Contacts of the helix formed by residues 386 - 394 (chain A) in PDB entry 1LVK
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 PRO 386 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A LEU* 3.8 10.8 - - + +
376A ASN* 3.9 22.2 - - + +
379A SER* 3.6 27.1 - - - +
380A THR* 6.3 0.9 - - + -
384A VAL 3.3 10.5 - - - +
385A ASN* 1.3 93.5 - - - +
387A SER* 1.3 58.3 + - - +
389A LEU* 3.5 4.1 - - + +
390A GLU* 2.7 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ASN* 3.2 16.0 + - - -
386A PRO* 1.3 81.6 - - - +
388A VAL* 1.3 58.0 + - - +
390A GLU* 3.3 13.8 - - - +
391A LYS* 2.9 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ASN* 2.7 49.6 - - + +
387A SER* 1.3 73.2 - - - +
389A LEU* 1.3 68.8 + - - +
391A LYS* 3.3 4.1 + - - +
392A ALA* 2.8 26.0 + - + +
599A CYS* 4.1 23.1 - - + -
602A ASP* 5.3 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A LEU* 4.6 18.4 - - + -
375A LEU* 3.9 15.3 - - + +
378A ALA* 4.9 1.1 - - + -
379A SER* 3.8 26.7 - - - +
384A VAL* 4.4 8.3 - - + -
385A ASN 2.7 15.4 + - - +
386A PRO* 3.5 7.0 - - + +
388A VAL* 1.3 78.7 - - - +
390A GLU* 1.3 64.3 + - - +
392A ALA* 3.0 5.0 + - - +
393A LEU* 2.8 34.6 + - + +
421A LEU* 4.2 6.1 - - + -
596A LEU* 4.0 14.1 - - + -
599A CYS* 3.6 13.0 - - - -
600A PHE* 3.3 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A LEU* 3.5 27.2 + - + +
372A LYS* 4.3 10.5 - - - +
375A LEU* 4.0 24.0 - - + +
386A PRO 2.7 18.6 + - - +
387A SER* 3.3 15.8 - - - +
389A LEU* 1.3 79.2 - - - +
391A LYS* 1.3 61.7 + - + +
393A LEU* 3.3 4.9 + - - +
394A MET* 3.1 50.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A SER* 2.9 23.0 + - - +
388A VAL* 4.0 4.5 - - - +
390A GLU* 1.3 77.0 - - + +
392A ALA* 1.3 58.1 + - - +
393A LEU 3.0 1.8 - - - -
395A GLU* 2.5 74.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A VAL* 2.8 20.3 + - + +
389A LEU* 3.3 6.3 - - - +
391A LYS* 1.3 76.3 - - - +
393A LEU* 1.3 58.5 + - - +
396A PRO* 3.9 17.8 - - - +
417A SER* 4.9 0.2 + - - -
593A GLN* 4.6 0.9 - - - +
595A ASP* 3.9 35.0 - - + +
596A LEU* 3.6 34.3 - - + +
599A CYS* 4.5 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A LEU* 5.7 2.0 - - + -
357A ILE* 4.8 11.0 - - + -
359A PHE* 4.3 19.3 - - + -
369A LEU* 5.7 1.1 - - + -
375A LEU* 4.4 9.4 - - + -
389A LEU* 2.8 33.7 + - + +
390A GLU* 3.6 9.6 - - - +
392A ALA* 1.3 80.0 - - - +
394A MET* 1.3 67.5 + - + +
396A PRO* 4.4 0.2 - - - -
409A LEU* 3.4 21.8 - - - +
414A SER* 3.8 8.5 + - - +
417A SER* 4.4 5.1 - - - -
418A ARG* 4.0 34.3 - - + +
421A LEU* 4.6 9.4 - - + -
596A LEU* 3.7 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A PHE* 3.6 30.3 - - + -
367A ALA 3.3 33.7 - - - +
368A VAL* 3.9 6.1 - - - -
369A LEU* 4.1 20.9 - - + +
390A GLU* 3.1 43.6 + - + +
393A LEU* 1.3 77.6 - - + +
395A GLU* 1.3 62.7 + - + +
396A PRO* 3.3 6.5 - - - +
407A GLN 2.7 1.7 - - - +
408A HIS* 3.4 5.7 - - + -
409A LEU 2.7 32.0 + - - +
414A SER* 3.2 22.0 - - - +
----------------------------------------------------------
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