Contacts of the helix formed by residues 423 - 443 (chain A) in PDB entry 1U3Q
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 SER 423 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411A TYR* 4.1 33.4 + - - -
421A ASP 3.1 8.2 - - - +
422A SER* 1.3 77.4 - - - +
424A ARG* 1.3 65.9 + - - +
425A LYS 3.2 1.3 - - - -
426A LEU* 3.6 12.4 + - - +
427A ALA* 3.7 11.6 + - - +
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Residues in contact with ARG 424 (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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421A ASP* 2.5 62.0 + - - +
423A SER* 1.3 76.8 - - - +
425A LYS* 1.3 64.1 + - + +
426A LEU 3.2 0.9 - - - -
427A ALA* 3.7 6.2 + - - +
428A HIS* 3.1 25.1 + - - +
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Residues in contact with LYS 425 (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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318A GLY* 4.6 7.4 + - - -
321A GLU* 3.4 40.2 + - - +
322A LEU* 3.7 17.3 - - + +
421A ASP* 3.2 23.1 + - - +
422A SER* 3.6 15.5 - - - +
423A SER 3.2 0.4 - - - -
424A ARG* 1.3 80.9 - - + +
426A LEU* 1.3 55.8 + - - +
428A HIS* 3.7 16.6 - - + +
429A LEU* 3.1 27.3 + - - +
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Residues in contact with LEU 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A LEU* 4.2 11.6 - - + +
330A LEU* 3.9 28.0 - - + -
406A LEU* 3.7 51.8 - - + +
409A SER 5.9 2.7 - - - +
411A TYR* 5.6 10.1 - - + -
422A SER 3.8 7.9 + - - +
423A SER* 3.6 10.0 + - - +
424A ARG 3.2 0.8 - - - -
425A LYS* 1.3 75.8 - - - +
427A ALA* 1.3 56.2 + - - +
428A HIS 2.9 4.5 - - - -
429A LEU* 2.8 6.2 + - + +
430A LEU* 2.7 36.7 + - + +
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Residues in contact with ALA 427 (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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423A SER 3.7 8.1 + - - +
424A ARG* 3.7 8.4 + - - +
426A LEU* 1.3 79.6 - - - +
428A HIS* 1.3 55.9 + - - +
430A LEU* 4.1 9.7 - - - +
431A ASN* 2.9 40.0 + - - +
386C ARG* 5.3 13.2 - - - +
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Residues in contact with HIS 428 (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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424A ARG 3.1 20.7 + - - +
425A LYS* 3.7 17.7 - - + +
426A LEU 2.9 0.2 - - - -
427A ALA* 1.3 76.3 - - - +
429A LEU* 1.3 68.0 + - - +
431A ASN* 3.2 7.6 + - - +
432A ALA* 3.1 24.3 + - + +
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Residues in contact with LEU 429 (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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268A LEU* 6.1 0.9 - - + -
316A ILE* 4.2 8.3 - - + -
317A PRO* 2.9 31.2 - - + +
318A GLY* 3.5 25.4 - - - +
319A PHE* 3.6 6.7 - - + +
322A LEU* 4.2 10.1 - - + -
406A LEU* 3.2 44.9 - - + -
425A LYS* 3.1 13.7 + - - +
426A LEU* 2.8 9.1 + - + +
428A HIS* 1.3 82.1 - - - +
430A LEU* 1.3 62.7 + - - +
432A ALA* 3.0 17.4 + - + +
433A VAL* 3.3 14.1 + - + +
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Residues in contact with LEU 430 (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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403A MET* 4.2 20.4 - - + +
406A LEU* 4.0 39.4 - - + +
407A ASN* 4.0 22.7 - - + +
426A LEU* 2.7 19.6 + - + +
427A ALA* 4.1 9.9 - - - +
429A LEU* 1.3 72.5 - - - +
431A ASN* 1.3 66.9 + - - +
433A VAL* 3.2 3.1 + - - +
434A THR* 3.0 29.0 + - - +
386C ARG* 5.4 8.5 - - - +
457C ASN* 5.4 4.9 - - - +
460C MET* 3.8 28.0 - - + -
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Residues in contact with ASN 431 (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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427A ALA* 2.9 28.6 + - - +
428A HIS* 3.2 8.9 + - - +
430A LEU* 1.3 84.2 - - - +
432A ALA* 1.3 55.3 + - - +
434A THR* 3.4 6.5 + - - -
435A ASP* 2.9 28.8 + - - +
386C ARG* 5.9 2.0 - - - +
453C MET* 2.7 38.2 - - - +
457C ASN* 4.0 20.6 + - - +
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Residues in contact with ALA 432 (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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263A LEU 6.2 0.4 - - - +
265A PRO* 5.6 0.9 - - - +
268A LEU* 3.1 26.1 - - + +
428A HIS* 3.1 14.1 + - + +
429A LEU* 3.0 14.1 + - + +
431A ASN* 1.3 77.2 - - - +
433A VAL* 1.3 58.4 + - - +
435A ASP* 3.5 6.7 + - - +
436A ALA* 3.0 21.1 + - - +
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Residues in contact with VAL 433 (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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268A LEU* 3.8 18.4 - - + -
272A LEU* 4.7 7.9 - - + -
316A ILE* 5.5 1.6 - - + -
399A CYS* 3.3 34.7 - - + +
402A ALA* 4.0 15.0 - - + -
403A MET* 3.4 14.1 - - + -
406A LEU* 3.9 20.6 - - + -
429A LEU* 3.3 15.9 + - + +
430A LEU 3.2 7.5 + - - +
432A ALA* 1.3 74.5 - - - +
434A THR* 1.3 60.6 + - - +
436A ALA* 3.2 3.9 + - - +
