Contacts of the strand formed by residues 283 - 288 (chain M) in PDB entry 1OEY
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 283 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244M TYR* 5.1 1.3 - - + -
271M LEU* 4.9 14.2 - - + +
274M THR* 2.9 39.7 - - + -
278M PHE* 5.5 0.9 - - + -
280M ARG* 3.8 54.5 - - + +
281M GLU* 3.2 9.1 + - - +
282M ASP* 1.3 82.5 - - - +
284M ALA* 1.3 60.4 + - - +
285M LEU* 4.7 5.6 - - + -
326M ILE* 3.7 21.1 - - + -
327M THR 3.1 15.7 - - - +
328M GLN* 4.2 0.4 - - - +
329M LYS* 3.9 7.4 - - - +
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Residues in contact with ALA 284 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271M LEU* 6.2 0.2 - - - -
283M ILE* 1.3 75.0 - - - +
285M LEU* 1.3 63.9 + - - +
286M ASN* 3.4 2.4 + - - +
296M ARG* 3.5 42.6 - - + +
326M ILE* 3.5 5.7 - - - +
327M THR* 2.6 45.5 + - - +
329M LYS* 4.2 6.0 - - + +
335M TYR* 4.1 1.3 - - - +
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Residues in contact with LEU 285 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267M LEU* 4.5 8.1 - - + -
270M LEU* 3.5 38.6 - - + +
271M LEU* 3.8 28.7 - - + +
274M THR* 3.6 24.5 - - + +
283M ILE* 4.7 2.9 - - + -
284M ALA* 1.3 76.7 - - - +
286M ASN* 1.3 66.3 + - - +
296M ARG* 3.7 2.9 - - - +
297M LEU* 2.9 42.3 + - + +
324M LEU* 4.1 11.4 - - + -
325M HIS 3.5 1.1 - - - -
326M ILE* 3.8 22.7 - - + -
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Residues in contact with ASN 286 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284M ALA 3.4 4.6 + - - -
285M LEU* 1.3 78.0 - - - +
287M TYR* 1.3 65.5 + - - +
294M LEU* 3.7 24.7 - - + -
295M VAL 3.1 10.1 - - - +
296M ARG* 3.2 17.3 - - - +
297M LEU* 4.0 5.5 - - - +
324M LEU* 3.8 11.1 - - - +
325M HIS* 2.7 47.6 + - + +
327M THR* 3.0 31.3 + - - +
335M TYR* 2.6 27.8 + - - -
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Residues in contact with TYR 287 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363D VAL* 4.0 8.5 - - - +
286M ASN* 1.3 74.8 - - - +
288M ARG* 1.3 69.1 + - - +
289M ASP* 4.1 18.3 - - + +
294M LEU* 3.5 7.1 - - - -
295M VAL* 2.7 67.4 + - + +
297M LEU* 3.6 29.2 - - + -
302M ASP* 4.5 5.2 + - + -
305M LEU* 3.6 24.8 - - + +
306M MSE 3.6 45.5 - - + -
309M GLN* 4.6 13.7 - - + -
323M LYS 4.3 4.7 - - - +
325M HIS* 4.0 6.7 - - - -
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Residues in contact with ARG 288 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245M TYR* 2.9 33.1 + - - -
287M TYR* 1.3 79.9 - - - +
289M ASP* 1.3 63.1 + - - +
292M GLY* 3.1 43.0 + - - +
293M ASP 3.4 3.1 - - - +
294M LEU* 3.7 26.9 - - + +
325M HIS* 4.1 25.5 + - + +
334M VAL* 4.8 7.1 + - - +
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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