Contacts of the helix formed by residues 328 - 348 (chain A) in PDB entry 1Q0H
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 GLY 328 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324A ALA 3.0 6.2 + - - +
325A PHE 3.3 8.4 + - - -
326A GLU 3.2 5.3 - - - -
327A GLN* 1.3 80.0 - - - +
329A GLN* 1.3 60.4 + - - -
330A ALA 3.5 2.7 - - - -
331A ALA 3.5 2.4 + - - -
332A THR* 2.9 29.0 + - - -
371A GLU* 4.0 5.6 - - - -
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Residues in contact with GLN 329 (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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129A VAL 2.9 25.6 + - - +
130A THR* 2.9 20.5 + - - +
131A CYS 4.2 4.0 - - - +
132A GLY* 3.5 24.9 - - - -
133A ARG 4.5 1.5 + - - +
134A LEU* 6.0 2.0 - - + -
237A TRP* 4.1 13.2 + - + -
328A GLY* 1.3 69.8 - - - -
330A ALA* 1.3 60.7 + - - +
332A THR* 4.0 6.4 - - - +
333A THR* 2.8 51.2 + - - +
371A GLU* 3.1 11.2 + - + +
372A PRO* 4.2 20.6 - - + +
378A VAL* 5.2 1.6 - - + -
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Residues in contact with ALA 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A GLN* 1.3 76.1 - - - +
331A ALA* 1.3 58.0 + - - +
333A THR 3.4 0.2 + - - -
334A ALA* 2.9 32.4 + - - +
367A MSE 6.4 0.7 - - - -
369A MSE 4.0 13.5 - - + +
370A ARG 3.8 22.0 - - - +
371A GLU* 3.0 21.0 + - - +
372A PRO* 4.0 8.2 - - + +
381A VAL* 3.7 17.5 - - + +
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Residues in contact with ALA 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ALA* 4.1 5.2 - - + +
327A GLN* 3.7 41.9 + - + +
328A GLY 3.5 5.2 + - - +
329A GLN 3.3 0.6 - - - -
330A ALA* 1.3 79.1 - - - +
332A THR* 1.3 56.7 + - - +
334A ALA* 4.4 4.0 - - - -
335A LEU* 2.8 30.0 + - - +
364A LEU* 3.4 13.2 - - + +
367A MSE 6.2 1.8 - - - -
371A GLU* 5.4 0.2 + - - -
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Residues in contact with THR 332 (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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129A VAL* 3.4 36.0 - - + +
233A ILE* 3.9 22.9 - - + -
324A ALA* 3.2 22.8 + - - -
325A PHE* 3.7 7.3 + - + -
328A GLY 2.9 19.1 + - - -
329A GLN* 3.6 11.7 - - - +
331A ALA* 1.3 76.2 - - - +
333A THR* 1.3 63.1 - - - +
335A LEU* 3.7 2.8 - - - +
336A ASN* 3.0 24.4 + - - +
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Residues in contact with THR 333 (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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130A THR* 2.7 46.3 + - - +
329A GLN* 2.8 27.7 + - - +
330A ALA* 3.7 4.5 - - - -
332A THR* 1.3 72.8 - - - +
334A ALA* 1.3 58.0 + - - +
336A ASN* 3.7 2.8 + - - +
337A ALA* 3.1 26.3 + - - +
372A PRO* 4.7 2.6 - - - +
378A VAL* 3.5 25.7 - - - +
381A VAL* 3.7 10.5 - - + -
382A ASP* 3.7 16.7 - - - +
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Residues in contact with ALA 334 (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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330A ALA 2.9 18.7 + - - +
331A ALA* 3.8 4.5 - - - +
333A THR* 1.3 76.0 - - - +
335A LEU* 1.3 58.4 + - - +
338A ALA* 2.9 30.1 + - - +
363A VAL* 4.5 0.9 - - + +
364A LEU* 3.9 8.6 - - + +
367A MSE 3.6 35.9 - - + -
381A VAL* 4.5 1.8 - - + -
385A ALA* 3.6 20.7 - - + +
