Contacts of the helix formed by residues 356 - 375 (chain B) in PDB entry 3LLM
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 THR 356 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354B PHE 4.2 5.8 - - - +
355B ALA* 1.3 77.4 - - - +
357B PRO* 1.3 73.7 - - - +
358B GLU* 3.5 12.9 + - - +
359B GLN* 3.0 47.2 + - - +
360B ILE* 2.9 22.9 + - - +
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Residues in contact with PRO 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B SER* 4.2 23.1 - - - +
355B ALA 4.3 0.2 - - - +
356B THR* 1.3 86.5 - - - +
358B GLU* 1.3 66.9 + - - +
360B ILE* 3.2 5.9 + - + +
361B SER* 2.7 38.9 + - - +
436B ALA* 3.9 21.9 - - + +
437B GLU* 6.2 2.5 - - + -
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Residues in contact with GLU 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B THR* 3.2 15.0 + - - +
357B PRO* 1.3 89.3 - - - +
359B GLN* 1.3 55.1 + - + +
361B SER* 3.2 6.0 + - - -
362B MSE 2.8 37.2 + - - +
433B ASP 5.9 0.4 - - - -
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Residues in contact with GLN 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B PHE 4.5 0.3 - - - +
355B ALA* 3.4 14.5 - - + +
356B THR* 3.0 48.9 + - - +
358B GLU* 1.3 78.0 - - + +
360B ILE* 1.3 59.4 + - - +
362B MSE 3.7 9.9 - - - +
363B ASP* 2.8 31.5 + - - +
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Residues in contact with ILE 360 (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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337B SER* 4.1 23.3 - - - +
352B LEU* 4.3 13.0 - - + -
355B ALA* 4.0 21.1 - - + -
356B THR 2.9 18.0 + - - +
357B PRO* 3.7 8.3 - - + +
359B GLN* 1.3 75.5 - - - +
361B SER* 1.3 64.4 + - - +
363B ASP* 3.4 6.3 + - - +
364B LEU* 3.1 40.7 + - + +
436B ALA* 4.4 11.7 - - + -
483B HIS* 3.9 42.0 - - + +
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Residues in contact with SER 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B PRO* 2.7 27.8 + - - +
358B GLU* 3.6 5.3 - - - -
360B ILE* 1.3 74.3 - - - +
362B MSE 1.3 62.3 + - - +
364B LEU* 3.3 3.5 + - - +
365B LYS* 3.1 23.3 + - - +
430B ILE 5.0 2.1 - - - +
433B ASP* 3.5 35.0 + - - -
434B ARG* 3.9 1.0 - - - -
435B ALA* 3.6 17.4 + - - +
436B ALA* 3.4 19.8 + - - +
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Residues in contact with MSE 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B GLU 2.8 18.6 + - - +
359B GLN* 3.7 8.1 - - - +
361B SER* 1.3 74.0 - - - +
363B ASP* 1.3 72.7 + - - +
365B LYS* 3.3 6.0 + - - +
366B ASN* 3.2 65.3 + - + +
433B ASP* 5.5 4.4 + - - +
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Residues in contact with ASP 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B GLN 2.8 22.7 + - - +
360B ILE* 3.6 7.6 - - - +
362B MSE 1.3 86.7 - - - +
364B LEU* 1.3 73.2 + - - +
366B ASN* 3.5 4.0 + - - +
367B GLU* 3.1 25.8 + - - +
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Residues in contact with LEU 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B ILE* 3.1 33.7 + - + +
361B SER 4.1 2.7 - - - +
362B MSE 3.2 0.2 - - - -
363B ASP* 1.3 89.3 - - - +
365B LYS* 1.3 65.2 + - - +
367B GLU* 3.3 12.6 + - + +
368B LEU* 3.3 21.7 + - - +
430B ILE* 4.3 12.3 - - + +
435B ALA* 4.3 11.4 - - + -
467B LYS* 5.9 1.8 - - - -
481B ARG* 3.7 32.8 - - - +
483B HIS* 4.5 9.6 - - + +
484B ALA* 3.9 26.2 - - + -
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Residues in contact with LYS 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B SER 3.1 15.3 + - - +
362B MSE 3.3 7.2 + - - +
364B LEU* 1.3 78.4 - - - +
366B ASN* 1.3 63.1 + - - +
368B LEU* 3.3 7.3 + - - +
369B MSE 3.3 24.1 + - + +
430B ILE* 3.9 23.2 - - + +
