Contacts of the strand formed by residues 290 - 295 (chain F) in PDB entry 2OME
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 290 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258F ILE* 4.4 16.6 - - + -
261F MET* 4.1 33.4 - - + -
265F ALA* 3.4 16.6 - - + +
267F LEU* 4.2 14.6 - - + +
281F LEU* 4.2 20.9 - - + -
284F ALA* 3.4 15.5 + - + +
285F LEU* 3.7 28.3 - - + +
288F GLY* 3.8 6.3 - - - +
289F ARG* 1.3 82.7 - - - +
291F ARG* 1.3 65.6 + - - +
292F GLY 3.3 28.7 + - - +
315F ASN* 5.6 0.2 - - - +
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Residues in contact with ARG 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148F ARG* 5.5 7.3 + - - +
151F TRP* 5.3 0.9 - - - -
174F GLY* 4.7 25.5 + - - -
264F GLY* 3.4 37.2 + - - +
265F ALA 2.8 9.4 + - - +
266F PHE* 3.7 30.7 - - + -
288F GLY* 4.5 4.0 - - - -
290F ILE* 1.3 72.3 - - - +
292F GLY* 1.3 56.6 + - - +
315F ASN* 3.3 25.3 - - - +
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Residues in contact with GLY 292 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145F LEU* 3.9 2.2 - - - +
151F TRP* 4.8 4.3 - - - -
266F PHE* 3.4 20.4 - - - -
267F LEU 3.1 20.8 + - - -
285F LEU* 3.7 5.2 - - - -
290F ILE* 3.2 9.5 - - - +
291F ARG* 1.3 83.3 - - - +
293F ALA* 1.3 60.9 + - - -
315F ASN* 3.3 14.6 - - - -
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Residues in contact with ALA 293 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F LEU* 4.0 7.2 - - - +
267F LEU* 3.1 16.4 - - + +
281F LEU* 4.1 34.5 - - + -
285F LEU* 3.9 8.2 - - + +
292F GLY* 1.3 74.1 - - - +
294F ALA* 1.3 61.8 + - - +
295F LEU* 4.2 4.5 - - + -
315F ASN 3.0 6.9 + - - +
316F LEU* 3.5 10.2 - - + +
317F ILE* 2.8 26.0 + - - +
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Residues in contact with ALA 294 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F HIS* 3.6 37.8 - - + +
145F LEU* 4.0 17.6 - - + +
267F LEU 3.0 7.3 + - - +
268F VAL* 3.4 8.7 - - + +
269F ASN 3.0 24.9 + - - +
293F ALA* 1.3 73.5 - - - +
295F LEU* 1.3 60.2 + - - +
296F ASP 4.3 0.4 + - - -
317F ILE* 3.2 15.0 - - + -
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Residues in contact with LEU 295 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F HIS* 4.8 1.6 - - - -
267F LEU* 5.4 3.6 - - + +
268F VAL 5.2 0.2 - - - -
269F ASN* 3.6 31.6 - - + +
276F VAL* 5.1 6.3 - - + -
278F GLU* 5.2 4.9 - - + +
281F LEU* 4.0 21.3 - - + -
293F ALA* 4.8 2.5 - - + -
294F ALA* 1.3 78.2 - - - +
296F ASP* 1.3 60.9 + - - +
297F VAL 3.9 10.3 - - - +
298F HIS* 3.7 20.3 - - + +
310F LEU* 3.8 22.2 - - + -
316F LEU* 3.8 24.7 - - + -
317F ILE* 2.7 12.1 + - - +
318F CYS* 3.2 5.1 - - - -
319F THR* 3.1 23.0 + - - +
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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