Contacts of the helix formed by residues 420 - 434 (chain B) in PDB entry 5UQ9
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 MET 420 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428A SER* 3.8 7.4 + - - +
200B GLU* 3.5 7.9 - - + +
204B LEU* 4.3 10.8 - - + -
409B ALA 3.8 17.5 - - - +
410B VAL* 3.5 44.6 - - + +
413B GLY* 3.9 15.0 - - - -
414B VAL* 4.7 6.7 - - + +
418B ILE* 3.2 21.6 + - + +
419B PRO* 1.3 74.1 - - - +
421B PRO* 1.3 59.9 - - - +
422B CYS 3.3 2.7 - - - -
423B PHE* 3.7 29.2 - - + -
424B THR* 2.2 48.0 + - + +
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Residues in contact with PRO 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A THR* 5.8 2.5 - - - +
428A SER* 3.8 28.0 - - - +
429A PHE* 6.0 0.2 - - - -
196B GLN* 4.3 9.0 - - - +
200B GLU* 3.0 15.0 - - + +
283B GLU* 3.5 33.2 - - + +
287B ALA* 4.9 9.4 - - + -
290B LEU* 6.3 2.5 - - + -
419B PRO* 3.5 10.1 - - + +
420B MET* 1.3 88.6 - - - +
422B CYS* 1.3 57.6 + - - +
424B THR* 3.7 1.1 + - - -
425B THR* 3.1 31.1 + - - +
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Residues in contact with CYS 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B GLN* 3.5 28.9 - - - -
197B LEU* 3.5 20.4 - - + +
200B GLU* 2.5 20.4 + - - +
280B LEU* 3.7 36.6 - - + +
283B GLU* 4.1 3.8 - - - -
284B ALA* 3.8 13.0 - - - -
421B PRO* 1.3 72.7 - - - +
423B PHE* 1.3 63.8 + - - +
425B THR* 3.4 7.6 - - - +
426B ALA* 3.1 26.7 + - - +
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Residues in contact with PHE 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LEU* 3.5 37.9 - - + -
200B GLU* 2.9 32.5 + - + +
201B ALA* 3.8 15.3 - - + -
204B LEU* 4.1 12.3 - - + -
323B ILE* 4.8 2.2 - - + -
326B ALA* 3.9 12.1 - - + -
327B LEU* 3.6 35.4 - - + -
330B SER* 3.4 16.6 - - - +
406B TRP* 3.5 13.1 + - - +
409B ALA* 6.0 1.1 - - + -
410B VAL* 4.2 9.3 - - + +
420B MET* 3.5 35.2 + - + -
421B PRO 3.5 0.2 - - - -
422B CYS* 1.3 76.6 - - - +
424B THR* 1.3 60.8 + - - +
426B ALA* 3.7 0.9 + - - +
427B LEU* 3.2 18.0 + - - +
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Residues in contact with THR 424 (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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414A VAL* 5.1 1.3 - - + -
424A THR* 3.6 36.3 - - + +
428A SER* 3.3 14.2 + - - +
410B VAL* 3.6 27.6 - - + -
414B VAL* 4.9 7.4 - - + -
420B MET* 2.2 38.7 + - + +
421B PRO 3.7 2.5 + - - -
423B PHE* 1.3 76.2 - - - +
425B THR* 1.3 53.8 + - - +
427B LEU* 3.2 5.2 + - + +
428B SER* 2.7 39.2 + - - -
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Residues in contact with THR 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A GLU* 2.3 32.0 + - - -
421A PRO* 6.1 0.4 - - - -
424A THR* 5.3 1.8 - - - -
425A THR* 6.2 1.6 - - - -
279B THR* 3.0 15.3 + - - +
280B LEU* 3.8 18.8 - - + -
283B GLU* 3.7 15.9 - - + -
421B PRO 3.1 20.7 + - - +
422B CYS* 3.4 14.4 - - - +
424B THR* 1.3 77.4 - - - +
426B ALA* 1.3 59.3 + - - +
428B SER* 3.9 6.8 - - - -
429B PHE* 2.9 29.6 + - - +
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Residues in contact with ALA 426 (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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279B THR* 5.3 0.4 - - - -
280B LEU* 3.8 13.9 - - + -
330B SER* 3.7 20.0 - - - +
333B ILE* 3.7 19.9 - - + +
406B TRP* 3.5 18.4 - - + -
422B CYS 3.1 20.3 + - - +
423B PHE 3.9 0.2 - - - +
425B THR* 1.3 80.2 - - - +
427B LEU* 1.3 57.8 - - - +
429B PHE 3.6 0.3 + - - -
430B TYR* 3.1 27.2 + - - +
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Residues in contact with LEU 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A VAL* 3.6 35.7 - - + -
406B TRP* 3.3 34.2 - - + +
407B ARG* 3.6 41.7 - - + +
410B VAL* 3.8 23.1 - - + -
423B PHE 3.2 16.0 + - - +
424B THR* 3.2 4.7 + - + +
426B ALA* 1.3 76.0 - - - +
428B SER* 1.3 66.2 + - - +
430B TYR* 3.4 2.4 + - + +
