Contacts of the helix formed by residues 394 - 407 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A THR 4.4 5.7 + - - +
253A LYS* 4.6 5.4 - - + +
254A VAL 3.3 34.3 - - - +
255A ARG* 3.8 14.1 - - + -
268A ILE* 3.8 19.3 - - + -
367A ILE* 3.6 29.6 - - + +
392A ASP 3.7 3.6 + - - -
393A MSE 1.3 73.4 - - - +
395A PRO* 1.3 82.5 - - + +
396A GLU* 3.7 18.4 - - + +
397A THR* 2.9 21.8 + - - +
398A ALA 2.8 20.8 + - - -
426A GLU 4.7 1.4 + - - -
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Residues in contact with PRO 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A LEU* 3.9 9.6 - - + +
333A VAL* 4.0 0.2 - - - +
335A GLU* 3.7 28.9 - - + +
363A THR* 3.5 29.8 - - + +
364A SER 3.5 25.4 - - - +
367A ILE* 4.8 11.4 - - + +
393A MSE 3.2 4.0 - - - +
394A LEU* 1.3 89.6 - - + +
396A GLU* 1.3 76.8 + - - +
398A ALA* 3.4 3.1 + - - +
399A TYR* 3.1 19.9 + - - +
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Residues in contact with GLU 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A GLY* 5.7 5.4 - - - +
183A TYR* 3.3 39.9 + - + -
186A ALA* 5.5 0.7 - - - -
254A VAL 5.2 1.8 - - - +
255A ARG* 3.3 36.4 + - + +
309A LEU* 5.1 3.1 - - - -
394A LEU* 3.7 18.2 - - + +
395A PRO* 1.3 93.1 - - - +
397A THR* 1.3 64.9 + - - +
399A TYR* 2.8 22.3 + - - +
400A VAL* 3.2 9.3 + - - +
311B LYS* 3.6 11.1 + - - +
365B GLN* 3.5 20.6 - - - +
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Residues in contact with THR 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A GLY 5.4 0.5 + - - -
186A ALA* 3.9 15.8 - - - +
190A PHE* 4.2 22.0 - - + -
252A THR* 3.0 32.3 + - - +
254A VAL 5.6 0.2 + - - -
393A MSE 3.4 23.8 - - + -
394A LEU* 2.9 22.7 + - - +
396A GLU* 1.3 79.5 - - - +
398A ALA* 1.3 58.1 + - - +
399A TYR 3.2 0.3 + - - -
400A VAL* 3.3 2.6 + - - +
401A LYS* 2.9 27.2 + - - +
426A GLU* 4.3 5.2 - - + -
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Residues in contact with ALA 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A VAL* 3.6 11.8 - - + +
361A CYS* 5.4 0.8 - - + +
363A THR* 3.8 24.7 - - + -
390A CYS* 4.8 8.5 - - - -
393A MSE 3.7 22.0 - - + -
394A LEU 2.8 15.4 + - - +
395A PRO 3.7 8.7 - - - +
397A THR* 1.3 74.1 - - - +
399A TYR* 1.3 62.1 + - - +
401A LYS* 3.7 1.5 - - - +
402A LEU* 2.9 24.8 + - - +
419A MSE 4.6 3.4 - - - +
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Residues in contact with TYR 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A PRO* 5.1 0.3 - - - +
154A TRP* 4.6 2.9 - + - -
183A TYR* 4.1 21.5 - + - -
305A GLU 5.4 0.9 + - - -
307A VAL* 3.2 35.4 + - + -
308A ALA* 4.6 0.7 - - - -
309A LEU* 4.4 20.0 - - + -
333A VAL* 3.6 11.9 - - + +
395A PRO 3.1 11.7 + - - +
396A GLU* 2.8 11.2 + - - +
398A ALA* 1.3 77.9 - - - +
400A VAL* 1.3 75.9 + - + +
402A LEU* 3.2 8.1 + - - +
403A MSE 3.2 44.7 + - + +
313B TYR* 3.2 31.8 - + + -
314B PRO* 2.7 34.6 + - + -
315B GLY* 3.6 5.5 + - - -
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Residues in contact with VAL 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A TRP* 3.4 34.1 - - + -
183A TYR* 3.7 20.9 - - + +
186A ALA* 4.0 12.8 - - + +
187A ALA* 3.7 28.7 - - + +
190A PHE* 4.2 6.7 - - + -
396A GLU 3.2 8.3 + - - +
397A THR 3.6 6.5 - - - +
399A TYR* 1.3 82.9 - - + +
401A LYS* 1.3 67.6 + - - +
