Contacts of the helix formed by residues 326 - 343 (chain B) in PDB entry 1H1Q
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 ASN 326 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B GLN* 2.9 20.0 + - + +
324B PRO* 3.2 5.3 + - + +
325B ALA* 1.3 73.4 - - - +
327B CYS* 1.3 64.8 + - - +
328B LYS* 2.8 26.7 + - - +
329B VAL* 3.1 18.8 + - + -
330B GLU* 3.1 23.3 + - - +
364B LEU* 6.2 0.2 - - + -
367B VAL* 3.9 8.9 - - - +
368B THR* 3.7 23.6 - - + +
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Residues in contact with CYS 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ALA* 3.9 4.2 + - + -
326B ASN* 1.3 75.9 + - - +
328B LYS* 1.3 59.9 + - - +
330B GLU* 4.0 13.1 - - + +
331B SER* 3.3 23.0 + - - -
419B HIS* 2.9 46.1 + - - -
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Residues in contact with LYS 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ASN* 2.8 15.3 + - - +
327B CYS* 1.3 70.3 - - - +
329B VAL* 1.3 57.1 + - - +
331B SER* 3.3 0.8 + - - -
332B LEU* 2.6 39.2 + - - +
367B VAL* 3.8 23.9 - - + +
419B HIS* 4.5 14.6 - - + +
421B VAL* 3.6 20.8 - - + +
424B LEU* 4.0 25.4 - - + +
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Residues in contact with VAL 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B GLN* 3.4 15.0 - - - +
326B ASN* 3.3 30.1 - - + +
328B LYS* 1.3 77.1 - - - +
330B GLU* 1.3 65.4 + - - +
332B LEU* 4.8 0.9 - - - -
333B ALA* 3.0 19.8 + - - +
360B PHE* 3.7 15.5 - - + -
363B ALA* 3.4 10.2 - - + +
364B LEU* 3.6 37.9 - - + +
367B VAL* 3.8 20.4 - - + -
368B THR* 3.9 13.5 - - + -
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Residues in contact with GLU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B PHE* 3.2 44.6 - - + +
322B GLN* 2.5 31.7 + - - +
325B ALA* 3.8 13.7 - - - +
326B ASN 3.1 9.8 + - - +
327B CYS* 4.0 13.0 - - - +
329B VAL* 1.3 73.3 - - - +
331B SER* 1.3 58.9 + - - +
333B ALA 3.0 2.6 + - - -
334B MET* 3.0 35.6 + - + +
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Residues in contact with SER 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B CYS 3.3 16.1 + - - -
328B LYS 3.7 2.9 - - - -
329B VAL 3.2 0.2 - - - -
330B GLU* 1.3 78.3 - - - +
332B LEU* 1.3 63.7 + - - +
334B MET* 3.3 12.2 - - - +
335B PHE 3.2 17.3 + - - -
413B TYR* 3.6 3.8 - - - -
417B LYS 4.4 0.3 + - - -
418B TYR* 3.1 48.9 - - - +
419B HIS* 3.4 7.9 + - - -
421B VAL* 3.6 11.3 - - - +
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Residues in contact with LEU 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LYS 2.6 21.0 + - - +
329B VAL 4.1 2.7 - - - +
331B SER* 1.3 71.9 - - - +
333B ALA* 1.3 62.2 + - - +
335B PHE* 3.5 24.1 + - + -
336B LEU* 3.3 30.1 + - + +
363B ALA* 4.0 14.8 - - + -
366B THR* 3.8 28.5 - - + +
367B VAL* 4.0 8.7 - - + -
398B TYR* 3.6 30.5 - - + +
421B VAL* 3.7 27.5 - - + +
424B LEU* 4.3 4.3 - - + -
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Residues in contact with ALA 333 (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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315B LEU* 3.7 18.0 - - + +
319B PHE* 3.6 21.1 - - + -
329B VAL 3.0 13.8 + - - +
330B GLU 3.0 8.7 + - - +
332B LEU* 1.3 72.3 - - - +
334B MET* 1.3 60.1 + - - +
336B LEU* 3.3 2.9 + - - +
337B GLY* 2.9 27.5 + - - -
359B ALA* 3.7 26.1 - - - +
360B PHE* 4.2 3.4 - - + -
363B ALA* 3.6 5.3 - - + +
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Residues in contact with MET 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ASN* 3.5 33.0 - - + +
233B HIS* 5.0 6.0 - - + -
312B ASN* 3.6 24.7 - - + +
315B LEU* 3.9 11.1 - - + +
319B PHE* 4.0 17.9 - - + -
330B GLU* 3.0 16.5 + - - +
331B SER* 3.3 14.8 - - - +
333B ALA* 1.3 75.4 - - - +
335B PHE* 1.3 54.9 + - - +
337B GLY* 3.7 0.5 + - - -
338B GLU* 2.9 31.2 + - - +
413B TYR* 3.6 11.0 + - + +
418B TYR* 4.8 11.7 - - + -
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Residues in contact with PHE 335 (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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331B SER 3.2 4.6 + - - +
332B LEU* 3.6 29.8 - - + +
333B ALA 3.3 0.2 - - - -
334B MET* 1.3 79.7 - - - +
336B LEU* 1.3 67.0 + - + +
338B GLU* 3.6 1.9 - - - +
339B LEU* 2.8 53.2 + - + +
398B TYR* 4.3 14.1 - + - -
401B ALA* 4.8 1.8 - - + -
409B ILE* 3.8 6.4 - - + +
410B ARG* 3.8 34.5 - - + -
413B TYR* 3.3 47.5 - + + -
421B VAL* 4.3 2.2 - - + -
422B SER* 3.7 28.7 - - - -
