Contacts of the helix formed by residues 301 - 311 (chain G) in PDB entry 5X8Q
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 SER 301 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458E HIS* 5.1 8.1 - - - -
299G ILE 3.4 3.7 + - - -
300G PHE* 1.3 75.3 - - - +
302G ARG* 1.3 59.5 + - - +
303G GLU* 3.4 20.8 + - - +
304G GLU* 2.8 52.9 + - - +
305G VAL* 2.9 15.5 + - - +
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Residues in contact with ARG 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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458E HIS* 3.9 34.0 + - + +
300G PHE 4.0 0.2 + - - -
301G SER* 1.3 73.4 - - - +
303G GLU* 1.3 69.0 + - - +
305G VAL* 3.9 9.3 - - + +
306G THR* 3.0 27.0 + - - -
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Residues in contact with GLU 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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301G SER* 3.4 20.6 + - - +
302G ARG* 1.3 87.4 + - - +
304G GLU* 1.3 60.1 + - + +
306G THR* 3.1 21.7 + - - -
307G GLY* 3.2 10.2 + - - -
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Residues in contact with GLU 304 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299G ILE 4.4 0.3 - - - +
300G PHE* 3.4 26.5 - - + -
301G SER* 2.8 44.6 + - - +
303G GLU* 1.3 74.5 - - + +
305G VAL* 1.3 64.5 + - - +
307G GLY* 3.3 11.3 + - - +
308G TYR* 3.3 23.8 + - + -
381G LYS* 3.4 27.2 + - - -
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Residues in contact with VAL 305 (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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300G PHE* 4.3 11.6 - - + +
301G SER 2.9 20.6 + - - +
302G ARG* 3.9 10.5 - - + +
304G GLU* 1.3 75.0 - - - +
306G THR* 1.3 56.8 + - - +
308G TYR* 3.3 4.7 + - - +
309G GLN* 3.0 59.7 + - + +
383G GLY* 6.2 0.7 - - - -
384G GLY 6.1 1.3 - - - +
386G GLU* 3.7 32.1 - - + +
387G LEU* 4.1 21.5 - - + +
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Residues in contact with THR 306 (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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302G ARG 3.0 14.1 + - - -
303G GLU* 3.1 12.7 + - - -
305G VAL* 1.3 76.9 - - - +
307G GLY* 1.3 57.5 + - - +
309G GLN* 3.3 14.1 + - + +
310G ARG* 3.0 39.4 + - + +
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Residues in contact with GLY 307 (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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303G GLU 3.2 12.1 + - - -
304G GLU* 3.3 5.7 + - - -
306G THR* 1.3 76.3 - - - +
308G TYR* 1.3 59.7 + - - +
310G ARG* 3.3 41.6 + - - +
311G LYS* 3.5 18.1 + - - +
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Residues in contact with TYR 308 (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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300G PHE* 3.8 31.5 - + - -
304G GLU* 3.3 24.3 + - + -
305G VAL 3.7 6.1 - - - +
307G GLY* 1.3 72.7 - - - +
309G GLN* 1.3 61.4 + - - +
311G LYS* 3.2 42.9 + - - +
316G MET* 3.9 24.0 - - + +
319G ARG* 4.3 8.4 + - - -
378G PHE* 3.9 13.2 - + - -
379G GLU* 2.5 41.2 + - - +
387G LEU* 3.6 38.4 - - + +
390G ALA* 3.9 8.7 - - - +
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Residues in contact with GLN 309 (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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305G VAL* 3.0 40.0 + - + +
306G THR* 3.3 15.8 + - + +
308G TYR* 1.3 76.1 - - - +
310G ARG* 1.3 60.8 + - - +
311G LYS 3.5 5.7 + - - +
386G GLU* 3.0 38.2 + - - +
387G LEU 4.8 2.7 - - - +
389G ARG* 3.1 55.8 + - + +
390G ALA* 4.0 14.8 + - - +
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Residues in contact with ARG 310 (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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306G THR* 3.0 20.7 + - + +
307G GLY* 3.3 33.3 - - - +
309G GLN* 1.3 74.1 - - - +
311G LYS* 1.3 68.9 + - + +
312G SER* 3.6 0.7 + - - -
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Residues in contact with LYS 311 (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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307G GLY 3.5 18.9 + - - +
308G TYR* 3.2 34.7 + - + +
309G GLN 3.9 1.4 - - - +
310G ARG* 1.3 82.6 - - + +
312G SER* 1.3 71.2 + - - +
313G MET 3.7 0.3 + - - -
315G GLU* 3.3 36.3 - - + +
316G MET* 4.3 20.9 - - + +
319G ARG* 3.5 28.7 - - - +
390G ALA* 3.4 13.9 - - - +
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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