Contacts of the helix formed by residues 356 - 367 (chain B) in PDB entry 5ZE3
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 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 LYS 3.3 4.6 - - - +
355B TRP* 1.3 77.4 - - - +
357B LEU* 1.3 68.2 + - - +
358B VAL* 3.4 13.9 - - + +
359B SER* 2.5 48.0 + - - -
360B ALA 3.0 19.4 + - - -
375B ALA* 3.5 9.1 - - - +
393B ILE 3.0 18.5 - - - +
394B GLN* 3.4 20.2 - - - +
395B CYS 4.4 2.4 - - - +
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Residues in contact with LEU 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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356B ASP* 1.3 72.8 - - - +
358B VAL* 1.3 59.3 + - + +
360B ALA* 3.4 2.5 + - - +
361B SER* 2.8 36.3 + - - +
371B SER* 5.6 1.3 - - - +
372B ALA* 3.3 24.7 - - + +
373B LYS 3.7 16.2 - - - +
374B GLU* 4.0 1.1 - - - -
375B ALA* 3.4 30.1 - - + +
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Residues in contact with VAL 358 (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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356B ASP* 3.1 10.4 + - + +
357B LEU* 1.3 79.0 - - + +
359B SER* 1.3 56.8 + - - +
361B SER* 3.3 7.1 + - - -
362B VAL* 3.0 26.5 + - - +
365B ARG* 5.0 0.7 + - - -
395B CYS 3.1 26.0 - - - +
396B THR 3.6 15.5 - - - +
397B GLY* 3.6 12.2 - - - -
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Residues in contact with SER 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B TRP* 3.6 22.4 - - - -
356B ASP* 2.5 40.9 + - - -
358B VAL* 1.3 69.6 - - - +
360B ALA* 1.3 68.7 + - - +
362B VAL* 3.1 18.4 + - - +
363B VAL* 3.1 9.9 + - - +
393B ILE* 3.7 5.4 + - - -
395B CYS* 3.0 39.7 + - - -
402B ILE* 3.9 1.1 - - - +
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Residues in contact with ALA 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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355B TRP* 3.8 7.3 - - + -
356B ASP 3.0 12.2 + - - +
357B LEU 3.5 8.7 - - - +
359B SER* 1.3 76.0 - - - +
361B SER* 1.3 56.7 + - - +
363B VAL* 2.8 22.6 + - - +
364B CYS* 2.9 14.2 + - - -
372B ALA* 3.5 17.0 - - + -
375B ALA* 3.9 18.4 - - + +
422B VAL* 3.5 27.1 - - + -
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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
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357B LEU* 2.8 24.3 + - - +
358B VAL* 3.6 8.1 - - - -
359B SER 3.2 0.2 - - - -
360B ALA* 1.3 68.8 - - - +
362B VAL* 1.3 66.0 + - - +
364B CYS* 3.8 2.5 - - - +
365B ARG* 2.9 50.3 + - - +
371B SER* 3.3 12.4 - - - -
372B ALA* 2.9 29.9 + - - +
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Residues in contact with VAL 362 (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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358B VAL 3.0 15.8 + - - +
359B SER 3.1 7.9 - - - +
361B SER* 1.3 77.5 - - - +
363B VAL* 1.3 63.6 + - - +
365B ARG* 3.3 18.9 + - - +
366B GLU* 2.9 22.7 + - - +
395B CYS* 3.6 24.7 - - + -
397B GLY* 4.3 4.3 - - - -
399B GLU* 3.9 22.7 - - - +
400B LYS 5.3 0.5 - - - +
401B SER* 3.8 10.1 - - - +
402B ILE* 3.8 32.3 - - + +
405B CYS* 4.1 4.3 - - - -
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Residues in contact with VAL 363 (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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326B VAL* 4.4 8.3 - - + -
328B LEU* 4.3 2.0 - - + -
339B VAL* 4.0 32.1 - - + -
355B TRP* 4.4 3.8 - - + -
359B SER 3.1 3.3 + - - +
360B ALA 2.8 15.0 + - - +
362B VAL* 1.3 75.4 - - - +
364B CYS* 1.3 62.2 + - - +
366B GLU* 3.2 11.6 + - - +
367B LEU* 3.1 39.5 + - + +
402B ILE* 3.6 42.2 - - + -
422B VAL* 4.1 13.2 - - + -
424B CYS* 5.8 0.2 - - - -
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Residues in contact with CYS 364 (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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360B ALA 2.9 15.9 + - - +
361B SER 3.3 4.9 + - - +
363B VAL* 1.3 77.6 - - - +
365B ARG* 1.3 57.7 + - - +
367B LEU* 3.4 3.0 + - - -
368B GLY 3.4 3.8 + - - -
369B PHE* 2.8 29.3 + - + +
370B GLY 3.2 20.6 - - - +
371B SER 4.3 2.7 - - - -
372B ALA* 3.8 15.5 - - - -
422B VAL* 4.2 10.5 - - - -
424B CYS* 2.0 54.3 - - + -
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Residues in contact with ARG 365 (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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358B VAL 5.0 0.2 + - - -
361B SER* 2.9 36.7 + - - +
362B VAL* 3.9 20.3 - - - +
364B CYS* 1.3 75.5 - - - +
366B GLU* 1.3 66.2 + - - +
368B GLY* 3.1 13.3 + - - -
369B PHE 3.8 15.0 - - - +
370B GLY* 3.8 11.8 + - - +
371B SER* 5.2 3.8 - - - +
397B GLY* 2.8 31.7 + - - -
398B ASN* 5.1 0.2 - - - +
399B GLU 4.5 6.7 + - - -
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Residues in contact with GLU 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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457A SER* 5.4 0.3 + - - -
325B LEU* 4.8 8.1 - - - +
326B VAL* 3.0 35.9 + - + +
362B VAL 2.9 16.5 + - - +
363B VAL* 3.2 7.0 + - - +
365B ARG* 1.3 78.5 - - - +
367B LEU* 1.3 60.1 + - + +
368B GLY 3.3 0.9 + - - -
400B LYS 3.6 19.7 - - - +
401B SER* 2.7 33.4 + - - -
402B ILE* 3.2 17.3 + - - +
403B ILE* 4.4 1.0 - - - +
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Residues in contact with LEU 367 (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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455A GLN 4.3 16.6 - - - +
456A GLY* 4.7 8.7 - - - +
457A SER* 3.3 36.5 + - - +
326B VAL* 3.9 38.8 - - + +
327B ARG* 4.9 2.7 - - - -
328B LEU* 3.6 40.8 - - + +
363B VAL* 3.1 20.7 + - + +
364B CYS* 3.4 1.1 + - - -
365B ARG 3.1 0.2 - - - -
366B GLU* 1.3 77.8 - - + +
368B GLY* 1.3 59.6 + - - +
369B PHE* 3.5 24.2 + - + -
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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
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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