.3 88.0 - - - +
290A VAL* 1.3 64.4 + - - +
316A PRO* 3.8 24.7 - - + +
318A ALA* 4.1 16.2 - - + +
342A LEU* 4.0 15.5 - - + -
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Residues in contact with VAL 290 (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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268A ALA 3.3 2.9 - - - -
278A PHE* 3.7 28.9 - - + -
281A LEU* 4.7 10.1 - - + -
282A LEU* 4.2 11.4 - - + -
287A ALA* 5.0 1.1 - - + -
289A ILE* 1.3 70.8 - - - +
291A MSE 1.3 60.4 + - - +
292A LEU* 4.7 0.9 - - + -
306A ILE* 3.9 16.8 - - + -
310A ALA* 3.7 22.4 - - + -
315A LEU* 3.9 23.8 - - + +
316A PRO 2.9 13.7 + - - +
317A VAL* 3.2 16.8 - - + +
318A ALA 3.1 22.8 + - - -
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Residues in contact with MSE 291 (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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118A TYR* 3.4 24.2 - - - +
242A TRP* 4.6 1.3 - - + -
244A GLU* 3.4 35.4 - - + +
267A CYS* 3.6 20.4 - - - -
268A ALA 2.7 16.3 + - - +
269A SER* 3.0 24.9 + - - +
270A GLU* 3.9 18.4 - - + +
278A PHE* 3.1 9.6 - - - -
289A ILE 3.5 0.8 + - - -
290A VAL* 1.3 75.0 - - - +
292A LEU* 1.3 67.0 + - - +
318A ALA* 3.2 35.4 - - + +
319A PRO 4.0 1.8 - - - +
320A HIS* 3.8 31.4 - - + +
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Residues in contact with LEU 292 (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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269A SER 4.4 2.9 - - - -
270A GLU* 4.6 0.7 - - - -
272A LEU 5.6 0.2 - - - -
278A PHE* 4.0 13.2 - - + -
290A VAL* 4.7 0.7 - - + -
291A MSE 1.3 79.6 - - - +
293A ASP* 1.3 55.9 + - - +
294A ILE* 3.8 17.0 - - + +
297A CYS* 4.3 9.6 - - + -
303A ALA* 3.7 33.0 - - + +
306A ILE* 3.6 33.4 - - + -
317A VAL* 3.8 25.1 - - + -
318A ALA 3.6 2.2 + - - -
319A PRO* 4.5 5.3 - - + +
320A HIS* 2.8 33.3 + - - -
334A LEU* 3.9 10.1 - - + -
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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