Contacts of the helix formed by residues 287 - 302 (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 HIS 287 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352E LYS 6.0 0.7 - - - +
355E ALA* 4.5 15.2 + - + +
356E GLN* 4.6 22.7 + - + -
282G GLN* 2.9 25.4 + - + +
285G LEU* 3.1 9.8 - - + +
286G ASP* 1.4 73.8 - - - +
288G TYR* 1.3 53.8 + - - +
289G ARG* 4.1 10.3 - - + +
290G ALA* 3.2 33.5 + - + +
291G ALA* 2.9 34.0 + - - +
293G ARG* 4.7 6.7 + - - -
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Residues in contact with TYR 288 (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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318E GLN 4.6 15.1 + - - -
319E GLN 6.3 0.9 - - - -
283G LEU* 4.2 10.8 - - + -
286G ASP* 3.0 50.4 + - + -
287G HIS* 1.3 70.9 - - - +
289G ARG* 1.3 59.9 + - - +
291G ALA* 3.5 2.3 + - - +
292G LEU* 3.0 34.1 + - - +
315G VAL* 3.6 25.4 - - + +
318G GLN* 3.0 51.5 + - + +
319G GLN* 3.6 33.4 - - + +
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Residues in contact with ARG 289 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287G HIS* 3.4 11.9 - - + +
288G TYR* 1.3 78.1 - - - +
290G ALA* 1.3 60.4 + - - +
292G LEU* 3.6 9.7 - - + +
293G ARG* 3.4 38.9 + - - +
319G GLN* 4.8 9.9 - - - +
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Residues in contact with ALA 290 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282G GLN* 3.4 24.6 + - - +
287G HIS* 3.2 37.8 + - + +
289G ARG* 1.3 74.2 - - - +
291G ALA* 1.3 64.8 + - - +
292G LEU 3.1 1.6 - - - -
293G ARG* 3.0 31.3 + - - +
294G SER* 3.1 15.8 + - - -
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Residues in contact with ALA 291 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279G ALA* 4.0 8.3 - - + +
282G GLN* 3.5 24.5 + - + -
283G LEU* 3.9 13.9 - - - +
287G HIS 2.9 18.1 + - - +
288G TYR 3.8 4.9 - - - +
290G ALA* 1.3 74.8 - - - +
292G LEU* 1.4 56.5 + - - +
294G SER* 3.5 3.0 + - - -
295G CYS* 2.9 35.7 + - - +
315G VAL* 4.0 19.3 - - + -
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Residues in contact with LEU 292 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288G TYR 3.0 21.5 + - - +
289G ARG* 3.6 9.4 - - + +
291G ALA* 1.4 72.8 - - - +
293G ARG* 1.4 56.0 + - - +
295G CYS* 3.4 5.1 + - - +
296G SER* 2.9 40.1 + - - +
312G LYS* 3.8 38.6 - - + +
315G VAL* 3.7 10.9 - - + +
316G LEU* 4.4 15.5 - - + -
319G GLN* 3.3 34.3 - - - +
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Residues in contact with ARG 293 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287G HIS* 4.7 8.1 + - - -
289G ARG* 3.4 23.7 + - - +
290G ALA* 3.0 32.2 + - - +
292G LEU* 1.4 76.6 - - - +
294G SER* 1.3 57.0 + - - +
296G SER* 3.4 6.3 + - - -
297G LEU* 3.0 42.2 + - + +
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Residues in contact with SER 294 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G LEU* 3.5 34.9 - - - +
278G LEU* 3.9 12.8 - - - +
279G ALA* 3.9 5.4 - - - -
282G GLN* 2.7 30.6 + - - -
290G ALA 3.1 5.1 + - - -
291G ALA 3.6 6.3 - - - -
293G ARG* 1.3 74.7 - - - +
295G CYS* 1.3 60.3 + - - +
297G LEU* 3.4 4.2 + - - +
298G VAL* 3.1 29.9 + - - +
