Contacts of the helix formed by residues 321 - 340 (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 ASP 321 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ARG 5.6 0.2 - - - +
60A ASN* 5.1 3.2 - - - +
61A LEU* 4.2 26.7 + - + +
304M VAL* 3.4 17.5 - - + +
319M PHE* 3.9 9.0 + - + -
320M ILE* 1.3 70.2 - - - +
322M PRO* 1.3 64.5 - - + +
323M GLN* 3.4 18.5 - - - +
324M ASN* 2.5 65.5 + - - +
325M GLU* 2.8 14.0 + - - +
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Residues in contact with PRO 322 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU* 4.4 2.7 - - + +
59A ARG* 3.4 44.2 - - - +
60A ASN* 3.1 25.1 - - - +
321M ASP* 1.3 86.9 - - + +
323M GLN* 1.3 59.0 + - - -
324M ASN 3.2 0.2 - - - -
325M GLU* 3.3 18.2 + - + +
326M ASP* 3.2 28.3 + - - +
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Residues in contact with GLN 323 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A HIS* 3.3 43.6 - - - +
44A PRO* 4.1 11.0 + - + +
52A LEU* 6.0 5.0 - - + +
60A ASN* 4.5 8.1 + - - +
187M PRO* 4.5 8.0 - - - +
321M ASP* 2.9 17.8 + - - +
322M PRO* 1.3 79.3 - - - +
324M ASN* 1.3 62.6 + - - +
326M ASP* 3.3 13.1 + - - +
327M LYS* 3.3 32.3 + - + +
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Residues in contact with ASN 324 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301M ARG 4.9 0.9 - - - +
302M PHE* 3.1 35.6 + - - +
303M THR* 3.4 23.3 + - - +
304M VAL* 3.7 4.4 - - - +
319M PHE 4.2 0.2 + - - -
320M ILE* 3.8 9.4 - - + -
321M ASP* 2.5 38.7 + - - +
323M GLN* 1.3 71.7 - - - +
325M GLU* 1.3 54.7 + - - +
326M ASP 3.1 1.6 - - - -
327M LYS* 3.5 18.8 - - - +
328M ILE* 2.7 39.9 + - - +
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Residues in contact with GLU 325 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG* 5.7 0.4 + - - -
272M TYR* 5.3 8.4 - - + -
275M ARG* 3.6 27.4 - - - +
320M ILE* 3.2 26.2 - - - +
321M ASP 2.8 34.6 + - - +
322M PRO* 3.3 16.9 + - + +
324M ASN* 1.3 76.0 - - - +
326M ASP* 1.3 61.0 + - - +
328M ILE* 3.3 20.6 - - + +
329M LEU* 3.3 27.7 - - - +
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Residues in contact with ASP 326 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 3.5 33.5 - - + +
42A GLY 4.2 5.2 - - - +
43A HIS* 3.9 19.2 - - - +
187M PRO* 4.5 8.9 - - + +
322M PRO* 3.2 16.4 + - - +
323M GLN* 3.5 16.0 - - - +
324M ASN 3.1 0.8 - - - -
325M GLU* 1.3 81.6 - - - +
327M LYS* 1.3 59.4 + - - +
328M ILE 3.5 0.2 - - - -
329M LEU* 4.0 16.5 + - - +
330M CYS* 3.7 13.2 - - - -
359M LYS* 5.9 2.3 - - - +
363M LEU* 4.3 8.6 - - - +
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Residues in contact with LYS 327 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186M ARG 4.7 5.2 - - - -
187M PRO* 3.6 30.6 + - + +
188M THR 6.2 0.2 - - - -
189M PRO* 5.9 4.4 - - - +
301M ARG 3.8 19.3 + - - -
302M PHE* 3.9 27.8 - - + -
323M GLN* 3.3 23.7 + - + +
324M ASN* 2.9 24.9 + - - +
326M ASP* 1.3 77.5 - - - +
328M ILE* 1.3 62.0 + - - +
329M LEU 3.3 1.8 - - - -
330M CYS* 3.4 24.2 + - - +
331M TYR 4.4 0.9 + - - -
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Residues in contact with ILE 328 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271M VAL* 5.2 7.6 - - + +
272M TYR* 3.6 38.6 - - + -