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Residues in contact with LEU 335 (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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226A MSE 3.6 27.6 - - + -
230A LEU* 6.1 2.0 - - + -
233A ILE* 5.3 3.6 - - + -
320A LEU* 3.5 17.3 - - + +
321A ALA* 3.5 36.6 - - + +
324A ALA* 3.8 7.2 - - + -
331A ALA 2.8 19.3 + - - +
332A THR* 3.3 6.5 + - + +
334A ALA* 1.3 74.7 - - - +
336A ASN* 1.3 66.5 + - - +
338A ALA* 3.3 2.3 + - + +
339A ASN* 2.9 23.4 + - - +
360A ASN* 3.9 21.8 - - + +
364A LEU* 3.6 22.6 - - + +
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Residues in contact with ASN 336 (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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104A ALA* 4.0 11.9 - - - +
126A GLU* 3.1 40.1 + - - +
129A VAL* 4.1 14.3 - - + +
130A THR* 4.4 5.5 + - - -
217A LYS* 4.6 1.0 + - - -
230A LEU* 3.8 20.5 - - + +
332A THR 3.0 16.5 + - - +
333A THR* 3.8 5.4 - - - +
335A LEU* 1.3 75.7 - - - +
337A ALA* 1.3 59.9 + - - +
339A ASN* 3.3 7.0 + - - +
340A GLU* 2.8 54.6 + - - +
382A ASP* 4.6 0.6 + - - -
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Residues in contact with ALA 337 (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 THR 3.1 15.2 + - - +
334A ALA 3.8 4.0 - - - +
336A ASN* 1.3 80.0 - - - +
338A ALA* 1.3 64.8 + - - +
340A GLU* 3.3 5.4 + - - +
341A ILE* 3.2 25.9 + - - +
382A ASP* 3.4 39.9 - - - +
385A ALA* 3.8 9.6 - - + -
386A ARG* 4.2 12.5 - - + +
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Residues in contact with ALA 338 (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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334A ALA 2.9 18.0 + - - +
335A LEU* 3.6 5.6 - - - +
337A ALA* 1.3 76.2 - - - +
339A ASN* 1.3 58.1 + - - +
341A ILE* 3.1 3.6 + - - +
342A THR* 2.8 33.5 + - + +
360A ASN* 3.4 17.3 - - - +
363A VAL* 3.9 33.0 - - + -
385A ALA* 4.7 1.2 - - - +
389A ALA* 3.9 11.7 - - + -
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Residues in contact with ASN 339 (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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217A LYS* 3.5 17.6 - - - +
221A ASP* 2.9 23.4 + - - +
226A MSE 3.5 27.8 - - + +
230A LEU* 4.6 2.6 - - + +
335A LEU 2.9 17.1 + - - +
336A ASN* 3.3 6.1 + - - +
338A ALA* 1.3 73.7 - - - +
340A GLU* 1.3 59.8 + - - +
342A THR* 3.3 6.3 - - - -
343A VAL* 3.0 47.1 + - - +
356A ILE* 3.7 6.4 - - - +
360A ASN* 3.2 22.7 + - - +
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Residues in contact with GLU 340 (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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103A GLY* 3.4 19.5 - - - -
104A ALA 3.0 15.6 + - - -
105A ALA* 5.1 0.9 + - - +
217A LYS* 4.0 27.3 - - + +
336A ASN* 2.8 40.5 + - - +
337A ALA 3.5 8.3 - - - +
339A ASN* 1.3 75.8 - - - +
341A ILE* 1.3 62.9 + - - +
343A VAL* 4.1 1.2 - - - +
344A ALA* 3.2 24.3 + - - +
386A ARG* 3.1 32.4 + - - +
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Residues in contact with ILE 341 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337A ALA 3.2 11.6 + - - +
338A ALA 3.1 8.1 + - - +
340A GLU* 1.3 78.4 - - - +
342A THR* 1.3 57.4 + - - +
344A ALA* 3.6 6.3 + - + +
345A ALA* 3.0 23.7 + - - +
386A ARG* 3.7 42.4 - - + +
389A ALA* 3.7 22.9 - - + +
390A ARG* 3.8 42.0 - - + +
393A VAL* 4.2 7.0 - - + -
