Contacts of the helix formed by residues 321 - 336 (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 GLU 321 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316G LEU* 2.8 37.7 + - + +
319G GLN* 4.7 12.6 - - + +
320G GLY* 1.3 74.2 - - - +
322G TYR* 1.4 58.4 + - - +
323G SER* 3.3 11.3 + - - +
324G GLU* 3.4 29.8 + - + +
325G ALA* 3.0 23.9 + - - +
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Residues in contact with TYR 322 (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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285E LEU 4.3 1.6 + - - -
286E ASP* 4.0 28.4 + - - +
317G ALA* 3.4 25.2 + - + -
320G GLY* 3.1 22.9 + - - -
321G GLU* 1.4 73.9 - - - +
323G SER* 1.4 62.5 + - - +
325G ALA* 3.9 0.6 - - - +
326G ILE* 3.2 31.1 + - - +
349G LEU* 3.4 36.0 - - + +
352G LYS* 4.1 20.8 + - + +
353G HIS* 3.2 51.1 - + + +
356G GLN* 5.8 5.2 - - + -
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Residues in contact with SER 323 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321G GLU* 4.4 13.0 + - - -
322G TYR* 1.4 77.0 - - - +
324G GLU* 1.3 63.6 + - - +
326G ILE* 4.0 5.5 - - - +
327G PRO* 3.4 19.2 - - - +
353G HIS* 5.3 5.4 - - - -
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Residues in contact with GLU 324 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316G LEU* 4.0 26.4 - - + +
321G GLU* 3.4 33.3 + - + +
322G TYR 3.3 0.2 - - - -
323G SER* 1.3 83.4 + - - +
325G ALA* 1.3 63.2 + - - +
326G ILE 3.6 0.4 - - - -
327G PRO* 3.5 13.6 - - - +
328G ILE* 3.4 20.8 - - + +
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Residues in contact with ALA 325 (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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313G GLY* 3.5 25.1 - - - +
316G LEU* 3.7 8.9 - - + +
317G ALA* 3.7 17.3 - - + +
321G GLU 3.0 18.7 + - - +
322G TYR 3.4 4.9 + - - +
324G GLU* 1.3 75.5 - - - +
326G ILE* 1.4 59.1 + - - +
327G PRO 3.6 0.2 - - - -
328G ILE* 3.4 3.4 + - - +
329G LEU* 2.9 34.6 + - + +
349G LEU* 4.2 7.6 - - + -
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Residues in contact with ILE 326 (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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322G TYR 3.2 16.6 + - - +
323G SER* 4.0 7.0 - - - +
325G ALA* 1.4 73.3 - - - +
327G PRO* 1.4 70.4 - - + +
329G LEU* 3.4 1.4 + - - +
330G ARG* 2.9 69.9 + - - +
346G LEU* 3.8 12.1 - - + -
349G LEU* 4.0 11.9 - - + +
350G VAL* 3.8 29.4 - - + -
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Residues in contact with PRO 327 (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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323G SER 3.4 15.5 - - - +
324G GLU* 3.5 12.6 - - - +
326G ILE* 1.4 101.9 - - + +
328G ILE* 1.3 53.4 + - + +
330G ARG* 3.3 10.2 + - + +
331G ALA* 2.8 34.4 + - - +
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Residues in contact with ILE 328 (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* 3.2 44.5 - - + +
312G LYS* 4.2 21.3 - - + -
313G GLY* 3.7 11.9 - - - +
316G LEU* 3.6 20.9 - - + -
324G GLU* 3.4 18.4 - - + +
325G ALA 3.4 6.8 + - - +
326G ILE 3.3 0.4 - - - -
327G PRO* 1.3 78.4 - - + +
329G LEU* 1.4 64.6 + - - +
331G ALA* 3.2 9.3 + - - +
332G ALA* 3.1 22.2 + - - +
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Residues in contact with LEU 329 (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 5.3 0.2 - - - -
