Contacts of the helix formed by residues 340 - 357 (chain B) in PDB entry 4MQP
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 340 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B GLN* 1.3 73.5 - - - +
341B TRP* 1.3 59.7 + - - +
342B ARG* 3.6 8.5 + - - +
343B THR* 2.7 38.3 + - - +
344B ARG* 3.2 17.9 + - - +
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Residues in contact with TRP 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B GLY* 4.4 8.7 - - - -
264B GLY 3.8 20.6 - - - -
265B ALA 3.8 4.0 - - - -
266B LEU* 3.3 52.8 - - + +
336B LEU* 3.2 52.0 - - + +
337B LEU* 4.3 12.7 + - - +
339B GLN* 2.9 20.7 + - + -
340B ASP* 1.3 72.7 - - - +
342B ARG* 1.3 112.7 + - + +
344B ARG* 3.2 9.6 + - + +
345B ILE* 2.9 44.5 + - + +
412B TYR* 5.6 1.6 - - + -
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Residues in contact with ARG 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B GLY 3.8 23.2 + - - +
265B ALA* 4.4 7.5 - - - +
266B LEU* 5.5 0.4 - - - +
340B ASP* 3.2 7.0 + - - +
341B TRP* 1.3 121.2 - - + +
343B THR* 1.3 57.5 + - - +
345B ILE* 3.3 3.5 + - - +
346B THR* 2.9 37.9 + - - +
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Residues in contact with THR 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ASP* 2.7 35.7 + - + +
342B ARG* 1.3 75.2 - - - +
344B ARG* 1.3 64.8 + - - +
346B THR* 3.3 8.3 + - - -
347B GLU* 3.0 46.0 + - + +
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Residues in contact with ARG 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B GLN* 4.3 15.0 - - - +
340B ASP 3.2 13.0 + - - +
341B TRP* 3.2 13.7 + - - +
343B THR* 1.3 77.8 - - - +
345B ILE* 1.3 57.2 + - + +
347B GLU* 2.8 42.7 + - - +
348B LEU* 3.0 46.6 + - + +
412B TYR* 2.8 54.1 + - + +
413B ILE* 4.5 2.4 - - - +
414B CYS 3.0 24.2 + - - -
415B THR* 5.8 0.4 - - - -
416B PRO* 4.8 13.7 - - - +
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Residues in contact with ILE 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B GLY* 3.6 14.1 - - - +
264B GLY* 3.7 26.2 - - - -
341B TRP* 2.9 30.8 + - + +
342B ARG* 3.9 3.8 - - - +
344B ARG* 1.3 74.4 - - + +
346B THR* 1.3 60.5 + - - +
348B LEU* 3.2 9.8 + - + +
349B ALA* 2.8 29.1 + - - +
372B GLY* 3.8 3.1 - - - -
373B ALA* 3.6 26.2 - - + +
412B TYR* 3.6 52.7 - - + -
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Residues in contact with THR 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ARG* 2.9 26.1 + - - +
343B THR* 3.3 8.9 + - - -
345B ILE* 1.3 77.3 - - - +
347B GLU* 1.3 57.8 + - + +
349B ALA* 3.5 6.9 + - + +
350B ALA* 3.0 28.9 + - + +
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Residues in contact with GLU 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B THR* 3.0 39.5 + - + +
344B ARG* 2.8 41.6 + - - +
346B THR* 1.3 75.0 - - + +
348B LEU* 1.3 59.6 + - - +
350B ALA* 3.3 7.1 + - - +
351B GLY* 3.0 25.1 + - - -
416B PRO* 5.8 2.1 - - - +
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Residues in contact with LEU 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B ARG* 3.0 38.0 + - - +
345B ILE* 3.6 22.7 - - + +
347B GLU* 1.3 72.7 - - - +
349B ALA* 1.3 61.0 + - - +
351B GLY* 3.2 2.6 + - - -
352B LEU* 2.9 37.9 + - + +
373B ALA* 4.1 16.2 - - + -
410B PRO* 5.0 2.2 - - + +
411B PRO 4.2 3.4 - - - +
412B TYR* 3.6 35.4 - - + +
414B CYS* 3.8 9.6 - - + +
419B ILE* 3.6 36.9 - - + +
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Residues in contact with ALA 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B ILE 2.8 19.0 + - - +
