Contacts of the helix formed by residues 20 - 27 (chain C) in PDB entry 5J3V
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 LEU 20 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A PHE* 3.8 17.3 - - + +
585A PRO* 3.7 37.0 - - + -
588A GLU* 3.9 22.0 - - + +
643A VAL* 5.8 3.1 - - + -
18C LYS* 4.3 18.8 - - - +
19C GLN* 1.3 78.8 - - - +
21C ALA* 1.3 66.6 + - - +
22C THR* 3.3 5.6 - - - +
23C LYS* 4.3 7.4 - - + +
24C ALA* 3.2 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A LEU* 5.1 14.4 - - + -
20C LEU* 1.3 79.7 - - - +
22C THR* 1.3 61.4 + - - +
24C ALA* 4.3 1.7 - - - +
25C ALA* 3.2 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A SER* 5.5 2.5 - - - +
539A LEU* 3.4 31.6 + - - +
540A ILE* 3.6 35.9 - - + +
543A ASP* 3.4 34.8 - - + +
20C LEU* 3.3 2.9 - - - +
21C ALA* 1.3 75.7 - - - +
23C LYS* 1.3 67.1 + - - +
24C ALA 3.2 0.9 - - - -
25C ALA* 3.0 16.5 + - - +
26C ARG* 3.4 14.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A GLU* 4.3 9.9 - - - -
543A ASP* 3.9 12.9 + - - +
547A THR* 5.8 0.7 - - - +
550A ASP* 5.8 2.0 + - - -
16C PRO* 5.5 7.9 - - - +
17C ARG 5.1 5.3 + - - -
19C GLN* 3.5 44.9 - - + +
20C LEU* 3.9 8.0 + - + +
22C THR* 1.3 79.0 - - - +
24C ALA* 1.3 57.3 + - - +
26C ARG* 3.4 21.0 - - - +
27C LYS* 3.2 55.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C GLN* 3.7 21.3 + - + +
20C LEU 3.2 18.8 + - - +
21C ALA* 4.4 2.7 - - - +
22C THR 3.2 0.8 - - - -
23C LYS* 1.3 77.8 - - - +
25C ALA* 1.3 62.7 + - - +
26C ARG 3.4 0.7 + - - -
27C LYS* 3.7 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A ILE* 6.5 0.2 - - + -
21C ALA 3.2 19.3 + - - +
22C THR* 3.0 9.5 + - - +
24C ALA* 1.3 80.3 - - - +
26C ARG* 1.3 58.6 + - - +
27C LYS 5.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A SER* 3.7 30.5 - - - +
505A ALA* 3.9 8.5 + - - +
506A THR* 3.7 32.6 + - - +
509A GLU* 3.3 37.0 + - - -
543A ASP* 2.6 40.4 + - - -
547A THR* 3.3 11.7 + - - -
22C THR* 3.6 7.9 - - - +
23C LYS* 3.4 23.8 - - - +
25C ALA* 1.3 80.0 - - - +
27C LYS* 1.3 73.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A GLU* 2.9 31.6 + - - +
19C GLN* 3.9 21.5 - - - +
23C LYS* 3.2 47.0 + - + +
24C ALA* 3.7 11.9 + - - +
25C ALA 3.7 0.5 - - - +
26C ARG* 1.3 95.4 - - - +
----------------------------------------------------------
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