437A LEU* 2.8 26.7 + - - +
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Residues in contact with THR 434 (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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403A MET* 3.8 17.1 - - + +
430A LEU* 3.0 19.4 + - - +
431A ASN* 3.7 5.5 - - - -
432A ALA 3.3 0.2 - - - -
433A VAL* 1.3 76.6 - - - +
435A ASP* 1.3 53.6 + - - +
437A LEU* 3.1 4.0 + - - +
438A VAL* 2.8 42.7 + - + +
455A LEU* 5.3 2.7 - - + -
453C MET* 3.9 19.3 - - + -
456C ALA* 3.3 33.7 - - + -
460C MET* 3.3 22.3 - - + +
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Residues in contact with ASP 435 (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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265A PRO* 3.8 17.7 - - + +
431A ASN 2.9 17.9 + - - +
432A ALA* 3.7 7.6 - - - +
434A THR* 1.3 79.0 - - - +
436A ALA* 1.3 62.4 + - - +
438A VAL* 3.3 10.0 + - - +
439A TRP* 2.9 21.7 + - - +
449C GLN* 3.1 37.9 + - - +
453C MET* 3.9 5.2 - - + +
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Residues in contact with ALA 436 (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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265A PRO* 4.0 19.7 - - + +
268A LEU* 4.1 11.9 - - + -
269A VAL* 3.9 22.9 - - + -
272A LEU* 5.6 0.7 - - + -
399A CYS* 4.0 6.5 - - - -
432A ALA 3.0 16.0 + - - +
433A VAL* 3.3 12.8 - - + +
435A ASP* 1.3 77.4 - - - +
437A LEU* 1.3 63.2 + - - +
439A TRP* 3.0 5.7 + - - +
440A VAL* 2.9 25.0 + - - +
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Residues in contact with LEU 437 (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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396A GLU* 4.1 32.5 - - + +
399A CYS* 3.6 24.8 - - + -
400A VAL* 4.5 11.0 - - + -
403A MET* 3.8 24.5 - - + -
433A VAL 2.8 14.7 + - - +
434A THR* 3.1 8.0 + - - +
436A ALA* 1.3 75.1 - - - +
438A VAL* 1.3 64.9 + - - +
440A VAL* 3.0 15.5 + - + +
441A ILE* 3.0 28.2 + - + +
455A LEU* 3.7 22.9 - - + -
458A LEU* 4.5 10.1 - - + -
459A LEU* 4.5 4.3 - - + -
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Residues in contact with VAL 438 (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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434A THR* 2.8 41.6 + - + +
435A ASP* 3.4 12.6 - - - +
437A LEU* 1.3 74.1 - - - +
439A TRP* 1.3 60.3 + - - +
441A ILE* 3.7 9.7 + - - +
442A ALA* 3.2 22.1 + - + +
451A GLN* 4.8 3.1 - - - +
455A LEU* 4.4 21.8 - - + -
449C GLN* 5.1 10.1 - - - +
452C SER* 4.2 26.2 - - - +
453C MET* 4.4 5.4 - - + -
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Residues in contact with TRP 439 (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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265A PRO* 3.7 29.4 - - + -
266A GLU* 3.7 46.2 - - + -
269A VAL* 4.1 10.5 - - + -
395A LYS* 4.9 14.4 - - + -
435A ASP* 2.9 14.1 + - - +
436A ALA 3.3 9.9 - - - +
437A LEU 3.0 0.2 - - - -
438A VAL* 1.3 74.3 - - - +
440A VAL* 1.3 87.2 - - + +
441A ILE 3.1 2.0 - - - -
442A ALA* 3.0 9.4 + - + +
443A LYS* 2.8 66.8 + - + +
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Residues in contact with VAL 440 (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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269A VAL* 4.1 13.2 - - + -
393A GLN* 5.8 2.5 - - + -
395A LYS* 3.8 36.6 + - + +
396A GLU* 3.9 24.0 - - + +
399A CYS* 4.3 7.2 - - - -
436A ALA 2.9 20.3 + - - +
437A LEU* 3.0 10.1 + - + +
439A TRP* 1.3 99.5 - - + +
441A ILE* 1.3 61.7 + - - +
443A LYS* 3.6 14.2 + - - +
444A SER* 3.8 5.7 + - - -
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Residues in contact with ILE 441 (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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396A GLU* 4.0 20.0 - - - +
437A LEU* 3.0 36.1 + - + +
438A VAL* 4.0 6.3 - - - +
440A VAL* 1.3 73.9 - - - +
442A ALA* 1.3 62.7 + - - +
444A SER* 2.7 31.5 + - - +
446A ILE* 4.0 6.6 - - + +
451A GLN* 4.0 31.4 - - + +
454A ARG* 3.9 17.5 - - + +
455A LEU* 3.9 37.0 - - + +
458A LEU* 4.2 10.3 - - + -
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Residues in contact with ALA 442 (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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438A VAL* 3.2 12.5 + - + +
439A TRP* 3.0 14.4 + - + +
441A ILE* 1.3 75.7 - - - +
443A LYS* 1.3 53.2 + - - +
444A SER 2.9 4.7 - - - -
445A GLY* 2.6 30.5 + - - -
451A GLN* 3.4 29.6 + - - +
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Residues in contact with LYS 443 (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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395A LYS* 5.4 11.5 - - - +
439A TRP* 2.8 62.6 + - + +
440A VAL* 3.7 9.2 - - - +
441A ILE 3.2 0.2 - - - -
442A ALA* 1.3 75.6 - - - +
444A SER* 1.3 62.6 + - - +
445A GLY* 3.0 1.6 + - - -
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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