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Residues in contact with LEU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B LEU* 3.3 24.5 - - + +
333B ALA 3.3 3.1 + - - +
335B PHE* 1.3 85.6 - - + +
337B GLY* 1.4 67.9 + - - +
338B GLU 3.0 0.7 - - - -
339B LEU* 3.2 8.5 + - + +
340B SER* 2.9 18.7 + - - -
359B ALA* 3.9 18.4 - - + +
362B LEU* 3.9 31.6 - - + -
363B ALA 4.0 7.4 - - - +
394B LEU* 3.5 23.6 - - + +
397B THR* 6.4 0.4 - - + -
398B TYR* 3.5 46.4 - - + -
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Residues in contact with GLY 337 (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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233B HIS* 4.3 8.3 + - - -
311B VAL* 4.1 21.7 - - - +
315B LEU* 4.8 1.8 - - - -
333B ALA 2.9 15.9 + - - -
334B MET 4.1 0.9 - - - -
336B LEU* 1.4 74.4 - - - +
338B GLU* 1.3 58.8 + - - +
340B SER* 2.6 32.5 + - - -
341B LEU* 3.5 4.3 + - - +
355B ILE* 4.2 8.3 - - - -
359B ALA* 4.1 6.0 - - - +
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Residues in contact with GLU 338 (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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219B VAL* 4.4 4.2 - - - +
229B ASN* 3.2 20.3 - - - +
232B LEU* 4.4 17.8 - - + +
233B HIS* 4.3 13.4 + - + -
334B MET* 2.9 17.8 + - - +
335B PHE 3.6 6.1 - - - +
336B LEU 3.0 0.2 - - - -
337B GLY* 1.3 77.8 - - - +
339B LEU* 1.3 61.5 + - - +
341B LEU* 3.1 18.7 + - + +
409B ILE* 3.2 33.8 - - + +
412B LYS* 2.7 34.9 + - - +
413B TYR* 2.6 28.8 + - - -
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Residues in contact with LEU 339 (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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335B PHE* 2.8 56.2 + - + +
336B LEU* 3.2 13.6 + - + +
338B GLU* 1.3 70.5 - - - +
340B SER* 1.3 66.3 + - - +
342B ILE* 2.8 27.7 + - + +
343B ASP* 4.1 5.7 + - - +
347B TYR* 5.4 0.2 - - - -
394B LEU* 5.6 0.2 - - + -
397B THR* 4.0 26.0 - - + +
398B TYR* 5.4 1.1 - - - -
401B ALA* 4.3 20.4 - - + -
404B HIS* 6.2 6.1 - - + -
406B GLN 5.6 5.8 - - - +
407B GLN* 6.5 0.7 - - - -
409B ILE* 3.7 29.6 - - + -
410B ARG* 4.9 4.9 - - + +
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Residues in contact with SER 340 (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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211B ARG* 5.7 0.3 + - - -
311B VAL* 5.1 2.4 - - - +
336B LEU 2.9 10.6 + - - -
337B GLY 2.6 16.5 + - - -
339B LEU* 1.3 76.3 - - - +
341B LEU* 1.3 63.2 + - - +
342B ILE 3.4 0.3 + - - -
343B ASP 3.9 3.6 + - - +
347B TYR* 3.1 54.1 - - - +
355B ILE* 3.4 36.4 - - - +
394B LEU* 4.4 3.2 - - - +
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Residues in contact with LEU 341 (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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211B ARG* 3.1 24.1 + - - +
215B VAL* 3.9 16.5 - - + +
232B LEU* 3.2 34.8 - - + -
233B HIS* 3.7 41.7 - - + +
236B VAL* 3.9 31.6 - - + +
311B VAL* 6.0 2.0 - - + -
337B GLY 4.3 1.3 - - - +
338B GLU* 3.1 17.3 + - + +
339B LEU 2.8 3.2 + - - -
340B SER* 1.3 81.7 + - - +
342B ILE* 1.3 61.2 + - + +
343B ASP 4.8 0.2 - - - -
409B ILE* 5.2 0.7 - - + -
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Residues in contact with ILE 342 (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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208B ASN 4.8 0.2 - - - +
211B ARG* 3.3 7.2 + - - +
212B ALA* 3.2 32.0 - - + +
215B VAL* 4.1 10.1 - - + +
216B ASP* 3.6 47.8 - - + +
339B LEU* 2.8 22.5 + - + +
341B LEU* 1.3 71.9 - - - +
343B ASP* 1.3 58.2 + - - +
344B ALA 4.0 0.2 + - - -
404B HIS* 3.7 34.3 - - + +
406B GLN* 4.0 4.9 - - + -
409B ILE* 3.4 32.5 - - + -
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Residues in contact with ASP 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ASN* 5.7 1.3 - - - -
211B ARG* 4.1 0.9 - - - -
212B ALA* 4.7 5.3 - - - +
339B LEU 4.1 2.9 + - - +
340B SER 3.9 4.1 + - - -
341B LEU 3.4 1.6 - - - -
342B ILE* 1.3 83.1 - - - +
344B ALA* 1.3 62.1 + - - +
345B ASP 2.9 14.2 + - - +
346B PRO* 4.9 1.1 - - + -
347B TYR* 3.4 34.6 + - + +
397B THR* 4.7 15.8 + - - +
404B HIS* 3.1 38.9 + - - -
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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
------------------------------------------------------------
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