Contacts of the helix formed by residues 305 - 320 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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709C ASP* 5.6 1.0 + - - -
272E VAL* 4.5 2.2 - - - +
276E ASN* 3.0 31.8 + - - +
298E VAL* 3.8 9.1 - - + +
299E LEU* 3.8 0.2 - - - +
302E GLN* 3.1 43.9 + - + +
303E PRO 3.5 1.6 - - - -
304E ASP* 1.4 73.2 - - - +
306E ILE* 1.4 56.8 + - - +
307E LYS* 3.2 8.1 + - - +
308E ALA* 3.0 24.0 + - + +
309E LEU* 3.0 30.1 + - - +
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Residues in contact with ILE 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704C GLU* 4.7 4.9 - - - +
705C MET* 3.9 15.7 - - + -
304E ASP 3.3 6.1 + - - +
305E ASN* 1.4 71.4 + - - +
307E LYS* 1.4 67.2 + - + +
309E LEU* 3.4 8.6 + - - +
310E PHE* 2.9 28.9 + - - +
332E ALA* 3.6 33.9 - - + +
335E LEU* 4.3 11.9 - - + -
336E GLU* 3.6 46.4 - - + +
342E ILE* 3.7 11.2 - - + -
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Residues in contact with LYS 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704C GLU* 3.3 26.5 - - - +
705C MET* 4.2 19.7 - - - -
707C GLU* 3.1 33.3 + - - +
708C VAL 4.2 0.4 - - - +
709C ASP* 2.8 40.5 + - - +
276E ASN* 4.0 5.2 - - - +
305E ASN* 3.2 9.0 + - - +
306E ILE* 1.4 83.6 - - + +
308E ALA* 1.3 56.7 + - - +
310E PHE* 3.8 0.9 - - - +
311E ARG* 2.9 60.5 + - - +
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Residues in contact with ALA 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276E ASN* 3.6 9.8 + - - +
295E CYS* 3.7 11.0 - - - +
298E VAL* 3.7 34.1 - - + -
299E LEU* 3.8 22.0 - - + +
305E ASN* 3.0 10.7 + - - +
307E LYS* 1.3 75.6 - - - +
309E LEU* 1.4 57.8 + - - +
311E ARG* 4.5 3.8 - - - -
312E LYS* 3.0 30.1 + - - +
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Residues in contact with LEU 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299E LEU* 3.7 24.2 - - + -
303E PRO 3.9 17.5 - - - +
304E ASP* 4.3 0.9 - - - +
305E ASN 3.0 22.7 + - - +
306E ILE 3.7 3.8 - - - +
308E ALA* 1.4 72.9 - - - +
310E PHE* 1.3 60.2 + - - +
312E LYS 3.2 1.4 + - - -
313E GLY* 2.9 25.3 + - - -
328E ILE* 3.2 34.9 - - + +
331E ALA* 4.5 11.7 - - + +
332E ALA* 4.0 20.4 - - + +
335E LEU* 3.8 27.6 - - + -
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Residues in contact with PHE 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705C MET* 3.6 38.6 - - + -
706C GLU* 5.3 2.0 - - - -
283E LEU* 5.8 0.9 - - + -
306E ILE 2.9 17.9 + - - +
307E LYS 3.8 2.0 - - - +
309E LEU* 1.3 76.6 - - - +
311E ARG* 1.4 68.6 + - + +
313E GLY* 3.4 1.2 + - - -
314E LYS* 2.8 61.1 + - + +
329E LEU* 3.8 17.0 - - + +
332E ALA* 4.3 7.7 - - + +
341E THR* 3.7 27.8 - - + -
342E ILE* 4.0 18.6 - - + -
345E GLU* 3.7 33.2 - - + -
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Residues in contact with ARG 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705C MET* 2.9 23.0 + - - +
706C GLU 4.5 0.8 - - - -
707C GLU 2.8 29.1 + - - -
708C VAL* 4.7 0.8 - - - +
709C ASP* 5.5 0.6 + - - -
276E ASN* 3.0 45.5 + - - +
277E ASN* 4.4 2.8 + - - +
279E ALA* 4.6 3.6 - - + -
280E ALA* 3.5 34.8 - - - +
283E LEU* 4.2 20.2 - - + +
295E CYS* 3.7 17.0 - - - -
307E LYS* 2.9 35.4 + - - +
310E PHE* 1.4 80.9 - - + +
312E LYS* 1.3 65.2 + - - +
314E LYS* 3.6 5.1 + - - +
315E VAL* 3.1 30.5 + - + +
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Residues in contact with LYS 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292E LEU* 3.8 25.4 - - + +
295E CYS* 3.6 17.2 - - + -
296E SER* 3.1 28.0 + - - +
299E LEU* 4.0 19.8 - - + +
308E ALA 3.0 20.0 + - - +
