Contacts of the helix formed by residues 355 - 374 (chain B) in PDB entry 4UH6
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 355 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B ALA* 1.3 81.7 - - - +
356B LYS* 1.3 55.7 + - - +
357B ASP* 2.9 14.9 + - - +
358B GLN* 2.9 40.5 + - - +
359B LEU* 2.6 39.4 + - - +
397B SER 5.5 1.3 - - - -
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Residues in contact with LYS 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B THR* 1.3 71.7 - - - +
357B ASP* 1.3 63.1 + - - +
359B LEU* 3.7 2.9 - - - +
360B PHE* 3.2 27.5 + - - +
393B ILE* 3.8 33.3 - - + +
394B ASP* 2.8 40.8 + - - +
397B SER* 3.5 32.6 + - - -
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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
----------------------------------------------------------
355B THR* 3.0 13.0 + - - +
356B LYS* 1.3 81.5 + - - +
358B GLN* 1.3 61.9 + - + +
361B PRO* 3.0 27.4 - - - +
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Residues in contact with GLN 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B ALA* 3.4 11.1 - - + -
355B THR* 2.9 44.4 + - - +
357B ASP* 1.3 79.3 - - + +
359B LEU* 1.3 64.2 + - - +
361B PRO* 3.3 11.4 - - - +
362B LEU* 3.5 24.2 - - + +
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Residues in contact with LEU 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B ALA* 4.8 11.9 - - + -
355B THR 2.6 23.4 + - - +
356B LYS* 3.7 5.2 - - - +
357B ASP 3.2 0.4 - - - -
358B GLN* 1.3 73.7 - - - +
360B PHE* 1.3 59.7 + - - +
362B LEU* 3.1 8.8 + - + +
363B ALA* 2.9 23.6 + - - +
393B ILE* 3.7 23.6 - - + -
397B SER 3.6 24.2 - - - +
398B THR* 3.6 20.4 - - - +
399B TYR* 4.2 9.4 - - + -
580B GLY 4.1 4.7 - - - +
581B GLY* 4.0 32.8 - - - +
582B LEU* 4.2 3.8 - - + -
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Residues in contact with PHE 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B LYS 3.2 12.7 + - - +
359B LEU* 1.3 79.6 - - - +
361B PRO* 1.4 61.2 - - + +
363B ALA* 4.1 0.2 - - - -
364B LYS* 2.6 63.9 + - + +
386B LEU* 3.8 24.2 - - + -
389B VAL* 4.5 7.2 - - + -
390B ASN* 3.2 54.7 - - + +
393B ILE* 3.8 17.5 - - + +
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Residues in contact with PRO 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ASP 3.0 28.5 - - - +
358B GLN* 3.3 9.9 - - - +
360B PHE* 1.4 92.3 - - + +
362B LEU* 1.3 59.8 + - + +
364B LYS* 3.4 7.7 + - + +
365B GLU* 2.8 30.8 + - - +
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Residues in contact with LEU 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LEU* 6.3 3.6 - - + -
358B GLN* 3.5 23.3 - - + +
359B LEU* 3.1 7.8 + - + +
361B PRO* 1.3 77.3 - - + +
363B ALA* 1.3 67.3 + - - +
365B GLU* 3.4 20.3 + - - +
366B PHE* 3.1 23.2 + - - +
578B GLU* 5.5 6.5 - - - +
580B GLY* 3.7 4.7 - - - -
581B GLY* 3.8 30.1 - - - +
706B THR* 6.1 1.6 - - + -
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Residues in contact with ALA 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B LEU 2.9 12.9 + - - +
360B PHE* 3.5 7.2 - - + +
362B LEU* 1.3 76.0 - - - +
364B LYS* 1.3 57.0 + - - +
366B PHE* 3.2 3.6 + - - +
367B ILE* 2.9 34.6 + - - +
389B VAL* 3.8 19.7 - - + -
393B ILE* 4.0 5.2 - - + -
399B TYR* 3.5 32.8 - - + +
580B GLY* 3.5 9.8 + - - -
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Residues in contact with LYS 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B PHE* 2.6 46.6 + - + +
361B PRO* 3.5 7.6 - - + +
363B ALA* 1.3 72.4 - - - +
365B GLU* 1.3 53.7 + - - +
367B ILE* 3.8 0.5 - - - +
368B ASP* 2.8 62.6 + - - +
386B LEU* 4.0 29.1 - - + +
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Residues in contact with GLU 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B LYS 4.8 5.9 - - - +
326B THR* 4.0 23.2 + - - +
361B PRO 2.8 21.0 + - - +
362B LEU* 3.6 22.6 - - - +
364B LYS* 1.3 75.4 - - - +
366B PHE* 1.3 58.9 + - - +
368B ASP* 3.5 8.1 - - - +
369B GLN* 3.0 35.3 + - + +
