Contacts of the helix formed by residues 284 - 293 (chain J) in PDB entry 4E2I
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 ASP 284 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349I ARG* 4.4 0.8 + - - -
516I LYS* 2.7 32.2 - - - +
517I ARG* 4.0 13.5 + - - +
282J CYS* 3.2 1.6 - - - -
283J ASP* 1.3 82.3 - - - +
285J VAL* 1.3 74.2 + - - +
286J LEU* 3.0 7.1 + - - +
287J LEU* 2.7 49.9 + - + -
288J LEU* 3.1 19.8 - - - +
341J VAL* 3.1 15.2 - - - +
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Residues in contact with VAL 285 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514I LEU* 5.0 11.0 - - + -
515I ASN 5.5 5.6 - - - +
516I LYS* 5.0 7.8 - - + +
284J ASP* 1.3 76.8 + - - +
286J LEU* 1.3 69.5 + - + +
287J LEU 3.2 1.3 + - - -
288J LEU* 3.3 3.5 + - - +
289J LEU* 3.0 22.9 + - + +
334J LYS* 4.2 30.1 - - + +
337J CYS* 4.3 3.7 - - + +
338J GLN* 3.3 48.2 - - + +
341J VAL* 3.7 15.9 - - + -
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Residues in contact with LEU 286 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342I ASP* 3.5 42.4 - - + +
345I LEU* 4.3 26.0 - - + -
346I ALA* 3.5 15.2 - - - +
349I ARG* 3.2 37.2 - - + +
511I LYS* 4.6 2.7 - - + +
516I LYS* 3.5 29.4 - - + +
284J ASP* 3.0 4.7 + - - +
285J VAL* 1.3 78.9 - - - +
287J LEU* 1.3 62.1 + - - +
289J LEU* 3.4 9.5 - - + +
290J GLY 3.1 19.2 + - - -
334J LYS* 4.6 9.4 - - + -
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Residues in contact with LEU 287 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349I ARG* 3.4 38.7 - - + +
350I VAL* 4.5 3.3 - - - +
353I LEU* 3.8 19.3 - - + -
517I ARG* 3.3 17.7 - - - +
282J CYS* 3.8 17.9 - - - -
284J ASP* 2.7 30.9 + - + +
286J LEU* 1.3 71.2 - - - +
288J LEU* 1.3 65.5 + - - +
289J LEU 3.2 0.2 + - - -
290J GLY* 3.3 2.0 + - - -
291J MET* 3.1 43.3 + - + +
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Residues in contact with LEU 288 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273J VAL* 5.1 4.7 - - + +
276J TYR* 4.1 21.3 - - + -
277J ALA* 3.8 22.0 - - + -
280J THR* 4.6 0.2 - - - +
282J CYS* 3.5 28.7 - - + +
284J ASP 3.1 15.0 + - - +
285J VAL 3.3 4.1 + - - +
287J LEU* 1.3 79.4 - - - +
289J LEU* 1.3 60.0 + - - +
291J MET* 4.1 4.1 - - + +
292J TYR* 3.3 23.4 + - + +
337J CYS* 3.4 23.8 - - + +
340J ALA* 3.4 33.0 - - + -
341J VAL* 3.9 8.7 - - + +
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Residues in contact with LEU 289 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339I GLN* 5.4 0.7 - - + +
342I ASP* 4.0 39.9 - - + +
343I THR* 4.5 3.1 - - - +
346I ALA* 4.3 1.1 - - + -
285J VAL 3.0 13.1 + - - +
286J LEU* 3.4 15.3 - - + +
287J LEU 3.1 0.2 - - - -
288J LEU* 1.3 75.7 - - - +
290J GLY* 1.3 66.7 + - - +
292J TYR* 3.3 3.8 + - - +
293J LEU* 3.0 38.1 + - + +
327J PHE* 3.7 18.4 - - + -
333J GLN* 3.2 37.0 - - + +
334J LYS* 4.6 13.0 - - + +
337J CYS* 3.6 9.4 - - + -
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Residues in contact with GLY 290 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346I ALA* 3.4 23.3 - - - +
347I LYS* 4.9 0.4 - - - -
350I VAL* 3.7 16.4 - - - -
286J LEU 3.1 8.9 + - - -
289J LEU* 1.3 78.6 - - - +
291J MET* 1.3 63.3 + - - +
293J LEU* 3.1 18.5 + - - +
294J GLU* 3.5 14.7 - - - +
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Residues in contact with MET 291 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350I VAL* 3.4 31.5 - - + +
353I LEU* 6.0 2.5 - - - -
354I GLN* 3.9 16.2 - - + +
276J TYR* 3.8 21.5 - - + +
282J CYS* 5.9 1.1 - - - -
287J LEU* 3.1 33.5 + - + +
288J LEU* 4.1 5.8 - - + +
290J GLY* 1.3 77.4 - - - +
292J TYR* 1.3 59.3 + - - +
294J GLU* 3.5 17.7 + - - +
295J PHE* 3.1 22.1 - - + -
310J GLN* 5.3 2.7 - - + +
312J SER* 3.1 32.8 - - - +
313J HIS* 5.5 2.0 - - + -
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Residues in contact with TYR 292 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272J LEU* 4.1 0.2 - - - +
273J VAL* 3.5 34.4 + - + +
276J TYR* 3.6 27.3 - + + -
288J LEU 3.3 16.8 + - - +
289J LEU 3.3 4.4 + - - +
290J GLY 3.2 0.4 - - - -
291J MET* 1.3 75.7 - - - +
293J LEU* 1.3 58.1 + - - +
294J GLU 3.1 9.5 + - - -
295J PHE* 3.3 24.8 + + - +
320J HIS* 3.4 48.2 + + + +
323J ASN* 2.8 30.8 + - - +
324J ALA* 3.9 14.2 - - + +
327J PHE* 3.7 33.2 - + + -
337J CYS* 4.7 3.1 - - - -
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Residues in contact with LEU 293 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278I MET* 6.1 2.9 - - + -
343I THR* 3.5 33.9 - - + +
346I ALA* 4.6 0.2 - - + -
289J LEU* 3.0 44.1 + - + +
290J GLY* 3.1 12.5 + - - +
292J TYR* 1.3 76.3 - - - +
294J GLU* 1.3 58.3 + - - +
295J PHE 3.3 1.1 - - - -
296J GLN* 3.2 44.2 - - - +
297J TYR* 3.7 9.4 + - - -
327J PHE* 3.5 27.1 - - + -
333J GLN* 3.8 19.1 - - - +
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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