Contacts of the helix formed by residues 293 - 304 (chain G) in PDB entry 5UQ9
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 LEU 293 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260G GLN* 4.4 12.8 - - - +
289G CYS 3.6 15.7 - - - +
290G LEU* 3.5 22.9 - - + +
291G SER 3.1 1.4 - - - -
292G SER* 1.3 75.9 - - - +
294G LYS* 1.3 57.0 + - - +
295G ASP 3.5 2.0 - - - -
296G GLU* 3.8 31.9 - - + +
297G ARG* 2.8 37.0 + - + +
277H PRO* 4.3 8.5 - - + -
340H MET* 3.7 30.3 - - + -
343H ARG* 4.7 9.4 - - - +
433H TYR* 4.7 2.5 - - + -
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Residues in contact with LYS 294 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255G ARG* 3.3 39.3 - - + +
256G ASP* 2.5 34.8 + - - +
257G SER* 5.0 2.7 - - - -
291G SER 3.5 7.2 + - - +
292G SER 3.0 8.7 + - - +
293G LEU* 1.3 74.9 - - - +
295G ASP* 1.3 63.6 + - - +
297G ARG* 3.1 22.0 + - - +
298G ILE* 2.9 48.2 + - + +
436H GLU* 3.0 26.1 + - - +
437H MET* 3.3 14.6 - - - -
458H LEU* 3.9 11.9 - - - +
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Residues in contact with ASP 295 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255G ARG* 4.4 9.1 + - - -
293G LEU 3.5 0.2 - - - -
294G LYS* 1.3 81.2 - - - +
296G GLU* 1.3 62.5 + - - +
298G ILE* 3.1 28.0 + - - +
299G GLN* 3.1 26.4 + - + +
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Residues in contact with GLU 296 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293G LEU* 3.3 30.6 + - + +
294G LYS 3.3 0.6 - - - -
295G ASP* 1.3 79.1 - - - +
297G ARG* 1.3 62.0 + - - +
299G GLN* 3.7 7.8 + - - +
300G ALA* 3.4 19.8 + - - +
340H MET* 4.2 1.4 - - - +
343H ARG* 3.0 30.5 + - - -
387H GLN* 3.7 25.9 + - + +
388H ASN* 3.3 15.1 + - - +
391H LEU* 5.1 4.1 - - + +
433H TYR* 2.9 35.4 + - + +
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Residues in contact with ARG 297 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256G ASP* 3.2 23.4 + - - -
290G LEU* 3.0 28.2 + - + +
291G SER* 2.8 24.7 + - - +
293G LEU* 2.8 17.2 + - + +
294G LYS* 3.1 16.3 + - - +
296G GLU* 1.3 74.5 - - - +
298G ILE* 1.3 61.2 + - - +
300G ALA* 3.7 1.6 - - - +
301G SER* 3.0 28.2 + - - -
432H GLY 3.4 19.7 - - - -
433H TYR* 3.5 29.2 - - + +
435H HIS 3.1 27.1 + - - +
436H GLU* 3.6 14.4 + - - -
438H LEU* 3.4 26.4 - - - +
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Residues in contact with ILE 298 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294G LYS* 2.9 41.0 + - + +
295G ASP* 3.1 24.0 + - - +
297G ARG* 1.3 78.2 - - - +
299G GLN* 1.3 72.7 + - - +
301G SER* 2.7 23.7 + - - +
302G LYS* 3.6 7.6 + - - +
436H GLU* 4.1 29.8 - - + +
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Residues in contact with GLN 299 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295G ASP* 3.1 26.6 + - - +
296G GLU* 4.1 7.2 - - - +
298G ILE* 1.3 90.1 - - - +
300G ALA* 1.3 61.4 + - - +
302G LYS* 3.4 15.1 + - - +
303G LYS* 3.3 28.2 + - + +
391H LEU* 4.2 18.8 - - + -
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Residues in contact with ALA 300 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296G GLU 3.4 9.3 + - - +
297G ARG 3.3 1.7 + - - +
298G ILE 3.2 0.6 - - - -
299G GLN* 1.3 75.0 - - - +
301G SER* 1.3 55.6 + - - +
302G LYS 3.0 5.6 - - - -
304G LEU* 2.7 51.6 + - + +
391H LEU* 4.0 3.8 - - + +
433H TYR* 3.3 51.1 - - + +
434H ARG* 4.1 3.6 - - - -
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Residues in contact with SER 301 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297G ARG 3.0 9.9 + - - -
298G ILE* 2.7 24.8 + - - +
300G ALA* 1.3 75.0 - - - +
302G LYS* 1.3 58.9 + - - +
304G LEU 3.6 10.9 - - - +
434H ARG 3.2 23.0 + - - -
436H GLU* 3.5 30.4 + - - +
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Residues in contact with LYS 302 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298G ILE 3.6 7.6 + - - +
299G GLN* 3.4 18.3 + - - +
300G ALA 3.0 1.0 - - - -
301G SER* 1.3 81.6 + - - +
303G LYS* 1.3 86.9 + - + +
304G LEU 4.7 0.6 - - - +
305G LYS* 5.6 4.9 + - - +
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Residues in contact with LYS 303 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299G GLN* 3.3 13.9 + - + +
300G ALA 3.2 1.4 + - - -
302G LYS* 1.3 103.3 - - + +
304G LEU* 1.3 76.0 + - + +
305G LYS* 4.1 8.2 + - - +
391H LEU* 4.1 21.8 - - + +
396H LYS* 3.2 42.3 - - + +
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Residues in contact with LEU 304 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300G ALA* 2.7 40.0 + - + +
301G SER* 3.6 14.6 - - - +
302G LYS 4.7 0.3 - - - -
303G LYS* 1.3 83.3 - - + +
305G LYS* 1.3 62.5 + - - +
390H LEU* 3.4 46.4 - - + +
391H LEU* 3.8 7.4 - - + -
396H LYS* 4.9 7.9 - - + -
399H VAL* 5.8 0.2 - - + -
430H TYR* 3.5 38.1 - - + +
433H TYR* 4.2 10.5 - - + -
434H ARG* 4.0 19.3 + - + +
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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