275M ARG* 6.0 1.3 - - + -
298M ILE* 6.2 0.2 - - + -
302M PHE* 4.2 24.2 - - + +
320M ILE* 4.8 7.4 - - + -
324M ASN* 2.7 25.3 + - + +
325M GLU* 3.3 33.2 - - + +
327M LYS* 1.3 70.1 - - - +
329M LEU* 1.3 61.9 + - + +
330M CYS 3.0 6.3 + - - -
331M TYR* 3.0 57.8 - - + +
332M ILE* 3.3 4.4 - - - +
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Residues in contact with LEU 329 (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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272M TYR* 4.0 24.7 - - + -
325M GLU 3.3 19.5 + - - +
326M ASP* 4.2 11.7 - - - +
327M LYS 3.3 0.6 - - - -
328M ILE* 1.3 76.4 - - - +
330M CYS* 1.3 60.2 + - - +
332M ILE* 3.6 20.3 - - + +
333M LEU* 3.4 13.9 + - - +
353M LEU* 4.6 5.4 - - + -
355M LEU* 3.7 36.3 - - + -
359M LYS* 5.1 13.0 - - + -
363M LEU* 3.4 35.3 - - + +
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Residues in contact with CYS 330 (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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187M PRO* 3.2 33.2 - - - -
188M THR* 3.9 7.9 - - - -
189M PRO* 3.9 21.5 - - + -
302M PHE* 6.0 0.7 - - + -
326M ASP 3.7 13.5 - - - -
327M LYS 3.4 14.8 - - - +
328M ILE 3.0 1.0 - - - -
329M LEU* 1.3 75.8 - - - +
331M TYR* 1.3 62.4 + - - +
332M ILE 3.1 1.3 - - - -
333M LEU 3.3 2.6 + - - -
334M ALA* 3.0 32.3 + - - +
363M LEU* 4.3 6.5 - - - -
366M VAL* 5.7 1.3 - - - -
367M LEU* 4.0 17.1 - - + +
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Residues in contact with TYR 331 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189M PRO* 5.9 0.4 - - - +
207M ILE* 4.2 16.4 - - + -
264M TYR* 5.4 8.3 - + + -
265M LEU* 5.7 0.7 - - - +
268M LEU* 3.4 39.6 - - + +
269M LEU* 5.5 0.2 - - - -
271M VAL* 3.3 26.4 - - + +
272M TYR* 5.1 2.6 + - + +
298M ILE* 5.4 5.3 - - + +
302M PHE* 4.1 33.7 - + + -
327M LYS 4.5 0.2 - - - -
328M ILE* 3.0 48.8 - - + +
330M CYS* 1.3 75.8 - - - +
332M ILE* 1.3 80.0 + - + +
334M ALA* 4.0 0.7 - - - -
335M ILE* 3.3 43.8 + - + +
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Residues in contact with ILE 332 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265M LEU* 5.9 1.1 - - + -
268M LEU* 3.5 28.3 - - + -
269M LEU* 4.9 11.2 - - + -
272M TYR* 5.4 7.9 - - + -
328M ILE 3.3 17.9 - - - +
329M LEU* 3.6 23.3 - - + +
330M CYS 3.1 0.4 - - - -
331M TYR* 1.3 86.7 - - + +
333M LEU* 1.3 65.5 + - + +
334M ALA 3.7 0.2 + - - -
336M ILE* 3.2 33.7 + - + +
353M LEU* 3.6 44.6 - - + -
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Residues in contact with LEU 333 (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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329M LEU 3.4 11.8 + - - +
330M CYS 3.3 2.6 + - - -
332M ILE* 1.3 81.5 - - + +
334M ALA* 1.3 57.9 + - - +
336M ILE* 4.7 4.2 - - + +
337M MET* 3.4 21.1 - - - +
344M VAL* 4.9 3.3 - - + +
349M LEU* 4.1 25.6 - - + -
360M VAL* 3.7 22.7 - - + +
363M LEU* 3.7 22.4 - - + -
364M PHE* 3.5 53.2 - - + +
367M LEU* 3.9 14.7 - - + +
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Residues in contact with ALA 334 (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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202M TYR* 4.6 30.5 - - + -
207M ILE* 5.3 0.4 - - + -
