Contacts of the helix formed by residues 411 - 417 (chain A) in PDB entry 3W3K
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 PHE 411 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A ILE* 3.1 45.6 + - + -
410A ASP* 1.3 70.3 + - - +
412A LYS* 1.3 64.5 + - - +
413A LEU 3.1 3.7 + - - -
414A PHE* 3.3 30.4 + + - +
415A GLN 4.7 0.3 + - - -
425A LEU* 3.8 23.8 - - + -
430A ILE* 4.4 13.0 - - + -
433A LEU* 5.1 11.3 - - + +
486A LEU* 4.7 4.3 - - + -
488A LEU* 4.1 30.7 - - + -
500A GLN* 4.0 31.2 - - - +
501A PHE* 6.4 0.4 - + - -
502A GLU 4.6 7.6 - - - +
503A ASN 4.2 1.5 - - - +
504A LEU* 3.8 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A GLU* 3.2 23.9 + - - +
410A ASP* 3.1 27.5 + - - +
411A PHE* 1.3 78.4 - - - +
413A LEU* 1.3 62.1 + - - +
414A PHE 3.2 1.3 + - - -
415A GLN* 3.3 20.1 + - - +
416A ASN* 4.1 7.4 + - - +
503A ASN* 3.6 44.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A LEU* 3.7 24.9 - - + +
383A ARG 3.7 26.5 - - - +
384A GLU* 3.7 29.6 - - + -
387A PHE* 4.0 13.5 - - + -
391A MET* 3.3 18.4 - - + +
409A ILE* 4.4 1.1 - - + -
410A ASP 3.1 22.1 + - - +
411A PHE 3.1 1.2 - - - -
412A LYS* 1.3 81.3 - - - +
414A PHE* 1.3 93.5 + - + +
415A GLN 3.2 0.5 + - - -
416A ASN 3.2 10.7 + - - -
417A PHE* 3.4 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A LEU* 4.1 17.0 - - + -
387A PHE* 4.9 4.3 - + - -
399A ILE* 4.3 10.8 - - + -
401A LEU* 5.0 2.2 - - + -
409A ILE* 3.8 22.4 - - + -
411A PHE* 3.3 34.3 + + - +
412A LYS 3.2 1.6 - - - -
413A LEU* 1.3 98.7 - - + +
415A GLN* 1.3 60.5 + - - +
417A PHE* 3.4 23.7 - + - +
420A LEU* 3.7 28.0 + - + +
423A ILE* 3.8 43.1 - - + -
425A LEU* 4.2 12.8 - - + -
486A LEU* 5.8 0.4 - - + -
504A LEU* 4.9 2.7 - - + -
505A PRO* 4.3 13.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A LYS* 3.3 10.4 + - - +
413A LEU 3.2 0.6 - - - -
414A PHE* 1.3 77.8 - - - +
416A ASN* 1.3 59.7 + - - +
417A PHE 3.0 15.8 - - - +
503A ASN* 3.4 27.8 + - - +
504A LEU 2.8 25.9 + - - -
505A PRO* 3.8 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A GLU* 2.2 34.2 + - - -
391A MET* 3.3 34.1 - - - +
392A GLN* 5.1 1.6 - - - +
412A LYS* 4.4 7.8 + - - +
413A LEU 3.2 8.5 + - - +
415A GLN* 1.3 76.0 - - - +
417A PHE* 1.3 63.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A PHE* 3.6 31.2 - + + -
390A LEU* 3.5 37.9 - - + -
391A MET* 3.8 16.4 - - + +
393A LEU 6.1 0.2 - - - -
396A LEU* 4.0 16.2 - - + +
399A ILE* 5.5 4.3 - - + -
413A LEU* 3.4 38.8 - - + -
414A PHE* 3.4 12.0 - + - +
415A GLN 3.0 14.8 - - - +
416A ASN* 1.3 78.7 - - - +
418A SER* 1.3 70.3 + - - +
419A ASN* 4.5 0.5 - - - -
420A LEU* 3.4 43.1 - - + +
----------------------------------------------------------
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