403A MSE 3.1 22.6 + - - +
404A TRP* 3.2 13.8 + - + +
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Residues in contact with LYS 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A PHE* 3.2 32.1 - - + -
393A MSE 4.1 9.8 - - - +
397A THR 2.9 17.5 + - - +
398A ALA* 3.7 7.6 - - - +
400A VAL* 1.3 79.5 - - - +
402A LEU* 1.3 52.7 + - - +
404A TRP* 3.0 9.8 + - + +
405A VAL* 2.7 45.3 + - + +
418A MSE 3.2 20.6 - - - -
419A MSE 2.7 58.4 + - + +
421A THR 3.3 2.0 + - - -
423A TYR* 4.5 5.4 - - - -
426A GLU* 2.6 30.9 + - - -
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Residues in contact with LEU 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A VAL* 3.8 11.0 - - + -
331A GLY* 3.7 15.0 - - - -
332A ILE 3.8 3.4 - - - +
333A VAL* 3.9 13.9 - - + -
359A ALA* 3.7 31.4 - - + +
361A CYS* 4.0 15.5 - - - -
398A ALA 2.9 21.4 + - - +
399A TYR 3.2 4.2 + - - +
401A LYS* 1.3 71.3 - - - +
403A MSE 1.3 53.3 + - - +
406A LEU* 2.7 49.2 + - + +
415A VAL* 3.8 23.6 - - + -
419A MSE 2.8 27.4 - - + +
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Residues in contact with MSE 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A PRO* 3.4 20.6 - - + -
154A TRP* 3.1 38.8 - - + -
303A ILE* 4.0 7.4 - - + -
304A GLU 2.8 45.6 + - - +
305A GLU* 3.8 22.9 - - - +
307A VAL* 3.9 14.1 - - + +
399A TYR* 3.2 38.8 + - + +
400A VAL* 3.1 13.4 + - - +
402A LEU* 1.3 76.2 - - - +
404A TRP* 1.3 62.4 + - - +
406A LEU 3.6 0.3 - - - -
407A GLY 2.9 8.0 + - - -
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Residues in contact with TRP 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A PHE* 3.0 57.4 + + + -
191A MSE 4.3 7.4 - - + +
193A ARG* 4.4 6.1 - - - -
300A ASP* 3.3 42.4 + - + -
302A LYS 3.3 21.0 - - - +
303A ILE* 3.7 15.8 - - + +
400A VAL* 3.2 9.9 + - + +
401A LYS* 3.0 11.4 + - - +
403A MSE 1.3 79.2 - - - +
405A VAL* 1.3 77.2 + - + +
407A GLY* 2.8 17.5 + - - -
408A HIS* 3.0 28.8 + + - -
418A MSE 3.7 17.9 - - + -
423A TYR* 3.7 35.2 - + - -
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Residues in contact with VAL 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A LYS* 2.7 31.0 + - + +
404A TRP* 1.3 78.2 - - + +
406A LEU* 1.3 56.2 + - - +
407A GLY 3.0 0.2 - - - -
408A HIS* 3.1 16.6 + - - +
409A THR* 3.1 12.6 + - - +
415A VAL* 3.8 24.9 - - + +
418A MSE 3.6 50.6 - - + +
419A MSE 2.9 34.8 - - + -
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Residues in contact with LEU 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A GLU* 3.5 19.1 - - + +
307A VAL* 3.4 29.6 - - + -
330A LYS* 3.6 12.3 - - + +
331A GLY* 3.5 22.7 - - - +
359A ALA* 4.1 10.8 - - + -
402A LEU* 2.7 30.6 + - + +
405A VAL* 1.3 68.5 - - - +
407A GLY* 1.3 58.9 + - - +
408A HIS 3.0 5.6 - - - -
409A THR 3.0 16.6 + - - +
410A GLN* 2.6 38.4 + - - +
412A LEU* 5.7 1.3 - - + -
415A VAL* 3.9 22.2 - - + -
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Residues in contact with GLY 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A LYS* 3.2 21.7 - - - +
303A ILE* 3.8 9.0 - - - -
304A GLU* 3.4 19.1 - - - -
403A MSE 2.9 4.6 + - - -
404A TRP 2.8 10.9 + - - -
406A LEU* 1.3 79.2 - - - +
408A HIS* 1.3 61.5 + - - -
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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