Contacts of the helix formed by residues 534 - 539 (chain L) in PDB entry 4E2I
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 534 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484G ASP 5.2 1.6 - - - +
486G PRO* 3.6 33.7 - - + -
491L ILE* 3.5 27.6 - - + +
495L ASP* 4.4 3.6 - - + +
532L SER* 4.0 2.0 - - - +
533L VAL* 1.3 85.9 - - - +
535L LYS* 1.3 60.2 + - - +
536L THR* 4.0 7.4 - - - +
537L LEU* 3.0 16.4 + - + +
538L GLN* 2.9 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 535 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428G ILE* 4.4 21.6 - - + +
483G ARG* 3.3 29.6 + - - +
484G ASP* 3.9 30.4 + - + +
485G LEU* 4.5 11.3 - - - +
533L VAL 3.7 1.9 + - - -
534L PRO* 1.3 72.3 - - - +
536L THR* 1.3 67.8 + - + +
537L LEU 3.0 0.2 - - - -
538L GLN* 4.0 7.8 - - - +
539L ALA* 3.1 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 536 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428G ILE* 4.0 24.9 - - + -
485G LEU* 3.7 29.4 - - + -
486G PRO* 3.5 15.7 - - + +
529G ASN* 4.7 2.0 - - - +
531G TYR* 4.8 0.2 - - - +
495L ASP* 2.9 25.6 + - - -
498L ARG* 2.9 24.9 + - - +
534L PRO* 4.0 0.5 - - - +
535L LYS* 1.3 86.9 - - + +
537L LEU* 1.3 57.1 + - - +
539L ALA* 4.2 2.8 + - - +
540L ARG* 3.0 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 537 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491L ILE* 3.8 31.4 - - + +
494L LEU* 3.6 43.1 - - + +
495L ASP* 4.2 9.0 - - + +
498L ARG* 5.3 1.1 - - - +
501L LEU* 3.8 19.7 - - + -
528L MET* 5.3 0.4 - - + -
533L VAL* 3.5 19.5 - - + -
534L PRO* 3.0 17.6 + - + +
535L LYS 3.0 0.4 - - - -
536L THR* 1.3 79.1 + - - +
538L GLN* 1.3 60.9 + - - +
539L ALA 3.0 2.0 - - - -
540L ARG* 2.9 23.7 + - + +
541L PHE* 3.1 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 538 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423L LEU* 3.8 26.0 - - - +
425L LYS* 5.7 0.3 + - - -
533L VAL* 3.6 25.5 - - + +
534L PRO 2.9 15.0 + - - +
535L LYS* 4.0 7.6 - - - +
537L LEU* 1.3 77.0 - - - +
539L ALA* 1.3 57.1 + - - +
540L ARG 3.0 4.7 + - - -
541L PHE* 3.1 36.3 + - - +
544L GLN* 3.9 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 539 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428G ILE* 4.3 15.9 - - + -
429G ASP* 3.8 21.7 - - - +
418L LYS* 3.5 29.7 - - - +
535L LYS 3.1 17.5 + - - +
536L THR* 4.3 7.6 - - - +
537L LEU 3.0 1.0 - - - -
538L GLN* 1.3 76.1 - - - +
540L ARG* 1.3 59.5 + - - +
541L PHE 3.4 3.3 - - - +
----------------------------------------------------------
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