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Residues in contact with CYS 295 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276G ASN* 6.0 0.2 - - - -
279G ALA* 3.8 13.2 - - - -
291G ALA* 2.9 27.1 + - - +
292G LEU* 3.6 7.6 - - - +
293G ARG 3.3 0.2 - - - -
294G SER* 1.3 74.9 - - - +
296G SER* 1.3 55.7 + - - +
298G VAL* 3.3 7.7 + - - +
299G LEU* 3.1 34.6 + - - +
308G ALA* 3.7 11.7 - - - +
311G ARG* 3.7 20.0 - - - -
312G LYS* 3.7 40.8 - - + -
315G VAL* 5.5 0.9 - - - -
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Residues in contact with SER 296 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292G LEU* 2.9 22.3 + - - +
293G ARG* 3.8 6.3 - - - -
295G CYS* 1.3 75.5 - - - +
297G LEU* 1.4 56.6 + - - +
299G LEU* 3.5 6.8 + - - +
300G GLU* 3.1 33.5 + - - +
312G LYS* 3.2 28.0 + - - +
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Residues in contact with LEU 297 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G LEU* 4.0 30.5 - - + -
293G ARG* 3.0 29.7 + - + +
294G SER* 3.8 4.5 - - - +
295G CYS 3.3 0.2 - - - -
296G SER* 1.4 72.1 - - - +
298G VAL* 1.3 64.9 + - - +
300G GLU* 3.3 13.9 + - + +
301G HIS* 3.1 31.0 - - + +
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Residues in contact with VAL 298 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272G VAL* 3.5 28.2 - - + +
275G LEU* 3.6 11.9 - - + -
276G ASN* 3.6 42.4 - - - +
294G SER 3.1 17.2 + - - +
295G CYS* 3.6 8.1 - - - +
297G LEU* 1.3 74.9 - - - +
299G LEU* 1.3 49.3 + - - +
301G HIS* 3.1 8.2 + - - +
302G GLN* 2.8 31.2 + - - +
305G ASN* 3.8 9.6 - - + +
308G ALA* 3.6 22.7 - - + -
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Residues in contact with LEU 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 CYS 3.1 21.0 + - - +
296G SER* 3.5 6.9 + - - +
297G LEU 3.3 0.2 - - - -
298G VAL* 1.3 72.3 - - - +
300G GLU* 1.3 62.7 + - - +
301G HIS 3.3 0.2 - - - -
302G GLN 3.5 17.0 - - - +
303G PRO* 3.2 35.2 - - + +
305G ASN 3.9 3.6 - - - +
308G ALA* 3.8 29.8 - - + +
309G LEU* 3.8 32.3 - - + -
312G LYS* 3.9 28.5 - - + +
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Residues in contact with GLU 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 SER* 3.1 19.1 + - - +
297G LEU* 3.5 16.6 - - + +
298G VAL 3.2 0.6 - - - -
299G LEU* 1.3 78.8 - - - +
301G HIS* 1.4 64.4 + - + +
303G PRO* 4.8 2.1 - - - +
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Residues in contact with HIS 301 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268G LEU* 3.6 34.2 - - + +
271G LYS* 4.6 14.4 + - - -
272G VAL* 3.8 26.6 - - + +
275G LEU* 5.7 3.9 - - + +
297G LEU* 3.1 31.6 - - + +
298G VAL 3.1 6.5 + - - +
300G GLU* 1.4 83.0 - - + +
302G GLN* 1.3 64.3 + - + +
303G PRO* 3.8 6.9 - - - +
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Residues in contact with GLN 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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269G GLN* 3.6 33.5 + - - +
272G VAL* 3.8 24.2 - - + +
298G VAL 2.8 9.4 + - - +
299G LEU* 3.5 12.9 - - - +
301G HIS* 1.3 83.2 - - + +
303G PRO* 1.4 64.1 - - - +
304G ASP 3.2 4.5 + - - -
305G ASN* 3.1 45.8 + - + +
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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