706B THR* 3.9 25.2 - - + +
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Residues in contact with PHE 366 (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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362B LEU 3.1 2.8 + - - +
363B ALA 3.6 3.1 - - - +
365B GLU* 1.3 77.9 - - - +
367B ILE* 1.3 76.6 + - + +
369B GLN* 3.1 18.9 + - + +
370B TYR* 2.9 29.8 + - + +
399B TYR* 4.5 2.2 - - - -
401B LEU* 3.6 26.7 - - + -
405B GLU* 3.7 31.0 - - + -
408B TYR* 3.8 26.2 - + - -
409B GLY* 4.1 0.9 - - - -
579B ILE* 3.4 26.7 - - + -
580B GLY* 3.5 27.8 - - - +
706B THR* 6.6 0.2 - - + -
707B PRO* 3.9 19.7 - - + -
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Residues in contact with ILE 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B ALA* 2.9 27.6 + - - +
364B LYS 3.9 2.5 - - - +
366B PHE* 1.3 85.9 - - + +
368B ASP* 1.3 62.8 + - - +
370B TYR* 3.3 3.6 + - + +
371B TYR* 3.0 47.3 + - + -
382B HIS* 3.9 5.8 - - + -
385B ARG* 3.9 16.2 - - + +
386B LEU* 3.8 22.4 - - + -
389B VAL* 4.4 17.0 - - + -
399B TYR* 4.9 5.2 - - + -
405B GLU* 3.6 34.3 - - + +
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Residues in contact with ASP 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B LYS* 2.8 55.0 + - - +
365B GLU* 3.5 8.1 + - - +
367B ILE* 1.3 78.2 - - - +
369B GLN* 1.3 57.1 + - - +
371B TYR* 3.5 0.9 + - - +
372B SER* 3.0 27.7 + - - -
377B PHE* 3.9 20.8 - - + -
382B HIS* 2.7 37.8 + - - -
386B LEU* 4.0 8.5 - - - +
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Residues in contact with GLN 369 (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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365B GLU* 3.0 25.2 + - + +
366B PHE* 3.1 22.5 + - + +
368B ASP* 1.3 74.9 - - - +
370B TYR* 1.3 65.3 + - - +
372B SER* 3.4 8.2 + - - -
373B SER* 3.0 17.7 + - - -
408B TYR* 3.2 33.7 + - + +
412B HIS* 4.7 5.1 + - - +
674B ARG* 5.4 5.3 - - - +
706B THR* 3.3 27.1 + - - +
707B PRO* 3.8 14.6 - - - +
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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 PHE* 2.9 21.9 + - + +
367B ILE* 3.6 6.3 - - - +
369B GLN* 1.3 78.2 - - - +
371B TYR* 1.3 86.4 + + - +
373B SER* 2.6 26.5 + - - -
374B ILE* 3.3 42.8 + - + +
404B THR* 3.2 38.8 + - - +
405B GLU* 4.2 16.6 - - + -
408B TYR* 3.6 46.2 - + + -
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Residues in contact with TYR 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B ILE* 3.0 40.1 + - + +
368B ASP 4.1 1.8 - - - +
370B TYR* 1.3 94.7 - + - +
372B SER* 1.3 60.7 + - - +
374B ILE* 3.7 25.5 - - + +
375B LYS 3.4 2.1 + - - -
376B ARG* 2.8 42.3 + - + +
377B PHE* 3.1 4.5 + - - -
379B SER* 4.2 1.1 - - - -
381B ALA* 3.4 29.5 + - + +
382B HIS* 3.6 50.3 - + + +
385B ARG* 3.7 19.8 - - + +
405B GLU* 4.7 2.2 + - - -
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Residues in contact with SER 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B ASP 3.0 18.8 + - - -
369B GLN* 3.6 9.2 - - - -
370B TYR 3.1 0.2 - - - -
371B TYR* 1.3 78.1 - - - +
373B SER* 1.3 57.4 + - - +
375B LYS* 3.1 21.1 + - - +
377B PHE* 4.1 22.0 - - - +
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Residues in contact with SER 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B GLN 3.0 12.4 + - - -
370B TYR* 2.6 19.1 + - - -
372B SER* 1.3 76.5 - - - +
374B ILE* 1.3 63.8 + - - +
375B LYS* 3.3 8.1 + - - +
408B TYR* 3.1 34.8 - - - -
412B HIS* 5.4 2.2 - - - -
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Residues in contact with ILE 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B TYR* 3.7 43.1 - - + +
371B TYR* 3.7 33.7 - - + +
373B SER* 1.3 82.6 + - - +
375B LYS* 1.3 68.5 + - - +
376B ARG* 3.2 33.9 + - + +
408B TYR* 6.2 0.2 - - + -
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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
------------------------------------------------------------
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