Contacts of the helix formed by residues 394 - 407 (chain B) in PDB entry 1ZQ1
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 LEU 394 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B THR 4.2 5.2 + - - +
253B LYS* 4.1 6.6 - - - +
254B VAL 3.3 40.2 - - - +
255B ARG* 4.0 11.2 - - + -
268B ILE* 3.5 40.2 - - + +
269B ASN* 5.1 1.6 - - - +
367B ILE* 4.0 12.1 - - + +
392B ASP 3.9 2.8 + - - +
393B MSE 1.3 77.1 - - - +
395B PRO* 1.3 67.9 - - + +
396B GLU* 4.1 12.8 - - + +
397B THR* 3.0 25.1 + - - +
398B ALA* 2.7 29.5 + - - +
426B GLU 4.8 0.2 + - - -
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Residues in contact with PRO 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A LYS* 4.4 0.2 - - - +
309B LEU* 4.1 6.0 - - + +
333B VAL* 4.1 3.9 - - + +
335B GLU* 3.7 33.7 - - + +
363B THR* 3.7 25.8 - - + +
364B SER 3.8 22.9 - - - +
367B ILE* 5.0 14.4 - - + +
393B MSE 3.6 3.6 - - - +
394B LEU* 1.3 87.6 - - + +
396B GLU* 1.3 80.3 + - - +
398B ALA* 3.1 2.3 + - - +
399B TYR* 2.9 22.7 + - - +
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Residues in contact with GLU 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A LYS* 3.5 11.3 + - - -
365A GLN* 4.0 8.1 - - - +
182B GLY 5.4 7.9 - - - +
183B TYR* 3.3 37.8 + - + +
186B ALA* 5.3 0.6 - - - +
254B VAL 5.4 1.8 - - - +
255B ARG* 3.2 44.1 + - + +
309B LEU* 4.7 3.8 - - + +
394B LEU* 4.1 15.2 - - + +
395B PRO* 1.3 97.9 - - - +
397B THR* 1.3 62.4 + - - +
399B TYR* 3.5 5.3 + - - +
400B VAL* 3.3 28.1 + - - +
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Residues in contact with THR 397 (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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182B GLY 4.8 3.8 + - - -
186B ALA* 3.9 15.1 - - + +
190B PHE* 4.2 10.8 - - + -
252B THR* 3.0 49.6 + - + +
254B VAL 5.2 0.2 + - - -
393B MSE 3.8 15.0 - - + -
394B LEU* 3.0 25.7 + - - +
396B GLU* 1.3 79.5 - - - +
398B ALA* 1.3 59.2 + - - +
400B VAL* 3.4 2.9 + - - +
401B LYS* 2.8 27.4 + - - +
426B GLU* 4.4 2.7 - - + -
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Residues in contact with ALA 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B VAL* 3.5 10.3 - - + +
363B THR* 3.5 22.9 - - + -
390B CYS* 4.6 5.2 - - - -
393B MSE 3.7 22.4 - - + +
394B LEU 2.7 19.2 + - - +
395B PRO 3.5 5.2 - - - +
397B THR* 1.3 72.2 - - - +
399B TYR* 1.3 64.7 + - - +
401B LYS* 4.2 0.7 - - - -
402B LEU* 2.9 25.6 + - - +
419B MSE 3.5 9.9 - - + +
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Residues in contact with TYR 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A TYR* 3.7 21.3 - + + -
314A PRO 2.5 31.4 + - - -
315A GLY* 3.7 8.3 + - - -
151B PRO* 4.9 1.0 - - - +
154B TRP* 4.3 5.6 - + - -
183B TYR* 4.1 17.0 - + - -
305B GLU 5.3 0.9 + - - -
307B VAL* 3.2 36.6 + - + +
308B ALA* 4.5 0.9 - - - -
309B LEU* 4.3 26.0 - - + -
333B VAL* 3.5 10.9 - - - +
395B PRO 2.9 12.5 + - - +
396B GLU* 3.6 9.0 - - - +
397B THR 3.3 0.2 - - - -
398B ALA* 1.3 79.6 - - - +
400B VAL* 1.3 84.1 + - + +
402B LEU* 3.1 10.0 + - - +
403B MSE 3.3 39.0 + - - +
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Residues in contact with VAL 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B TRP* 3.6 37.9 - - + -
183B TYR* 4.1 17.7 - - + +
186B ALA* 4.1 8.7 - - + +
187B ALA* 3.7 33.4 - - + +
190B PHE* 4.5 4.0 - - + -
191B MSE 6.2 0.7 - - + -
303B ILE* 5.6 0.3 - - - +
396B GLU 3.3 14.2 + - - +
397B THR 3.7 6.3 - - - +
399B TYR* 1.3 85.3 - - + +
401B LYS* 1.3 62.1 + - - +
402B LEU 3.2 0.7 + - - -
403B MSE 3.4 13.2 + - - +
404B TRP* 3.4 13.1 + - + +
