Contacts of the strand formed by residues 295 - 301 (chain P) in PDB entry 2IMW
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 295 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248P ILE* 6.5 0.9 - - + -
287P VAL* 3.7 27.4 - - + -
288P ALA 3.4 2.7 - - - +
289P VAL* 4.2 16.8 - - + -
293P LEU 4.2 7.0 - - - +
294P ASP* 1.3 83.2 - - - +
296P VAL* 1.3 66.7 + - - +
297P SER* 5.2 3.8 - - - +
1913T T 3.9 20.2 + - + +
1914T C 5.1 8.5 + - + -
1915T C 6.3 1.1 - - - +
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Residues in contact with VAL 296 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287P VAL* 3.5 2.6 - - - +
288P ALA* 2.8 38.7 + - + +
290P THR* 4.0 13.2 - - + -
295P ILE* 1.3 79.5 - - - +
297P SER* 1.3 62.0 + - - +
298P ARG* 3.7 25.4 - - - +
322P ILE* 3.9 31.4 - - + +
326P ASP* 3.5 31.4 - - + +
328P ARG* 4.0 13.2 - - - +
1913T T 3.7 8.5 - - - +
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Residues in contact with SER 297 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285P HIS* 3.6 15.9 - - - +
286P VAL 3.5 8.2 + - - -
287P VAL* 4.4 6.1 - - - -
295P ILE* 5.4 4.0 - - - -
296P VAL* 1.3 75.5 - - - +
298P ARG* 1.3 86.7 + - - +
322P ILE* 4.6 0.2 - - - -
504P EDO 3.2 24.4 + - - -
1912T T 3.4 14.0 - - - +
1913T T 2.9 28.5 + - - +
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Residues in contact with ARG 298 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285P HIS* 4.0 4.5 - - - -
286P VAL* 2.8 35.5 + - - -
296P VAL* 3.7 14.1 - - - +
297P SER* 1.3 99.3 + - - +
299P GLY* 1.3 57.4 + - - +
318P LEU* 3.6 25.4 - - + +
321P LYS* 3.8 24.8 + - + +
322P ILE* 3.4 26.2 - - + +
325P GLU* 2.8 46.2 + - - +
326P ASP* 5.9 0.4 + - - +
1912T T 3.5 23.7 + - - +
1913T T 3.3 24.5 + - - -
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Residues in contact with GLY 299 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284P ILE 3.0 13.2 - - - -
285P HIS* 3.4 18.9 - - - -
298P ARG* 1.3 76.3 - - - +
300P ARG* 1.3 60.5 + - - +
318P LEU* 3.6 12.0 - - - +
321P LYS* 4.8 5.7 + - - -
1911T C 5.9 0.8 - - - +
1912T T 2.9 16.6 + - - -
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Residues in contact with ARG 300 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282P LYS 4.0 0.9 - - - +
283P ALA* 3.3 3.1 - - - -
284P ILE* 2.8 33.4 + - + +
285P HIS* 5.0 1.9 - - - -
299P GLY* 1.3 75.6 - - - +
301P THR* 1.3 73.0 + - - +
302P PHE* 3.3 42.2 - - + +
303P PRO* 5.7 3.4 - - - +
314P GLU* 3.3 48.1 + - + +
317P LYS* 5.2 5.7 - - - +
318P LEU* 4.6 1.8 - - + -
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Residues in contact with THR 301 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282P LYS* 3.5 11.4 - - + +
283P ALA* 3.7 4.3 - - - +
285P HIS* 5.6 1.7 - - - -
300P ARG* 1.3 86.5 + - - +
302P PHE* 1.3 73.2 + - - +
303P PRO* 4.6 2.1 - - - +
339P LYS* 2.7 47.6 + - + +
1911T C 3.8 15.5 + - - -
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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
------------------------------------------------------------
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