431B ASP* 3.1 31.4 + - - +
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Residues in contact with SER 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A LEU* 5.2 0.5 - - - +
418A ILE 5.8 0.2 - - - -
419A PRO* 4.0 9.6 - - - +
420A MET 3.7 8.7 + - - +
421A PRO* 3.8 30.3 - - - +
424A THR* 3.2 23.2 + - - +
424B THR 2.7 24.9 + - - -
425B THR* 3.9 7.9 - - - -
427B LEU* 1.3 73.9 - - - +
429B PHE* 1.3 61.3 + - - +
431B ASP* 3.5 6.5 + - - +
432B GLY* 3.0 19.9 + - - -
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Residues in contact with PHE 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A LEU* 3.6 28.7 - - + +
277B PRO* 3.6 33.2 - - + -
279B THR* 4.1 9.0 - - + +
333B ILE* 3.6 17.5 - - + -
336B ALA* 5.5 1.1 - - + -
337B GLN* 3.3 35.2 - - + +
340B MET* 3.9 26.2 - - + -
388B ASN* 5.5 0.7 - - - -
390B LEU* 4.5 12.1 - - + -
425B THR 2.9 20.0 + - - +
426B ALA 4.0 2.2 - - - +
428B SER* 1.3 76.3 - - - +
430B TYR* 1.3 60.1 + - - +
432B GLY 3.7 0.2 - - - -
433B TYR* 2.8 45.2 + + + +
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Residues in contact with TYR 430 (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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304A LEU* 3.8 33.8 - - + +
305A LYS* 2.6 35.2 + - - +
333B ILE* 4.0 12.1 - - + -
390B LEU* 4.1 19.7 - - + -
396B LYS 5.7 0.3 + - - -
399B VAL* 3.7 27.8 - - + +
400B GLU* 5.5 2.3 - - - +
403B GLN* 4.7 4.9 + - + -
406B TRP* 4.1 17.0 - + + -
407B ARG* 4.3 12.6 - - - -
426B ALA 3.1 17.9 + - - +
427B LEU* 3.7 5.4 - - + +
428B SER 3.3 0.2 - - - -
429B PHE* 1.3 81.4 - - - +
431B ASP* 1.3 69.1 + - - +
433B TYR* 4.0 2.5 - - - -
434B ARG* 3.2 35.5 + - - +
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Residues in contact with ASP 431 (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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414A VAL* 5.4 2.1 - - - -
417A GLY* 3.6 26.5 - - - +
418A ILE 4.0 5.5 + - - +
419A PRO* 3.5 14.4 - - + -
407B ARG* 2.7 43.7 + - - -
427B LEU* 3.1 21.6 + - - +
428B SER* 4.0 3.4 - - - +
430B TYR* 1.3 78.9 - - - +
432B GLY* 1.3 59.6 + - - +
434B ARG* 3.1 18.6 + - - +
435B HIS* 2.7 30.0 + - - -
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Residues in contact with GLY 432 (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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290A LEU* 3.9 14.8 - - - -
297A ARG* 3.4 16.8 - - - -
419A PRO* 3.5 18.5 - - - +
428B SER 3.0 14.5 + - - -
429B PHE 3.8 2.2 - - - -
431B ASP* 1.3 75.3 - - - +
433B TYR* 1.3 62.0 + - - +
434B ARG 3.4 0.5 + - - -
435B HIS 3.5 6.2 + - - -
438B LEU* 3.6 15.1 - - - +
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Residues in contact with TYR 433 (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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290A LEU* 3.9 26.6 - - + +
293A LEU* 5.0 4.0 - - + -
296A GLU* 2.5 51.9 + - + +
297A ARG* 3.3 23.2 - - + +
300A ALA* 3.4 32.4 - - + +
304A LEU* 4.0 17.9 - - + -
340B MET* 5.1 0.9 - - + -
388B ASN* 3.2 30.4 + - + +
390B LEU* 4.0 14.8 - - + -
391B LEU* 4.7 7.8 - - + +
429B PHE* 2.8 32.3 + + + +
430B TYR* 4.1 4.0 - - - +
432B GLY* 1.3 76.8 - - - +
434B ARG* 1.3 59.0 + - - +
435B HIS 3.4 0.2 - - - -
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Residues in contact with ARG 434 (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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300A ALA* 4.5 8.3 - - - +
301A SER* 3.2 26.9 - - - +
304A LEU* 4.1 26.0 + - + +
305A LYS 4.4 1.3 - - - -
306A GLY* 3.8 32.9 - - - +
307A PRO* 3.4 9.7 + - - +
416A ALA 4.3 1.8 + - - -
417A GLY* 2.8 41.2 + - - -
407B ARG* 4.3 0.2 - - - +
430B TYR* 3.2 30.9 + - + +
431B ASP* 3.1 23.0 + - - +
433B TYR* 1.3 76.2 - - - +
435B HIS* 1.3 75.4 + - - +
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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