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Residues in contact with THR 342 (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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338A ALA* 2.8 21.2 + - + +
339A ASN* 3.3 5.7 + - - -
341A ILE* 1.3 71.4 - - - +
343A VAL* 1.3 63.1 + - - +
345A ALA* 3.2 5.7 + - - -
346A PHE* 2.9 25.6 + - - +
351A ILE* 3.5 16.7 - - - +
356A ILE* 3.7 15.5 - - - +
359A LEU* 3.7 28.7 - - + -
360A ASN* 2.8 28.1 + - - +
389A ALA* 4.9 7.9 - - + -
393A VAL* 4.3 12.3 - - + -
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Residues in contact with VAL 343 (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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217A LYS* 4.1 23.6 - - + +
220A VAL* 3.7 35.9 - - + -
221A ASP* 3.5 15.7 - - - +
224A THR* 5.9 0.4 - - - +
339A ASN* 3.0 42.9 + - - +
340A GLU 4.1 2.0 - - - +
342A THR* 1.3 76.7 + - - +
344A ALA* 1.3 62.5 + - - +
346A PHE* 3.2 8.1 + - - +
347A LEU* 3.0 33.8 + - + +
356A ILE* 4.3 8.7 - - + -
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Residues in contact with ALA 344 (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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340A GLU 3.2 19.3 + - - +
341A ILE* 3.7 9.2 - - + +
343A VAL* 1.3 78.1 - - - +
345A ALA* 1.3 56.2 + - - +
347A LEU* 3.3 12.6 + - - +
348A ALA* 3.0 30.2 + - - +
350A GLN* 5.0 0.4 - - - -
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Residues in contact with ALA 345 (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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341A ILE* 3.0 18.1 + - + +
342A THR 3.5 5.6 - - - +
343A VAL 3.2 0.2 - - - -
344A ALA* 1.3 75.4 - - - +
346A PHE* 1.3 59.8 + - - +
348A ALA 3.3 5.5 + - - -
350A GLN* 2.9 45.3 + - + +
351A ILE* 4.1 9.4 - - + -
393A VAL* 3.8 35.0 - - + -
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Residues in contact with PHE 346 (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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201A MSE 3.6 13.9 - - - -
202A THR 3.6 6.5 - - - -
203A PRO* 3.3 51.0 - - + +
206A ALA* 3.6 24.0 - - + -
220A VAL* 3.9 18.6 - - + -
342A THR 2.9 13.6 + - - +
343A VAL 3.2 6.3 + - - +
345A ALA* 1.3 78.6 - - - +
347A LEU* 1.3 58.5 + - + +
349A GLN* 3.0 17.7 + - - -
351A ILE* 3.5 28.0 - - + +
352A ARG* 4.7 0.4 - - - -
353A PHE* 3.6 35.2 - + - -
356A ILE* 3.8 23.1 - - + -
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Residues in contact with LEU 347 (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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203A PRO* 4.1 23.9 - - + +
207A CYS* 3.8 20.6 - - - -
216A ARG* 4.0 32.5 + - + +
217A LYS* 4.5 3.4 - - + +
220A VAL* 3.6 24.9 - - + -
343A VAL* 3.0 34.0 + - + +
344A ALA* 3.3 9.2 + - - +
346A PHE* 1.3 76.3 - - + +
348A ALA* 1.3 57.2 + - - +
349A GLN* 3.2 6.2 + - - +
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Residues in contact with ALA 348 (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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344A ALA 3.0 16.3 + - - +
345A ALA 3.9 3.8 - - - +
346A PHE 3.2 0.4 - - - -
347A LEU* 1.3 74.3 - - - +
349A GLN* 1.3 70.2 + - - +
350A GLN* 3.2 25.3 + - + +
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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