310G PHE* 3.8 45.5 - - + +
313G GLY* 3.9 19.7 - - - +
314G LYS 4.1 0.4 - - - +
317G ALA* 4.9 2.7 - - + -
325G ALA* 2.9 21.4 + - + +
328G ILE* 1.4 71.9 - - - +
330G ARG* 1.4 56.5 + - - +
332G ALA* 3.7 3.2 - - + +
333G LEU* 3.2 19.4 + - - +
342G ILE* 3.3 18.1 - - + +
345G GLU* 3.9 29.8 - - + +
346G LEU* 3.8 21.3 - - + +
349G LEU* 3.8 27.1 - - + -
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Residues in contact with ARG 330 (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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326G ILE* 2.9 55.3 + - - +
327G PRO* 3.6 7.8 - - + +
329G LEU* 1.4 75.0 - - - +
331G ALA* 1.3 53.8 - - - +
333G LEU* 3.0 11.1 + - + +
334G LYS* 2.8 34.8 + - - +
346G LEU* 4.2 17.5 - - + +
350G VAL* 5.7 1.6 - - - +
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Residues in contact with ALA 331 (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* 4.6 16.1 - - + +
327G PRO 2.8 20.8 + - - +
328G ILE* 3.4 10.1 - - - +
330G ARG* 1.3 73.4 - - - +
332G ALA* 1.4 59.3 + - - +
334G LYS* 3.4 22.1 - - - +
335G LEU* 3.6 14.9 - - - +
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Residues in contact with ALA 332 (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 ILE* 3.5 29.6 - - + +
309G LEU* 4.0 18.8 - - + +
310G PHE* 4.3 11.0 - - - +
328G ILE 3.1 11.5 + - - +
329G LEU* 3.7 11.7 - - - +
330G ARG 3.2 0.2 - - - -
331G ALA* 1.4 72.8 - - - +
333G LEU* 1.4 64.4 + - - +
334G LYS 3.3 0.4 - - - -
335G LEU* 3.2 15.6 + - - +
336G GLU 3.4 8.0 + - - -
342G ILE* 3.8 12.2 - - + +
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Residues in contact with LEU 333 (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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329G LEU 3.2 11.4 + - - +
330G ARG* 3.0 14.1 + - + +
332G ALA* 1.4 74.9 - - - +
334G LYS* 1.3 58.9 + - - +
336G GLU 3.0 20.0 - - - +
337G PRO* 2.9 52.3 - - + +
339G ASN 4.1 1.3 - - - +
342G ILE* 3.8 23.7 - - + +
343G HIS* 3.7 32.3 - - + +
346G LEU* 3.9 18.4 - - + -
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Residues in contact with LYS 334 (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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330G ARG 2.8 11.7 + - - +
331G ALA* 3.4 18.6 - - - +
332G ALA 3.3 0.2 - - - -
333G LEU* 1.3 76.3 - - - +
335G LEU* 1.4 59.5 + - + +
337G PRO* 4.2 10.5 - - - +
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Residues in contact with LEU 335 (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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304G ASP* 3.6 42.8 - - + +
306G ILE* 4.3 18.4 - - + -
309G LEU* 3.9 19.3 - - + -
331G ALA 3.6 16.6 - - - +
332G ALA 3.2 6.7 + - - +
333G LEU 3.2 0.8 - - - -
334G LYS* 1.4 78.4 - - + +
336G GLU* 1.4 65.4 + - + +
337G PRO* 4.0 3.6 - - - +
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Residues in contact with GLU 336 (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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702B ASP* 3.8 16.1 - - - +
703B THR* 2.7 46.7 + - - -
306G ILE* 3.6 23.4 - - + +
332G ALA 3.4 2.6 + - - -
333G LEU* 3.0 17.8 + - - +
335G LEU* 1.4 82.0 - - - +
337G PRO* 1.4 66.6 - - - +
338G SER* 3.3 4.5 + - - -
339G ASN* 3.2 29.5 + - + +
342G ILE* 4.2 0.3 - - - +
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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