Contacts of the helix formed by residues 418 - 436 (chain B) in PDB entry 1U0C
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 418 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B PHE* 4.5 0.2 - - - -
414B SER 3.8 3.6 + - - -
415B ALA 3.8 6.9 - - - +
417B GLU* 1.3 79.1 - - - +
419B PRO* 1.3 69.6 - - - +
420B ASP* 3.0 7.0 - - - -
421B LYS* 3.1 32.6 + - - +
422B PHE 3.1 8.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B LYS* 5.9 1.3 - - - -
335B PHE* 3.5 38.1 - - + -
417B GLU 3.3 5.8 - - - +
418B SER* 1.3 83.8 - - - +
420B ASP* 1.3 64.6 + - + +
421B LYS 3.4 0.2 - - - -
422B PHE* 3.4 16.0 - - + +
423B LEU* 3.5 13.5 + - - +
451B VAL* 5.6 10.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B SER* 3.0 5.1 - - - +
419B PRO* 1.3 83.0 - - - +
421B LYS* 1.3 60.4 + - - +
422B PHE 3.0 4.9 - - - -
423B LEU* 3.3 24.7 + - + +
424B GLU* 3.2 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B GLN* 2.6 35.8 + - - -
414B SER* 2.8 41.1 + - - +
415B ALA* 4.0 1.3 - - - -
418B SER* 3.1 24.5 + - - +
420B ASP* 1.3 76.0 - - - +
422B PHE* 1.3 63.6 + - - +
424B GLU* 3.4 28.6 + - - +
425B VAL* 3.1 33.1 + - - +
428B TRP* 5.5 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B PHE* 3.8 32.3 - + + -
337B HIS* 3.8 29.8 - - + -
339B LEU* 4.0 35.2 - - + -
415B ALA* 3.3 34.1 + - + +
416B LYS* 5.9 4.3 - - + -
418B SER 3.1 7.5 + - - +
419B PRO* 3.4 15.5 - - + +
420B ASP 3.0 0.4 - - - -
421B LYS* 1.3 76.5 - - - +
423B LEU* 1.3 67.2 + - + +
425B VAL* 2.9 6.4 + - - +
426B CYS* 2.8 40.2 + - - +
448B VAL* 4.3 15.7 - - + -
451B VAL* 6.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B PRO 3.5 10.1 + - - +
420B ASP* 3.3 32.5 + - + +
422B PHE* 1.3 79.0 - - + +
424B GLU* 1.3 64.5 + - - +
426B CYS* 2.8 21.1 + - + +
427B THR* 2.8 13.8 + - - -
445B SER* 4.5 10.5 - - - +
448B VAL* 4.2 29.2 - - + +
449B ARG* 4.1 29.4 - - - +
451B VAL* 4.8 8.5 - - + -
452B LEU* 6.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 424 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B ASP 3.2 9.3 + - - +
421B LYS* 3.4 33.3 - - - +
423B LEU* 1.3 77.8 - - - +
425B VAL* 1.3 58.2 + - - +
427B THR* 2.8 31.4 + - - -
428B TRP* 3.2 44.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 425 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B LEU* 3.7 27.6 - - + -
408B ILE* 3.9 20.6 - - + +
411B GLN* 3.9 14.1 - - + +
412B LEU* 5.4 0.2 - - + -
415B ALA* 3.8 19.7 - - + -
421B LYS* 3.1 29.2 - - - +
422B PHE 2.9 8.1 + - - +
424B GLU* 1.3 70.5 - - - +
426B CYS* 1.3 59.7 + - - +
427B THR 2.9 4.9 - - - -
428B TRP* 3.0 43.7 + - + +
429B VAL* 3.2 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 426 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ILE* 3.4 24.7 - - + -
339B LEU* 4.2 4.5 - - - -
422B PHE* 2.8 40.4 + - - +
423B LEU* 2.8 13.7 + - - +
425B VAL* 1.3 75.8 - - - +
427B THR* 1.3 59.5 + - - +
429B VAL* 3.2 17.6 - - - +
430B ASP* 2.9 22.5 + - - +
445B SER* 3.3 19.0 - - - -
448B VAL* 3.9 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B LEU 2.8 13.4 + - - -
424B GLU* 2.8 19.9 + - - -
426B CYS* 1.3 78.3 - - - +
