Contacts of the helix formed by residues 396 - 412 (chain B) in PDB entry 4U1D
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 396 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ILE 4.7 0.6 + - - -
394B ASN 3.7 5.4 + - - +
395B PHE* 1.3 77.9 - - - +
397B VAL* 1.3 62.3 + - - +
398B ASP* 3.1 36.5 + - - +
399B THR* 3.0 24.2 + - - +
400B VAL* 2.9 30.1 + - - +
403B GLN* 5.6 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE* 4.2 10.2 - - + -
396B ASP* 1.3 75.2 + - - +
398B ASP* 1.3 65.7 + - - +
399B THR 3.1 1.4 + - - -
400B VAL* 3.5 18.1 + - + +
401B LYS* 4.6 7.6 + - - +
432B VAL* 3.7 30.5 - - + +
435B ALA* 3.6 33.7 - - + -
436B ALA* 5.0 0.9 - - - +
439B LYS* 6.1 7.0 - - + -
451B LEU* 3.5 38.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B ASP* 3.1 19.0 + - - +
397B VAL* 1.3 80.8 - - - +
399B THR* 1.3 64.3 + - + +
401B LYS* 6.4 0.2 - - - -
439B LYS* 3.9 27.8 + - - +
451B LEU* 4.7 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B ASP* 3.0 27.6 + - - +
398B ASP* 1.3 87.4 - - + +
400B VAL* 1.3 64.5 + - - +
401B LYS* 3.3 2.7 - - - -
402B GLN* 3.3 12.3 + - + +
403B GLN* 3.2 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ILE* 4.0 13.5 - - + +
391B ILE* 5.4 1.8 - - + -
395B PHE* 3.8 28.7 - - + -
396B ASP 2.9 10.3 + - - +
397B VAL* 3.5 31.2 + - + +
399B THR* 1.3 77.8 - - - +
401B LYS* 1.3 68.1 + - + +
403B GLN* 3.3 11.1 + - - +
404B LEU* 2.9 51.2 + - + +
428B ILE* 4.6 5.6 - - + -
432B VAL* 4.6 7.2 - - + -
454B LEU* 5.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B VAL 4.6 7.4 - - - +
398B ASP 6.4 0.4 - - - -
399B THR 3.3 0.8 - - - -
400B VAL* 1.3 88.8 - - + +
402B GLN* 1.3 56.7 + - - +
404B LEU* 4.7 1.8 - - - -
405B GLU* 3.0 30.7 + - - +
450B LYS* 2.5 34.6 + - - +
451B LEU* 3.5 23.7 - - + +
453B THR* 3.1 25.4 + - - +
454B LEU* 4.6 11.4 - - + -
455B PRO* 3.7 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B THR* 3.3 13.9 + - - +
400B VAL 3.2 0.6 - - - -
401B LYS* 1.3 76.9 - - - +
403B GLN* 1.3 67.6 + - + +
405B GLU* 2.9 29.9 + - - +
406B ASN* 3.0 44.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B GLU* 5.5 4.3 - - - +
389B ASP* 5.5 0.4 + - - -
390B ILE* 3.3 50.6 - - + +
394B ASN 5.1 5.7 + - - +
396B ASP 4.9 1.9 + - - +
399B THR* 3.2 31.5 + - - +
400B VAL* 3.6 8.4 - - - +
402B GLN* 1.3 79.1 - - + +
404B LEU* 1.3 62.6 + - - +
406B ASN* 3.2 8.0 + - - +
407B LEU* 3.0 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B LEU* 3.8 28.9 - - + -
390B ILE* 4.4 13.0 - - + -
391B ILE* 4.7 1.8 - - + -
400B VAL* 2.9 36.3 + - + +
401B LYS 3.9 3.6 - - - +
403B GLN* 1.3 75.7 - - - +
405B GLU* 1.3 57.9 + - - +
407B LEU* 4.4 6.7 - - + -
408B LEU* 2.9 43.7 + - + +