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Residues in contact with LYS 401 (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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190B PHE* 3.1 35.2 - - + -
393B MSE 4.2 8.5 - - - +
397B THR 2.8 21.2 + - - +
398B ALA* 3.8 7.4 - - - +
399B TYR 3.3 0.2 - - - -
400B VAL* 1.3 73.9 - - - +
402B LEU* 1.3 56.7 + - - +
404B TRP* 3.6 4.5 + - + +
405B VAL* 2.9 42.0 + - + +
418B MSE 3.5 16.8 - - - -
419B MSE 2.7 50.8 + - + +
421B THR 3.1 7.3 + - - -
423B TYR* 4.1 11.7 - - - -
426B GLU* 2.5 33.8 + - - +
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Residues in contact with LEU 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B VAL* 3.5 23.3 - - + -
331B GLY* 3.7 4.5 - - - -
332B ILE 3.7 18.8 - - - +
333B VAL* 3.6 16.6 - - + -
359B ALA* 3.9 21.1 - - + +
361B CYS* 3.9 22.0 - - - -
398B ALA 2.9 17.5 + - - +
399B TYR 3.1 4.7 + - - +
401B LYS* 1.3 74.6 - - - +
403B MSE 1.3 60.9 + - - +
404B TRP 3.1 1.6 - - - -
405B VAL* 4.2 0.7 - - + +
406B LEU* 2.8 49.1 + - + +
415B VAL* 4.0 11.4 - - + -
419B MSE 3.7 10.5 - - + -
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Residues in contact with MSE 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B PRO* 3.2 37.9 - - + -
154B TRP* 4.1 11.4 - - + -
303B ILE* 3.0 13.9 - - + -
304B GLU* 2.5 41.1 + - - +
305B GLU* 3.6 23.6 - - + +
307B VAL* 3.4 25.8 - - + -
399B TYR* 3.3 44.7 + - - +
400B VAL* 3.4 5.6 + - - +
402B LEU* 1.3 75.2 - - - +
404B TRP* 1.3 57.7 + - - +
407B GLY 3.1 8.3 + - - -
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Residues in contact with TRP 404 (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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190B PHE* 3.6 52.7 + + + +
191B MSE 4.2 7.4 - - + +
193B ARG* 4.3 7.9 - - - -
300B ASP* 3.4 35.3 + - - -
302B LYS 3.2 20.6 - - - +
303B ILE* 3.4 17.4 - - + +
400B VAL* 3.4 10.8 + - + +
401B LYS* 3.6 10.1 - - - +
403B MSE 1.3 78.2 - - - +
405B VAL* 1.3 85.6 + - + +
407B GLY 3.1 6.6 + - - -
408B HIS* 2.8 39.5 + + - -
418B MSE 4.7 4.7 - - + -
423B TYR* 3.2 48.9 - + + -
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Residues in contact with VAL 405 (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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401B LYS* 2.9 43.9 + - + +
402B LEU* 3.9 3.4 - - - +
404B TRP* 1.3 85.2 - - + +
406B LEU* 1.3 61.4 + - - +
408B HIS 3.2 0.2 + - - -
409B THR* 3.2 15.1 + - - +
415B VAL* 3.9 28.5 - - + +
418B MSE 3.1 60.6 - - + +
419B MSE 3.8 7.4 - - + +
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Residues in contact with LEU 406 (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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304B GLU* 3.7 16.6 - - + -
307B VAL* 4.1 6.5 - - + -
330B LYS* 3.3 41.5 - - + +
331B GLY* 3.4 12.6 - - - +
359B ALA* 3.9 11.0 - - + -
402B LEU* 2.8 32.0 + - + +
403B MSE 4.6 0.2 - - - -
405B VAL* 1.3 68.5 - - - +
407B GLY* 1.3 58.6 + - - +
408B HIS 2.8 10.2 + - - -
409B THR 2.7 28.9 + - - +
410B GLN* 3.4 19.4 + - - +
412B LEU* 5.4 0.7 - - + -
415B VAL* 3.7 28.0 - - + -
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Residues in contact with GLY 407 (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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302B LYS* 3.3 21.6 - - - +
303B ILE* 3.7 8.7 - - - -
304B GLU* 3.4 23.0 - - - +
403B MSE 3.1 7.9 + - - -
404B TRP 3.1 8.0 + - - -
406B LEU* 1.3 74.8 - - - +
408B HIS* 1.3 61.6 + - - +
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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