Contacts of the helix formed by residues 291 - 303 (chain M) in PDB entry 5M64
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 PRO 291 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215M PHE* 5.1 9.9 - - + +
235M PRO* 4.6 2.2 - - + -
263M TYR* 3.5 26.2 - - + +
267M LEU* 3.7 11.9 - - + -
289M SER 4.4 1.1 - - - +
290M PRO* 1.3 85.7 - - + +
292M GLU* 1.3 65.6 + - - +
293M ILE* 4.6 7.6 - - + +
294M LEU* 3.4 35.7 + - + +
295M VAL* 3.5 16.3 - - - +
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Residues in contact with GLU 292 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280M LYS* 4.5 11.1 + - - +
284M LEU* 6.2 5.8 - - + -
290M PRO* 3.3 6.1 + - - +
291M PRO* 1.3 72.1 - - - +
293M ILE* 1.3 68.6 + - - +
295M VAL* 3.6 4.3 + - - +
296M ASP* 3.1 41.1 + - - +
315M ASP* 4.4 17.8 - - - +
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Residues in contact with ILE 293 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211M LYS* 3.4 31.9 - - + +
212M GLU* 3.5 16.9 - - + +
215M PHE* 3.6 41.5 - - + -
291M PRO* 4.6 5.8 - - + -
292M GLU* 1.3 85.8 + - - +
294M LEU* 1.3 74.4 + - + +
296M ASP* 3.9 5.4 - - + +
297M GLY 3.4 15.9 + - - -
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Residues in contact with LEU 294 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208M ILE* 4.6 7.0 - - + -
212M GLU* 3.5 49.6 - - + +
215M PHE* 5.3 3.6 - - + +
216M ILE* 4.6 13.5 - - + -
263M TYR* 4.4 15.5 - - + -
264M TYR* 4.8 14.9 - - + -
267M LEU* 3.9 25.1 - - + -
291M PRO* 3.4 36.1 + - + +
292M GLU 3.3 0.6 - - - -
293M ILE* 1.3 84.2 - - + +
295M VAL* 1.3 62.4 + - - +
297M GLY 3.6 4.0 + - - -
298M ILE* 3.3 19.2 + - - +
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Residues in contact with VAL 295 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267M LEU* 3.7 26.2 - - + +
271M VAL* 6.3 3.1 - - + -
280M LYS* 3.6 34.1 - - + +
283M LEU* 4.6 11.9 - - + -
287M LEU* 4.8 7.2 - - + -
290M PRO* 4.4 14.1 - - + -
291M PRO 3.5 17.3 + - - +
292M GLU* 4.4 1.6 - - - +
294M LEU* 1.3 74.0 - - - +
296M ASP* 1.3 65.2 + - - +
298M ILE* 3.3 18.8 + - + +
299M LEU* 3.3 22.7 + - + +
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Residues in contact with ASP 296 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280M LYS* 4.2 8.9 - - - +
292M GLU* 3.1 39.1 + - - +
293M ILE* 3.9 7.9 - - + +
294M LEU 3.3 0.2 - - - -
295M VAL* 1.3 77.4 - - - +
297M GLY* 1.3 62.7 + - - +
299M LEU* 3.3 14.0 + - - +
300M SER* 3.3 17.8 + - - -
315M ASP* 6.0 0.4 - - - -
316M ARG* 4.3 27.4 + - - +
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Residues in contact with GLY 297 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212M GLU* 3.2 22.9 + - - -
293M ILE 3.4 8.5 + - - -
294M LEU 3.6 1.3 + - - -
295M VAL 3.3 0.2 - - - -
296M ASP* 1.3 77.0 - - - +
298M ILE* 1.3 64.3 + - - +
300M SER* 3.5 11.7 + - - -
301M ARG* 3.2 37.5 + - - -
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Residues in contact with ILE 298 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212M GLU* 5.7 0.9 - - - +
264M TYR* 3.3 27.8 - - + +
267M LEU* 3.7 33.7 - - + +
268M LEU* 5.4 2.7 - - - -
271M VAL* 4.9 24.0 - - + -
294M LEU 3.3 12.5 + - - +
295M VAL* 3.6 13.5 - - + +
296M ASP 3.2 0.8 - - - -
297M GLY* 1.3 75.6 - - - +
299M LEU* 1.3 61.0 + - + +
301M ARG* 5.5 2.0 - - - +
302M PHE* 2.7 67.9 + - + +
303M THR* 4.5 1.7 - - + +
331M TYR* 5.4 7.0 - - + -
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Residues in contact with LEU 299 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271M VAL* 5.8 4.0 - - + -
280M LYS* 3.6 25.4 - - + +
283M LEU* 5.6 1.3 - - + -
295M VAL* 3.3 24.9 - - + +
296M ASP* 3.3 10.2 + - - +
298M ILE* 1.3 83.5 - - + +
300M SER* 1.3 61.1 + - - +
301M ARG 3.1 1.8 + - - -
303M THR* 2.6 48.6 + - + +
305M ILE* 3.7 7.6 - - + +
316M ARG* 3.3 47.8 - - + +
318M TYR* 3.5 27.4 - - + -
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Residues in contact with SER 300 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296M ASP* 3.3 14.0 + - - -
297M GLY* 3.5 11.1 + - - -
298M ILE 3.3 0.8 - - - -
299M LEU* 1.3 76.3 - - - +
301M ARG* 1.3 69.2 + - - +
303M THR 5.3 1.8 - - - -
305M ILE* 4.5 10.2 - - - +
316M ARG* 4.1 20.0 + - - +
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Residues in contact with ARG 301 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207M ILE 5.1 4.6 + - - -
209M PRO* 4.0 20.7 - - - +
212M GLU* 3.6 21.6 + - - -
297M GLY* 3.2 37.9 + - - +
298M ILE* 3.2 4.6 + - - +
299M LEU 3.1 0.4 - - - -
300M SER* 1.3 89.5 - - - +
302M PHE* 1.3 85.1 + - + +
303M THR 3.9 1.8 - - - -
324M ASN* 4.9 1.3 - - - +
327M LYS* 3.8 14.4 + - - -
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Residues in contact with PHE 302 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189M PRO* 5.8 8.7 - - + -
207M ILE 5.8 5.6 - - - -
264M TYR* 5.5 3.6 - - - -
298M ILE* 2.7 57.0 + - + +
301M ARG* 1.3 100.4 - - + +
303M THR* 1.3 66.6 + - + +
320M ILE* 4.4 4.0 - - - +
324M ASN* 3.1 31.8 - - - +
327M LYS* 3.9 39.7 - - + -
328M ILE* 4.2 15.7 - - + +
330M CYS* 6.0 0.2 - - + -
331M TYR* 4.1 25.8 - + + -
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Residues in contact with THR 303 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271M VAL* 5.3 7.0 - - + -
298M ILE* 4.5 2.7 - - + +
299M LEU* 2.6 46.7 + - + +
300M SER 5.3 1.4 - - - -
301M ARG 5.2 0.9 - - - -
302M PHE* 1.3 87.0 + - + +
304M VAL* 1.3 61.0 + - - +
305M ILE* 3.8 7.6 + - - +
318M TYR* 3.3 39.1 - - + +
319M PHE 3.3 9.9 - - - -
320M ILE* 4.0 11.0 - - + -
324M ASN* 3.4 8.6 + - - +
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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