346B THR* 3.7 7.6 - - + +
348B LEU* 1.3 73.1 - - - +
350B ALA* 1.3 57.6 + - - +
352B LEU* 3.4 2.8 + - - +
353B THR* 2.9 35.5 + - - +
370B VAL* 3.7 9.0 - - + +
372B GLY* 3.2 35.3 + - - +
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Residues in contact with ALA 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346B THR* 3.0 19.3 + - + +
347B GLU* 3.7 7.4 - - - +
348B LEU 3.2 0.2 - - - -
349B ALA* 1.3 76.1 - - - +
351B GLY* 1.3 59.2 + - - +
353B THR* 3.4 6.4 + - - +
354B ALA* 2.9 31.9 + - - +
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Residues in contact with GLY 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B GLU 3.0 14.7 + - - -
348B LEU 3.2 3.6 + - - -
350B ALA* 1.3 73.8 - - - +
352B LEU* 1.3 58.5 + - - +
354B ALA* 3.9 4.2 - - - +
355B GLY* 3.0 27.2 + - - -
419B ILE* 3.6 20.2 - - - +
420B THR* 5.6 0.9 + - - -
423B THR* 4.1 0.7 + - - +
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Residues in contact with LEU 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LEU* 2.9 25.2 + - + +
349B ALA 3.7 3.8 - - - +
351B GLY* 1.3 71.5 - - - +
353B THR* 1.3 57.2 + - - +
355B GLY 3.4 0.5 + - - -
356B LEU* 2.9 39.4 + - + +
370B VAL* 4.1 13.0 - - + -
372B GLY 3.9 7.9 - - - +
373B ALA* 3.9 11.2 - - + +
374B ILE 3.8 34.3 - - - +
375B GLY* 4.0 8.3 - - - +
408B ALA* 5.0 7.6 - - + -
410B PRO* 4.3 22.7 - - + -
419B ILE* 4.0 12.3 - - + -
422B ILE* 5.1 2.9 - - + -
423B THR* 3.9 20.2 - - + -
426B MET* 5.4 0.7 - - - -
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Residues in contact with THR 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B ALA 2.9 23.0 + - - -
350B ALA* 3.6 8.0 - - - -
352B LEU* 1.3 77.3 - - - +
354B ALA* 1.3 63.5 + - - +
356B LEU* 4.0 1.7 - - - +
357B ASP* 3.2 24.3 + - + +
360B ARG* 5.7 5.8 + - - +
368B VAL* 5.7 0.7 - - - +
370B VAL* 3.7 23.3 - - + +
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Residues in contact with ALA 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B ALA 2.9 17.2 + - - +
351B GLY* 4.1 4.5 - - - +
353B THR* 1.3 78.5 - - - +
355B GLY* 1.3 62.4 + - - +
356B LEU 3.5 0.2 + - - -
357B ASP* 3.6 14.5 + - - +
358B THR* 4.9 4.2 + - - +
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Residues in contact with GLY 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B GLY 3.0 13.9 + - - -
354B ALA* 1.3 79.1 - - - +
356B LEU* 1.3 57.3 + - - +
357B ASP 3.4 0.4 + - - -
358B THR* 4.3 6.4 + - - +
420B THR* 5.9 0.7 - - - -
423B THR* 3.3 34.1 + - - +
424B SER* 5.6 0.3 - - - -
427B VAL* 3.7 13.5 - - - +
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Residues in contact with LEU 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B LEU* 2.9 25.0 + - + +
353B THR* 4.4 1.6 - - - +
355B GLY* 1.3 74.5 - - - +
357B ASP* 1.3 66.5 + - - +
358B THR 3.2 3.1 - - - -
359B ALA* 3.0 20.2 + - - +
360B ARG 4.0 0.2 + - - -
368B VAL* 3.6 25.2 - - + +
370B VAL* 4.2 8.7 - - + -
375B GLY* 4.0 28.0 - - - -
376B VAL 4.1 10.1 - - - +
377B ILE* 3.9 17.5 - - + -
423B THR* 3.8 25.4 - - + +
426B MET* 3.8 29.6 - - + -
427B VAL* 4.4 3.4 - - + -
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Residues in contact with ASP 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B THR* 3.2 17.5 + - + +
354B ALA* 3.8 11.9 - - - +
355B GLY 3.4 1.6 - - - -
356B LEU* 1.3 77.1 - - - +
358B THR* 1.3 62.6 + - + +
359B ALA 3.2 0.2 - - - -
360B ARG* 3.1 52.9 + - - +
361B ALA 4.6 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