330M CYS 3.0 17.7 + - - +
331M TYR* 4.7 3.1 - - - -
333M LEU* 1.3 78.6 - - - +
335M ILE* 1.3 64.5 + - + +
336M ILE 3.6 0.2 - - - -
337M MET* 3.9 16.8 - - - +
338M HIS* 4.4 3.8 + - - +
342M PHE* 5.6 1.4 - - - -
367M LEU* 4.4 12.6 - - + -
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Residues in contact with ILE 335 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207M ILE* 3.7 46.2 - - + -
261M LEU* 3.8 31.2 - - + -
264M TYR* 4.5 3.4 - - + -
265M LEU* 3.6 24.2 - - + -
268M LEU* 3.7 22.2 - - + -
331M TYR* 3.3 21.8 + - + +
334M ALA* 1.3 77.5 - - - +
336M ILE* 1.3 67.9 + - + +
337M MET 3.1 1.8 - - - -
338M HIS* 3.1 14.8 + - + +
339M LEU* 3.2 15.9 + - + +
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Residues in contact with ILE 336 (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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246M LYS* 4.4 20.9 - - - +
265M LEU* 5.1 12.1 - - + -
331M TYR 5.5 0.2 - - - +
332M ILE* 3.2 28.9 + - + +
333M LEU* 5.2 3.4 - - + -
334M ALA 4.4 0.2 - - - +
335M ILE* 1.3 78.6 - - + +
337M MET* 1.3 59.8 + - - +
339M LEU* 3.0 24.8 + - + +
340M ASP* 2.8 37.2 + - - +
344M VAL* 4.2 13.9 - - + -
349M LEU* 3.7 28.0 - - + -
352M GLU* 4.2 8.1 - - - +
353M LEU* 5.2 1.8 - - + -
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Residues in contact with MET 337 (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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333M LEU 3.4 22.4 + - - +
334M ALA* 3.9 12.1 - - - +
335M ILE 3.1 0.2 - - - -
336M ILE* 1.3 77.2 - - - +
338M HIS* 1.3 60.8 + - - +
340M ASP* 2.9 7.0 - - - +
342M PHE* 2.5 84.7 + - + +
344M VAL* 2.8 35.0 - - + -
364M PHE* 4.5 11.0 - - + -
369M ALA* 5.9 0.2 - - + -
395M ALA* 4.9 0.7 - - + +
396M THR* 4.5 11.4 - - - +
397M MET* 4.4 21.1 - - + -
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Residues in contact with HIS 338 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199M GLU* 3.7 38.9 + - + +
204M ILE* 6.0 5.4 - - + -
257M THR* 3.9 17.3 + - - -
258M LYS* 3.3 58.9 + - + +
261M LEU* 5.1 12.3 - - + -
334M ALA 4.4 3.0 + - - +
335M ILE* 3.1 12.9 + - - +
337M MET* 1.3 79.1 - - - +
339M LEU* 1.3 64.0 + - + +
341M ASN* 3.9 9.8 + - - +
342M PHE* 3.8 15.2 - - + -
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Residues in contact with LEU 339 (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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246M LYS* 3.7 40.4 - - + +
250M LEU* 6.0 0.2 - - + -
258M LYS* 3.5 32.1 - - + +
261M LEU* 5.4 1.8 - - + -
262M LEU* 4.6 19.3 - - + +
265M LEU* 4.3 25.1 - - + -
335M ILE* 3.3 16.8 - - + +
336M ILE* 3.0 22.3 + - + +
338M HIS* 1.3 84.6 - - + +
340M ASP* 1.3 57.9 + - + +
341M ASN* 3.3 9.1 + - - +
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Residues in contact with ASP 340 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245M LYS* 4.9 14.0 + - - +
246M LYS* 5.0 5.0 + - + +
336M ILE* 2.8 28.2 + - + +
337M MET* 2.9 13.0 - - - +
339M LEU* 1.3 74.6 - - + +
341M ASN* 1.3 66.3 + - - +
342M PHE 3.4 3.8 + - - -
343M ILE* 3.0 40.9 + - + +
344M VAL* 3.3 21.4 - - - +
349M LEU* 5.6 1.0 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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