Contacts of the helix formed by residues 305 - 319 (chain G) in PDB entry 5MGX
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 ASN 305 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709B ASP* 5.7 0.6 + - - -
272G VAL* 4.5 2.0 - - - +
276G ASN* 2.9 32.0 + - - +
298G VAL* 3.8 7.9 - - + +
299G LEU* 3.9 0.5 - - - +
302G GLN* 3.1 44.8 + - + +
303G PRO 3.5 1.2 - - - -
304G ASP* 1.3 73.6 - - - +
306G ILE* 1.3 58.1 + - - +
307G LYS* 3.2 7.8 + - - +
308G ALA* 3.0 25.7 + - + +
309G LEU* 3.0 30.2 + - - +
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Residues in contact with ILE 306 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703B THR* 3.8 29.2 - - + +
705B MET* 3.9 10.3 - - + -
304G ASP 3.3 6.6 + - - +
305G ASN* 1.3 69.9 + - - +
307G LYS* 1.4 59.7 - - + +
309G LEU* 3.4 4.0 + - - +
310G PHE* 2.9 29.5 + - - +
332G ALA* 3.5 33.7 - - + +
335G LEU* 4.3 16.4 - - + -
336G GLU* 3.6 38.4 - - + +
342G ILE* 3.7 10.5 - - + -
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Residues in contact with LYS 307 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703B THR* 3.8 24.7 - - + -
704B GLU 3.4 21.3 + - - -
705B MET* 4.3 12.8 - - - -
707B GLU* 3.1 31.1 + - - +
708B VAL 4.2 0.8 + - - +
709B ASP* 2.8 38.9 + - - +
276G ASN* 3.9 9.4 - - - +
305G ASN* 3.2 9.2 + - - +
306G ILE* 1.4 78.2 - - + +
308G ALA* 1.3 57.9 + - - +
310G PHE* 3.8 1.2 - - - +
311G ARG* 2.9 57.1 + - - +
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Residues in contact with ALA 308 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276G ASN* 3.6 10.5 + - - +
295G CYS* 3.7 10.8 - - - +
298G VAL* 3.6 33.4 - - + -
299G LEU* 3.8 23.3 - - + +
305G ASN* 3.0 10.9 + - - +
307G LYS* 1.3 76.3 - - - +
309G LEU* 1.4 56.9 + - - +
311G ARG* 4.6 3.4 - - - -
312G LYS* 3.0 30.0 + - - +
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Residues in contact with LEU 309 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299G LEU* 3.8 25.1 - - + -
303G PRO 3.9 18.6 - - - +
304G ASP* 4.3 1.3 - - - +
305G ASN 3.0 20.5 + - - +
306G ILE* 3.7 4.5 - - - +
308G ALA* 1.4 73.2 - - - +
310G PHE* 1.3 60.1 + - - +
312G LYS* 3.2 1.6 + - - +
313G GLY* 3.0 24.9 + - - -
328G ILE* 3.2 34.7 - - + +
331G ALA* 4.6 11.2 - - + -
332G ALA* 4.0 20.9 - - + +
335G LEU* 3.9 26.9 - - + -
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Residues in contact with PHE 310 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705B MET* 3.6 39.3 - - + -
706B GLU* 4.7 3.8 - - - -
283G LEU* 5.9 0.2 - - + -
306G ILE 2.9 18.3 + - - +
307G LYS 3.8 1.3 - - - +
309G LEU* 1.3 73.9 - - - +
311G ARG* 1.3 68.1 + - + +
313G GLY* 3.4 1.2 + - - -
314G LYS* 2.9 60.2 + - + +
329G LEU* 3.8 18.8 - - + +
332G ALA* 4.3 6.8 - - + +
341G THR* 3.7 28.5 - - + -
342G ILE* 4.0 18.6 - - + -
345G GLU* 3.7 32.5 - - + -
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Residues in contact with ARG 311 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705B MET 2.8 28.2 + - - -
706B GLU 4.4 0.8 - - - -
707B GLU 2.8 23.2 + - - -
708B VAL* 4.8 1.0 - - - +
709B ASP* 5.2 1.0 + - - -
276G ASN* 2.9 44.9 + - - -
277G ASN* 4.8 3.8 + - - +
279G ALA* 4.6 2.9 - - + +
280G ALA* 3.5 34.8 - - - +
283G LEU* 4.1 23.8 - - + +
295G CYS* 3.7 17.5 - - - -
307G LYS* 2.9 35.6 + - - +
310G PHE* 1.3 81.3 - - + +
312G LYS* 1.3 65.6 + - - +
314G LYS* 3.9 1.1 - - - +
315G VAL* 3.0 30.9 + - + +
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Residues in contact with LYS 312 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292G LEU* 3.8 24.7 - - + -
295G CYS* 3.7 14.8 - - + -
296G SER* 3.2 28.5 + - - +
299G LEU* 3.9 20.3 - - + +
308G ALA 3.0 19.8 + - - +
