Contacts of the helix formed by residues 348 - 367 (chain B) in PDB entry 1QQW
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 348 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ARG 5.0 1.2 - - - +
218B HIS* 2.6 38.6 + - + +
219B THR 4.4 4.2 + - - +
297B PHE* 3.3 31.3 - - + +
299B LEU* 4.4 7.1 + - - +
346B SER* 2.8 21.6 + - - +
347B PRO* 1.3 72.2 - - - +
349B LYS* 1.3 63.3 + - - +
350B MET* 2.9 16.2 + - - +
351B LEU* 3.5 17.2 - - + +
352B GLN* 2.8 30.3 + - - +
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Residues in contact with LYS 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ARG 3.8 11.7 - - - +
157B ASP* 4.0 19.8 + - - +
158B PRO* 3.1 21.1 - - + +
297B PHE 4.8 0.8 + - - -
347B PRO 3.2 10.1 + - - +
348B ASP* 1.3 75.3 + - - +
350B MET* 1.3 56.7 + - - +
352B GLN* 3.1 8.7 + - + +
353B GLY 2.9 26.3 + - - -
432B PHE* 3.7 23.2 + - - +
434B THR* 4.4 15.3 - - - +
41C VAL* 3.7 36.0 + - + +
43C THR* 3.6 27.1 + - + +
46C PRO 4.0 19.5 + - - -
48C GLY 5.5 1.1 - - - -
50C LEU* 5.4 0.6 - - + +
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Residues in contact with MET 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B PHE* 4.2 9.6 - - + -
155B ILE* 3.9 24.9 - - + +
156B ARG* 3.4 22.4 - - - +
157B ASP 3.2 14.8 - - - +
158B PRO* 3.1 32.5 - - + -
218B HIS* 3.7 15.9 - - + -
299B LEU* 3.8 18.4 - - + -
348B ASP* 2.9 10.1 + - - +
349B LYS* 1.3 76.9 - - - +
351B LEU* 1.3 59.4 + - - +
354B ARG* 3.2 25.8 + - - +
600B HEM 3.3 36.0 - - + +
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Residues in contact with LEU 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B HIS* 3.9 22.4 - - + +
219B THR 4.0 15.9 - - - +
220B PHE* 4.0 27.8 - - + -
336B PRO* 4.9 7.2 - - + +
339B MET* 5.8 0.2 - - + -
345B ALA* 4.0 14.8 - - + -
346B SER* 3.7 30.1 - - - +
348B ASP* 3.1 22.3 + - + +
349B LYS 3.1 0.4 - - - -
350B MET* 1.3 78.3 - - - +
352B GLN* 1.3 66.6 + - - +
354B ARG* 3.0 20.6 + - + +
355B LEU* 3.1 24.0 + - + +
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Residues in contact with GLN 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B ALA* 4.3 4.8 - - - +
346B SER 2.6 29.3 + - - +
347B PRO* 4.2 4.0 - - - +
348B ASP 2.8 28.2 + - - +
349B LYS* 3.5 8.3 - - + +
351B LEU* 1.3 76.9 - - - +
353B GLY* 1.3 61.8 + - - +
355B LEU* 3.2 26.1 + - - +
356B PHE 4.1 0.2 + - - -
49C PRO* 3.5 10.0 - - + +
50C LEU* 3.1 49.3 + - + +
52D VAL* 4.1 12.5 - - + +
53D GLN* 3.3 36.6 + - - +
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Residues in contact with GLY 353 (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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158B PRO* 4.2 6.1 - - - -
349B LYS 2.9 15.0 + - - -
350B MET 4.1 1.8 - - - -
352B GLN* 1.3 77.5 - - - +
354B ARG* 1.3 61.3 + - - +
355B LEU 3.3 0.4 + - - -
356B PHE* 3.7 3.7 + - - +
357B ALA* 3.4 22.2 + - - +
600B HEM 4.7 5.0 - - - +
50C LEU* 4.2 2.4 - - - +
57C PHE* 3.6 35.3 - - - -
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Residues in contact with ARG 354 (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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146B VAL* 3.2 34.8 + - - +
218B HIS* 3.1 40.3 + - - -
220B PHE* 5.4 3.0 - - - -
336B PRO* 4.1 25.7 - - + +
350B MET 3.2 15.5 + - - +
351B LEU* 3.0 14.3 + - + +
353B GLY* 1.3 73.8 - - - +
355B LEU* 1.3 62.8 + - - +
356B PHE 3.0 6.5 + - - -
357B ALA* 3.7 3.9 + - - +
358B TYR* 2.6 65.9 + - + +