431B GLN* 2.9 43.6 + - - +
433B ASP* 3.1 30.7 + - - +
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Residues in contact with ASN 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B MSE 3.2 39.3 + - + +
363B ASP* 3.6 9.2 - - - +
365B LYS* 1.3 81.9 - - - +
367B GLU* 1.3 57.0 + - - +
369B MSE 3.3 18.4 + - - +
370B TYR* 3.0 27.9 + - - +
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Residues in contact with GLU 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B ASP* 3.1 19.9 + - - +
364B LEU* 3.3 15.5 + - + +
365B LYS 3.3 0.6 - - - -
366B ASN* 1.3 76.6 - - - +
368B LEU* 1.3 57.3 + - - +
370B TYR* 3.9 7.7 - - + +
371B GLN* 3.0 29.5 + - + +
467B LYS* 4.0 23.8 - - - +
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Residues in contact with LEU 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B LEU 3.3 12.3 + - - +
365B LYS 3.6 9.4 - - - +
366B ASN 3.2 0.4 - - - -
367B GLU* 1.3 74.4 - - - +
369B MSE 1.3 65.6 + - - +
371B GLN* 3.4 8.4 + - + +
372B LEU* 3.1 37.5 + - + +
378B LEU* 6.1 4.3 - - + -
427B ASP* 4.1 17.0 - - - +
430B ILE* 4.1 19.3 - - + -
431B GLN* 3.4 28.5 - - - +
461B ARG* 4.5 15.3 - - + +
463B GLU* 6.0 2.0 - - - +
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Residues in contact with MSE 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B LYS* 3.3 12.9 + - + +
366B ASN* 3.3 21.9 + - - +
368B LEU* 1.3 80.0 - - - +
370B TYR* 1.3 62.7 + - - +
372B LEU* 3.4 11.8 + - + +
373B GLU* 3.2 22.3 + - - +
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Residues in contact with TYR 370 (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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366B ASN 3.0 16.2 + - - +
367B GLU* 3.9 9.9 - - + +
369B MSE 1.3 73.9 - - - +
371B GLN* 1.3 68.8 + - - +
373B GLU* 3.0 19.8 + - + +
374B GLN* 3.1 43.8 + - + +
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Residues in contact with GLN 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B GLU* 3.0 20.8 + - + +
368B LEU* 3.4 8.7 + - + +
370B TYR* 1.3 81.1 - - - +
372B LEU* 1.3 56.9 + - - +
374B GLN* 5.0 1.3 - - - -
375B ASP* 3.0 36.5 + - + +
378B LEU* 4.1 16.6 - - + +
461B ARG 5.8 1.8 - - - +
462B GLY 6.1 0.7 - - - +
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Residues in contact with LEU 372 (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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368B LEU* 3.1 27.7 + - + +
369B MSE 3.5 12.1 - - + +
370B TYR 3.1 0.6 - - - -
371B GLN* 1.3 73.9 - - - +
373B GLU* 1.3 56.6 + - - +
374B GLN 3.1 9.0 + - - -
375B ASP 3.4 17.1 - - - +
376B HIS* 5.3 0.2 - - - -
378B LEU* 4.3 17.3 - - + -
379B GLN* 4.3 23.3 - - + +
382B LEU* 4.0 28.5 - - + -
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Residues in contact with GLU 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B MSE 3.2 12.5 + - - +
370B TYR* 3.0 9.6 + - + +
372B LEU* 1.3 76.9 - - - +
374B GLN* 1.3 63.3 + - + +
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Residues in contact with GLN 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B TYR* 3.1 51.4 + - + +
371B GLN* 4.5 1.6 - - - +
372B LEU 3.1 1.0 - - - -
373B GLU* 1.3 83.2 - - + +
375B ASP* 1.3 64.4 + - - +
376B HIS* 3.3 6.3 + - - +
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Residues in contact with ASP 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B GLN* 3.0 19.6 + - + +
372B LEU 3.4 13.8 - - - +
374B GLN* 1.3 74.3 - - - +
376B HIS* 1.3 62.1 + - - +
377B ASP* 3.1 26.0 + - - +
378B LEU* 3.7 31.7 + - + +
379B GLN* 4.2 3.6 + - - +
462B GLY* 4.6 16.1 - - - +
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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