428B TRP* 1.3 79.7 + - + +
430B ASP* 2.9 21.9 + - + +
431B GLN* 3.0 30.5 + - + +
445B SER* 4.5 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B LEU* 3.8 7.9 - - + +
407B LYS* 3.5 48.0 - - + +
408B ILE* 3.2 39.5 - - + -
411B GLN* 4.4 11.2 - - + +
421B LYS* 5.7 1.1 - - - -
424B GLU* 3.3 46.7 - - + -
425B VAL* 3.0 31.2 + - + +
427B THR* 1.3 92.5 - - + +
429B VAL* 1.3 63.3 + - - +
431B GLN* 3.1 29.0 + - - +
432B ILE* 3.2 15.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ALA* 3.6 35.1 - - + +
326B GLN 4.8 0.4 - - - +
327B ILE* 3.6 28.0 - - + +
339B LEU* 4.9 4.3 - - + -
408B ILE* 3.7 8.7 - - + +
425B VAL* 3.2 13.7 - - + +
426B CYS* 3.2 23.6 - - - +
428B TRP* 1.3 75.0 - - - +
430B ASP* 1.3 62.4 + - - +
432B ILE* 3.1 3.8 + - - +
433B ALA 3.1 18.4 + - - -
441B ARG* 3.3 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B CYS 2.9 16.1 + - - +
427B THR* 2.9 16.6 + - + +
429B VAL* 1.3 77.6 - - - +
431B GLN* 1.3 63.4 + - + +
432B ILE 3.2 0.3 + - - -
433B ALA* 3.2 3.5 + - - +
434B ALA* 3.0 22.2 + - - +
441B ARG* 3.0 24.2 + - - +
444B THR* 4.3 6.6 + - - -
445B SER* 3.0 34.1 + - - -
446B GLU* 4.7 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B LEU* 3.4 33.6 - - + +
407B LYS* 4.8 2.4 + - - -
427B THR* 3.0 30.4 + - + +
428B TRP* 3.3 21.9 - - - +
430B ASP* 1.3 76.2 - - + +
432B ILE* 1.3 57.7 + - - +
434B ALA* 3.1 10.0 - - - +
435B LEU* 2.9 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ILE* 3.8 12.6 - - + +
325B ALA* 3.4 34.1 - - + +
401B GLN* 3.9 13.9 - - + +
404B LEU* 3.5 33.4 - - + -
405B VAL* 3.8 18.6 - - + -
408B ILE* 3.9 13.9 - - + -
428B TRP 3.5 8.7 - - - +
429B VAL 3.1 6.5 + - - +
430B ASP 3.1 1.0 - - - -
431B GLN* 1.3 72.9 - - - +
433B ALA* 1.3 68.8 + - - +
434B ALA 3.0 1.1 - - - -
435B LEU* 3.0 15.3 + - - +
436B ASN* 3.0 29.4 + - - +
567D C 4.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ALA 5.7 0.2 + - - -
429B VAL 3.1 3.8 + - - -
430B ASP 3.8 2.7 - - - +
432B ILE* 1.3 80.7 - - - +
434B ALA* 1.3 62.9 + - - +
436B ASN* 3.4 7.0 + - - +
438B SER* 3.0 27.0 - - - +
441B ARG* 3.5 34.3 - - - +
567D C 3.3 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B ASP 3.0 13.7 + - - +
431B GLN* 3.1 15.0 - - - +
432B ILE 3.0 0.4 - - - -
433B ALA* 1.3 77.3 - - - +
435B LEU* 1.3 64.9 + - + +
436B ASN 3.3 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLN* 5.6 1.2 - - - +
51A ARG* 5.3 3.6 + - - -
400B LYS* 3.5 50.3 - - + -
401B GLN* 3.7 26.9 + - + +
404B LEU* 4.4 14.1 - - + -
431B GLN* 2.9 19.6 + - + +
432B ILE 3.0 5.4 + - - +
434B ALA* 1.3 74.6 - - + +
436B ASN* 1.3 67.6 + - - +
437B ASP* 4.6 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLN* 5.5 0.5 - - - +
51A ARG* 6.1 0.2 - - - +
323B ILE 3.1 23.5 + - - +
324B ILE* 4.0 3.8 - - - +
398B LYS* 4.7 1.9 + - - -
401B GLN* 2.9 29.0 + - - +
432B ILE* 3.0 17.7 + - - +
433B ALA 3.4 4.1 - - - +
434B ALA 3.3 10.3 - - - +
435B LEU* 1.3 80.6 - - - +
437B ASP* 1.3 63.5 + - - +
438B SER 3.0 8.5 + - - -
566D A 3.4 41.4 + - - +
567D C 3.4 19.8 + - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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