600B HEM 3.3 54.1 - - + +
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Residues in contact with LEU 355 (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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336B PRO* 4.3 3.1 - - + +
337B SER* 3.3 47.9 + - - +
339B MET* 4.1 17.9 - - + -
345B ALA* 4.2 18.4 - - + -
351B LEU* 3.1 19.2 + - + +
352B GLN* 3.2 27.3 + - - +
354B ARG* 1.3 78.8 - - - +
356B PHE* 1.3 55.3 + - - +
359B PRO* 3.7 7.4 - - - +
52D VAL* 4.6 8.5 - - + -
53D GLN* 4.1 26.7 - - - +
55D VAL* 4.5 14.4 - - + +
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Residues in contact with PHE 356 (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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356A PHE* 3.4 32.3 - + - -
363A ARG* 5.0 1.6 - - - -
353B GLY 3.7 7.2 + - - +
354B ARG 3.0 0.2 - - - -
355B LEU* 1.3 80.5 - - - +
357B ALA* 1.3 71.4 + - - +
358B TYR 3.2 2.5 + - - -
359B PRO* 3.5 3.1 - - - +
360B ASP* 3.2 56.1 + - + +
363B ARG* 5.5 1.3 - - - -
57C PHE* 5.0 9.9 - + + -
58C THR* 3.5 31.2 - - + -
61C MET* 4.3 22.2 - - + -
62C ALA* 4.4 11.7 - - + -
65C ASP* 4.5 0.7 - - - -
52D VAL* 4.0 21.3 - - + -
58D THR* 4.8 12.1 - - + -
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Residues in contact with ALA 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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353B GLY 3.4 11.9 + - - +
354B ARG* 3.7 0.4 + - - -
356B PHE* 1.3 81.6 - - - +
358B TYR* 1.3 64.5 + - + +
361B THR* 3.0 29.5 + - - -
600B HEM 3.7 35.7 - - + -
61C MET* 4.3 9.6 - - + -
65C ASP* 3.3 23.9 - - - +
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Residues in contact with TYR 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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146B VAL* 4.2 5.8 - - + -
334B PHE 3.3 18.6 - - - +
335B ASP* 3.5 8.7 - - - +
336B PRO* 3.3 19.5 - - + -
354B ARG* 2.6 73.9 + - + -
356B PHE 3.3 0.2 - - - -
357B ALA* 1.3 74.5 - - + +
359B PRO* 1.3 76.7 - - + +
361B THR* 2.9 10.7 - - - +
362B HIS* 2.9 23.4 + - + -
600B HEM 2.7 72.3 + + + -
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Residues in contact with PRO 359 (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 ASP* 3.1 18.4 - - + +
336B PRO* 5.0 0.2 - - + -
337B SER* 3.4 23.1 - - - +
354B ARG 4.4 0.4 - - - +
355B LEU 3.7 15.3 - - - +
356B PHE* 3.5 9.4 - - - +
358B TYR* 1.3 96.1 - - + +
360B ASP* 1.3 60.3 + - - +
362B HIS* 3.3 2.8 + - - +
363B ARG* 3.3 49.8 + - - +
370B TYR* 3.5 11.5 + - - +
58D THR* 6.2 1.1 - - + -
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Residues in contact with ASP 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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360A ASP* 4.1 9.9 - - - +
363A ARG* 4.5 3.3 + - - -
356B PHE* 3.2 46.5 + - + +
357B ALA 3.7 2.0 - - - +
358B TYR 3.1 0.6 - - - -
359B PRO* 1.3 81.8 - - - +
361B THR* 1.3 60.2 + - - +
363B ARG* 3.3 25.0 + - - +
364B HIS 3.8 2.4 + - - -
62C ALA* 4.1 0.7 - - - +
65C ASP* 2.7 20.8 - - - +
66C ARG* 2.5 55.2 + - - -
66D ARG* 4.5 0.2 + - - -
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Residues in contact with THR 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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73B VAL* 4.4 5.5 - - - +
357B ALA 3.0 17.8 + - - +
358B TYR* 2.9 24.0 - - - +
360B ASP* 1.3 76.3 + - - +
362B HIS* 1.3 63.4 + - + +
364B HIS* 3.1 6.1 + - - +
365B ARG* 2.9 30.0 + - - +
