Contacts of the helix formed by residues 321 - 334 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316F LEU* 2.8 35.4 + - + +
319F GLN* 4.8 12.6 - - + +
320F GLY* 1.4 74.3 - - - +
322F TYR* 1.3 58.1 + - - +
323F SER* 3.3 11.3 + - - -
324F GLU* 3.4 29.6 + - + +
325F ALA* 3.0 27.4 + - - +
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Residues in contact with TYR 322 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317F ALA* 3.3 27.2 + - + -
320F GLY* 3.1 21.3 + - - -
321F GLU* 1.3 73.6 - - - +
323F SER* 1.3 63.4 + - - +
325F ALA* 3.9 0.3 - - - +
326F ILE* 3.2 29.6 + - - +
349F LEU* 3.5 31.7 - - + +
352F LYS* 4.1 27.5 + - + +
353F HIS* 3.4 59.9 + + + +
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Residues in contact with SER 323 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321F GLU* 4.4 13.2 + - - -
322F TYR* 1.3 77.2 - - - +
324F GLU* 1.3 64.4 + - - +
326F ILE* 4.0 6.1 - - - +
327F PRO* 3.4 19.1 - - - +
353F HIS* 4.4 8.1 + - - -
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Residues in contact with GLU 324 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316F LEU* 3.9 25.8 - - + +
321F GLU* 3.4 31.7 + - + +
322F TYR 3.3 0.2 - - - -
323F SER* 1.3 84.9 + - - +
325F ALA* 1.3 63.1 + - - +
326F ILE 3.6 0.2 - - - -
327F PRO* 3.5 12.3 - - - +
328F ILE* 3.4 23.4 - - + +
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Residues in contact with ALA 325 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313F GLY* 3.5 26.6 - - - +
316F LEU* 3.9 7.2 - - + +
317F ALA* 3.8 14.1 - - + +
321F GLU 3.0 17.7 + - - +
322F TYR 3.4 3.8 + - - +
324F GLU* 1.3 76.1 - - - +
326F ILE* 1.4 59.0 + - - +
328F ILE* 3.4 3.2 + - - +
329F LEU* 2.9 33.5 + - + +
349F LEU* 4.1 11.4 - - + -
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Residues in contact with ILE 326 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322F TYR 3.2 17.9 + - - +
323F SER* 4.0 6.7 - - - +
325F ALA* 1.4 72.7 - - - +
327F PRO* 1.4 69.9 - - + +
329F LEU* 3.4 1.0 + - - +
330F ARG* 2.9 69.2 + - - +
346F LEU* 3.9 10.1 - - + -
349F LEU* 4.0 13.0 - - + +
350F VAL* 3.8 28.7 - - + -
353F HIS* 6.0 8.1 - - + -
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Residues in contact with PRO 327 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323F SER 3.4 16.2 - - - +
324F GLU* 3.5 13.7 - - - +
326F ILE* 1.4 100.2 - - + +
328F ILE* 1.3 54.8 + - + +
330F ARG* 3.3 9.8 + - + +
331F ALA* 2.8 34.5 + - - +
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Residues in contact with ILE 328 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299F LEU* 6.4 0.2 - - + -
309F LEU* 3.2 43.6 - - + +
312F LYS* 4.1 21.1 - - + +
313F GLY* 3.8 12.3 - - - +
316F LEU* 3.9 20.4 - - + -
324F GLU* 3.4 19.5 - - + +
325F ALA 3.4 7.1 + - - +
326F ILE 3.3 0.2 - - - -
327F PRO* 1.3 78.2 - - + +
329F LEU* 1.3 64.8 + - - +
331F ALA* 3.2 9.2 + - - +
332F ALA* 3.1 21.7 + - - +
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Residues in contact with LEU 329 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310F PHE* 3.9 44.2 - - + +
313F GLY* 3.9 20.6 - - - +
317F ALA* 5.0 2.9 - - + -
325F ALA* 2.9 19.1 + - + +
328F ILE* 1.3 74.5 - - - +
330F ARG* 1.4 57.8 + - - +
332F ALA* 3.7 2.9 + - - +
333F LEU* 3.2 19.6 + - - +
342F ILE* 3.4 17.6 - - + +
345F GLU* 3.9 30.7 - - + +
346F LEU* 3.8 19.8 - - + +
349F LEU* 3.8 27.1 - - + -
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Residues in contact with ARG 330 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326F ILE* 2.9 54.9 + - - +
327F PRO* 3.6 8.5 - - + +
329F LEU* 1.4 75.0 - - - +
331F ALA* 1.4 53.8 + - - +
333F LEU* 3.0 10.8 + - + +
334F LYS* 2.8 34.7 + - - +
346F LEU* 4.2 17.7 - - + +
350F VAL* 5.7 1.2 - - - +
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Residues in contact with ALA 331 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309F LEU* 4.5 15.9 - - + +
327F PRO 2.8 17.0 + - - +
328F ILE* 3.2 10.3 + - - +
330F ARG* 1.4 76.1 - - - +
332F ALA* 1.4 58.3 + - - +
334F LYS* 3.4 19.5 + - - +
335F LEU* 3.6 14.7 - - - +
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Residues in contact with ALA 332 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306F ILE* 3.4 33.6 - - + +
309F LEU* 3.9 20.3 - - + +
310F PHE* 4.3 10.3 - - - +
328F ILE 3.1 11.7 + - - +
329F LEU* 3.7 11.0 - - - +
330F ARG 3.2 0.2 - - - -
331F ALA* 1.4 73.7 - - - +
333F LEU* 1.4 63.2 + - - +
334F LYS 3.3 0.2 - - - -
335F LEU* 3.4 16.5 + - - +
336F GLU 3.5 1.7 + - - -
342F ILE* 3.6 12.7 - - + +
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Residues in contact with LEU 333 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329F LEU 3.2 13.4 + - - +
330F ARG* 3.0 13.9 + - + +
332F ALA* 1.4 72.8 - - - +
334F LYS* 1.3 60.2 + - - +
335F LEU 3.1 0.4 - - - -
336F GLU 3.0 20.2 - - - +
337F PRO* 3.0 51.7 - - + +
339F ASN 4.1 0.9 - - - +
342F ILE* 3.8 23.3 - - + +
343F HIS* 3.7 33.2 - - + +
346F LEU* 3.9 19.1 - - + -
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Residues in contact with LYS 334 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330F ARG 2.8 12.7 + - - +
331F ALA* 3.4 16.2 - - - +
332F ALA 3.3 0.4 - - - -
333F LEU* 1.3 75.9 - - - +
335F LEU* 1.4 59.9 + - + +
337F PRO* 4.2 10.9 - - - +
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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