309G LEU 3.2 4.2 + - - +
311G ARG* 1.3 75.7 - - - +
313G GLY* 1.3 57.7 + - - +
315G VAL* 3.4 5.6 + - - +
316G LEU* 2.9 41.7 + - + +
328G ILE* 4.2 25.7 - - + +
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Residues in contact with GLY 313 (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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309G LEU 3.0 13.6 + - - -
310G PHE 3.8 2.5 - - - -
312G LYS* 1.3 71.5 - - - +
314G LYS* 1.4 52.6 + - - +
316G LEU* 3.1 5.1 + - - -
317G ALA* 2.8 36.1 + - - +
325G ALA* 3.5 10.2 - - - +
328G ILE* 3.7 14.0 - - - +
329G LEU* 3.9 19.1 - - - -
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Residues in contact with LYS 314 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706B GLU* 3.2 27.9 + - - -
283G LEU* 4.0 20.0 - - + -
284G LYS* 4.5 5.6 - - - +
310G PHE* 2.9 42.4 + - + +
311G ARG* 3.9 6.1 - - - +
313G GLY* 1.4 70.0 - - - +
315G VAL* 1.4 56.3 + - - +
317G ALA* 3.5 2.9 + - - +
318G GLN* 3.0 53.8 + - - +
329G LEU* 4.1 1.6 - - - +
341G THR* 6.2 0.2 - - - +
345G GLU* 3.4 38.1 + - + +
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Residues in contact with VAL 315 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283G LEU* 3.5 27.4 - - + -
288G TYR* 3.6 38.7 - - + +
291G ALA* 4.0 22.4 - - + -
292G LEU* 3.7 16.8 - - + -
295G CYS* 5.5 1.3 - - - -
311G ARG* 3.0 23.2 + - + +
312G LYS* 3.7 5.8 - - - +
314G LYS* 1.4 72.8 - - - +
316G LEU* 1.3 59.7 + - - +
318G GLN* 3.3 3.3 + - - +
319G GLN* 3.0 36.0 + - - +
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Residues in contact with LEU 316 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292G LEU* 4.4 15.3 - - + -
312G LYS* 2.9 30.5 + - + +
313G GLY 3.5 4.3 - - - +
315G VAL* 1.3 75.2 - - - +
317G ALA* 1.3 56.1 + - - +
319G GLN* 3.6 17.5 + - - +
320G GLY 3.4 3.3 + - - -
321G GLU* 2.8 53.9 + - + +
324G GLU* 4.0 29.2 - - + +
325G ALA* 3.7 10.5 - - + -
328G ILE* 3.6 31.4 - - + -
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Residues in contact with ALA 317 (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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286E ASP* 5.1 4.0 - - - +
313G GLY 2.8 19.6 + - - +
314G LYS* 3.6 9.6 - - - +
316G LEU* 1.3 73.3 - - - +
318G GLN* 1.3 59.8 + - + +
320G GLY* 3.2 12.8 + - - -
322G TYR* 3.4 24.1 + - + -
325G ALA* 3.7 6.9 - - + +
329G LEU* 4.9 2.9 - - + -
345G GLU* 4.5 9.4 - - - +
349G LEU* 4.1 24.7 - - + -
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Residues in contact with GLN 318 (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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286E ASP* 5.3 9.4 - - - +
288E TYR* 4.6 17.3 + - - -
318E GLN 5.3 2.4 - - - +
283G LEU* 3.6 12.0 - - - +
286G ASP* 4.8 1.2 - - - +
288G TYR* 3.0 45.7 + - + +
314G LYS* 3.0 51.8 + - + +
315G VAL 3.9 3.6 - - - +
317G ALA* 1.3 75.3 - - + +
319G GLN* 1.3 60.4 + - - +
320G GLY* 3.3 0.7 + - - -
345G GLU* 4.9 2.9 + - - +
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Residues in contact with GLN 319 (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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288E TYR* 6.3 0.9 - - - -
288G TYR* 3.6 39.0 - - + +
289G ARG* 4.4 9.1 - - - +
292G LEU* 3.3 31.2 - - - +
315G VAL* 3.0 21.0 + - - +
316G LEU* 3.8 18.3 - - - +
317G ALA 3.3 0.2 - - - -
318G GLN* 1.3 76.1 - - - +
320G GLY* 1.3 58.5 + - - +
321G GLU* 4.0 11.7 + - + +
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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
------------------------------------------------------------
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