600B HEM 3.8 41.8 + - + +
65C ASP* 3.1 33.8 + - - +
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Residues in contact with HIS 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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333B ALA* 3.5 27.0 - - + +
334B PHE 3.0 23.8 + - - -
335B ASP* 2.7 36.1 + - - -
358B TYR* 2.9 16.9 + - + +
359B PRO 3.6 0.7 - - - +
361B THR* 1.3 74.9 - - + +
363B ARG* 1.3 56.9 + - - +
364B HIS 3.0 5.2 - - - -
365B ARG* 4.4 4.3 - - - +
366B LEU* 2.9 36.8 + - + +
367B GLY 3.1 5.7 + - - +
370B TYR* 3.4 27.9 - - + -
600B HEM 3.4 39.3 + - - +
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Residues in contact with ARG 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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356A PHE* 5.1 2.2 - - - -
360A ASP* 4.8 2.4 + - - -
356B PHE* 5.5 1.2 - - - -
359B PRO* 3.3 30.6 + - - +
360B ASP* 3.3 35.9 + - - +
361B THR 3.2 0.4 - - - -
362B HIS* 1.3 76.8 - - - +
364B HIS* 1.3 57.7 + - - +
367B GLY* 3.3 27.3 - - - -
368B PRO* 3.6 26.3 + - + +
370B TYR* 4.0 13.4 + - + -
66C ARG* 5.3 0.7 - - - +
58D THR* 4.4 14.3 + - - +
59D ASP* 4.6 13.3 + - - +
62D ALA* 3.3 30.7 - - - +
63D HIS* 5.1 1.8 - - - +
66D ARG* 3.5 42.2 + - - +
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Residues in contact with HIS 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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368A PRO* 4.3 7.7 - - + +
391A PRO* 4.4 12.8 - - + -
70B PRO* 4.4 15.1 - - + +
360B ASP 3.8 5.8 + - - +
361B THR* 3.1 11.5 + - - +
362B HIS 3.0 0.2 - - - -
363B ARG* 1.3 80.7 - - - +
365B ARG* 1.3 74.8 + - + +
366B LEU 3.4 1.1 + - - -
367B GLY* 4.4 1.9 + - - -
65C ASP 3.5 15.9 - - - +
66C ARG* 3.2 50.3 + - + +
68C ARG* 3.3 27.4 + - + -
69C ILE* 5.7 0.2 - - + -
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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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69B ILE* 4.1 17.9 - - + +
70B PRO* 2.9 46.1 + - + +
71B GLU 4.1 1.8 - - - +
72B ARG* 3.6 25.6 - - - +
73B VAL 5.4 0.2 - - - +
330B GLU* 3.0 40.6 + - - -
332B ILE 3.3 24.7 + - - -
333B ALA* 4.7 1.2 - - - +
361B THR* 2.9 17.5 + - - +
362B HIS* 4.4 2.4 - - - +
364B HIS* 1.3 89.4 - - + +
366B LEU* 1.3 81.4 + - + +
600B HEM 3.0 36.8 + - - +
391D PRO* 5.7 1.9 - - - +
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Residues in contact with LEU 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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69B ILE* 4.2 11.7 - - + -
331B GLN* 3.7 35.7 - - - +
333B ALA* 3.7 24.9 - - + -
362B HIS* 2.9 12.5 + - + +
364B HIS 4.5 1.3 - - - -
365B ARG* 1.3 116.8 - - - +
367B GLY* 1.3 59.3 + - - +
370B TYR* 3.6 24.0 - - + -
373B ILE* 4.4 6.5 - - + -
376B ASN* 4.3 1.8 - - - +
391D PRO* 4.7 7.2 - - - +
392D MET* 3.6 27.9 + - - +
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Residues in contact with GLY 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B HIS 3.1 4.2 + - - -
363B ARG* 3.3 14.6 + - - -
364B HIS 4.4 1.3 + - - -
365B ARG 3.9 0.2 - - - -
366B LEU* 1.3 80.3 - - - +
368B PRO* 1.3 75.8 - - - +
369B ASN 3.3 2.7 - - - -
370B TYR* 3.0 25.7 + - - -
392D MET* 4.5 6.3 - - - -
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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
------------------------------------------------------------
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