309E LEU 3.2 4.0 + - - +
311E ARG* 1.3 75.8 - - - +
313E GLY* 1.3 58.4 + - - +
315E VAL* 3.4 5.8 + - - +
316E LEU* 3.0 42.3 + - + +
328E ILE* 4.1 24.4 - - + +
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Residues in contact with GLY 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309E LEU 2.9 14.3 + - - -
310E PHE 3.7 3.1 - - - -
312E LYS* 1.3 74.2 - - - +
314E LYS* 1.3 58.5 + - - +
316E LEU* 3.3 9.1 + - - +
317E ALA* 2.9 30.9 + - - +
325E ALA* 3.6 6.5 - - - +
328E ILE* 3.8 10.9 - - - +
329E LEU* 3.9 22.0 - - - -
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Residues in contact with LYS 314 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706C GLU* 3.6 21.8 + - - -
283E LEU* 4.0 20.5 - - + +
284E LYS* 4.6 7.6 - - - +
310E PHE* 2.8 45.6 + - + +
311E ARG* 3.9 6.5 - - - +
313E GLY* 1.3 71.4 - - - +
315E VAL* 1.4 56.7 + - - +
317E ALA* 3.5 2.4 + - - +
318E GLN* 3.0 54.0 + - - +
329E LEU* 4.1 1.4 - - - +
341E THR* 6.1 0.6 - - - +
345E GLU* 3.4 36.1 + - + +
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Residues in contact with VAL 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283E LEU* 3.8 23.3 - - + -
288E TYR* 3.6 41.5 - - + +
291E ALA* 4.0 23.8 - - + -
292E LEU* 3.7 17.3 - - + -
295E CYS* 5.5 0.7 - - - -
311E ARG* 3.1 22.6 + - + +
312E LYS* 3.7 6.1 - - - +
314E LYS* 1.4 73.8 - - - +
316E LEU* 1.3 59.6 + - - +
318E GLN* 3.3 3.0 + - - +
319E GLN* 3.0 36.7 + - - +
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Residues in contact with LEU 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292E LEU* 4.4 16.6 - - + -
312E LYS* 3.0 32.5 + - + +
313E GLY* 3.6 4.3 - - - +
315E VAL* 1.3 74.5 - - - +
317E ALA* 1.4 56.1 + - - +
319E GLN* 3.5 16.2 + - - +
320E GLY 3.3 3.8 + - - -
321E GLU* 2.9 44.5 + - + +
324E GLU* 3.9 34.5 - - + +
325E ALA* 3.7 12.8 - - + -
328E ILE* 3.4 33.2 - - + -
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Residues in contact with ALA 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313E GLY 2.9 17.3 + - - +
314E LYS* 3.6 8.5 - - - +
316E LEU* 1.4 74.5 - - - +
318E GLN* 1.3 59.8 - - + +
320E GLY* 3.2 13.3 + - - -
322E TYR* 3.4 23.8 + - + -
325E ALA* 3.7 7.6 - - + +
329E LEU* 4.9 3.4 - - + -
345E GLU* 4.5 10.5 - - - +
349E LEU* 4.1 24.5 - - + -
286G ASP* 5.1 3.3 - - - +
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Residues in contact with GLN 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283E LEU* 3.8 12.0 - - - +
286E ASP* 4.8 1.4 - - - +
288E TYR* 3.0 45.4 + - + +
314E LYS* 3.0 52.3 + - + +
315E VAL 3.3 4.0 + - - +
317E ALA* 1.3 76.9 - - + +
319E GLN* 1.3 60.2 + - - +
320E GLY* 3.6 0.3 + - - -
345E GLU* 4.9 2.7 + - - +
286G ASP* 5.3 10.2 - - - +
288G TYR* 4.6 17.2 + - - -
318G GLN 5.3 2.9 - - - +
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Residues in contact with GLN 319 (chain E).
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* 3.6 39.1 - - + +
289E ARG* 4.5 11.9 - - - +
292E LEU* 3.4 31.6 - - - +
315E VAL* 3.0 20.0 + - - +
316E LEU* 3.7 18.4 - - - +
317E ALA 3.2 0.2 - - - -
318E GLN* 1.3 76.1 - - - +
320E GLY* 1.3 59.1 + - - +
321E GLU* 3.5 12.4 - - + +
288G TYR* 6.3 1.1 - - - -
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Residues in contact with GLY 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317E ALA 3.2 14.4 + - - -
318E GLN 3.3 0.8 - - - -
319E GLN* 1.3 79.5 - - - +
321E GLU* 1.4 56.9 + - - +
322E TYR* 3.1 36.4 + - - -
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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