428B ILE* 3.7 33.7 - - + -
454B LEU* 4.1 11.7 - - + -
455B PRO* 4.0 10.5 - - + -
458B LEU* 4.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B LYS 3.0 14.6 + - - +
402B GLN* 2.9 29.0 + - - +
404B LEU* 1.3 76.7 - - - +
406B ASN* 1.3 63.3 + - - +
407B LEU 3.6 0.2 + - - -
408B LEU* 3.9 8.0 + - - +
409B VAL* 4.0 10.6 + - - +
455B PRO* 3.8 24.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B GLN* 3.0 46.5 + - - +
403B GLN* 3.2 6.0 + - - +
405B GLU* 1.3 79.4 + - - +
407B LEU* 1.3 59.3 + - - +
409B VAL* 3.2 22.2 - - - +
410B LYS* 4.1 9.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B GLU* 3.6 44.0 - - + +
386B GLU* 3.3 31.4 - - + +
387B LEU* 3.7 36.6 - - + +
390B ILE* 4.8 5.8 - - + -
403B GLN 3.0 17.1 + - - +
404B LEU* 4.0 7.6 - - + +
406B ASN* 1.3 77.6 - - - +
408B LEU* 1.3 61.5 + - + +
409B VAL 3.3 0.9 - - - -
410B LYS* 3.3 11.9 + - - +
411B LEU* 3.0 31.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B LEU* 6.1 1.3 - - + -
404B LEU* 2.9 30.9 + - + +
405B GLU* 3.9 4.5 + - - +
406B ASN 3.5 0.2 - - - -
407B LEU* 1.3 76.4 - - + +
409B VAL* 1.3 57.2 + - - +
410B LYS 3.2 0.4 - - - -
411B LEU* 3.6 11.7 - - + -
412B SER* 2.4 41.1 + - - +
417B PHE* 3.4 38.1 - - + -
424B LEU* 5.8 0.7 - - + -
455B PRO* 3.8 13.2 - - + +
456B ALA 3.3 26.0 - - - +
457B PRO* 3.7 9.4 - - + -
458B LEU* 3.7 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B GLU 4.0 8.1 + - - +
406B ASN* 3.2 25.8 - - - +
408B LEU* 1.3 79.6 - - - +
410B LYS* 1.3 73.0 + - + +
412B SER* 3.9 11.5 + - - -
413B SER* 4.2 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 410 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B GLU* 3.9 32.2 - - + +
386B GLU* 4.1 16.8 + - - -
406B ASN 4.1 16.6 - - - -
407B LEU* 3.3 9.3 + - - +
408B LEU 3.2 0.2 - - - -
409B VAL* 1.3 86.4 - - + +
411B LEU* 1.3 61.4 + - - +
412B SER 3.2 0.4 - - - -
413B SER* 2.6 25.8 + - - -
414B LYS* 3.8 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 411 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B GLU* 3.9 16.2 - - + +
384B LEU* 3.5 33.0 - - + -
387B LEU* 4.5 14.1 - - + -
407B LEU* 3.0 37.1 + - + +
408B LEU* 3.4 18.8 + - + -
410B LYS* 1.3 75.8 - - - +
412B SER* 1.3 63.5 + - - +
414B LYS* 3.3 26.1 + - + +
416B TYR* 4.2 1.1 - - - +
417B PHE* 3.4 48.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B LEU* 2.4 28.1 + - - +
409B VAL* 4.0 8.5 - - - -
410B LYS 3.2 0.6 - - - -
411B LEU* 1.3 77.5 - - - +
413B SER* 1.3 62.7 + - - +
414B LYS 3.4 6.2 + - - +
417B PHE* 4.3 11.3 - - - -
418B SER 5.9 0.2 + - - -
457B PRO* 4.8 12.1 - - - +
----------------------------------------------------------
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