Contacts of the helix formed by residues 19 - 27 (chain V) in PDB entry 2GLJ
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 LYS 19 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17V ASP* 2.5 33.4 + - - +
18V ASP* 1.3 80.7 - - - +
20V GLN* 1.3 60.5 + - + +
22V LYS* 4.5 8.3 - - - +
23V GLU* 3.6 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 20 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18V ASP* 2.6 41.1 + - - +
19V LYS* 1.3 73.6 - - + +
21V LEU* 1.3 70.0 + - + +
22V LYS 3.1 1.1 - - - -
23V GLU* 2.8 8.2 + - - +
24V VAL* 2.7 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15V LYS* 3.9 12.3 - - + +
16V TYR* 3.3 42.8 - - + +
17V ASP 3.5 7.4 + - - +
18V ASP* 3.6 17.9 - - + +
20V GLN* 1.3 79.0 - - + +
22V LYS* 1.3 66.0 + - - +
24V VAL* 3.0 16.6 + - + +
25V PHE* 2.9 16.9 - - - -
453V TYR* 3.1 33.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 22 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13V TRP* 4.7 19.9 - - + -
14V ASP 5.6 2.5 - - - +
16V TYR* 4.3 5.2 - - + -
17V ASP* 3.3 53.8 + - - +
19V LYS* 4.7 8.1 - - - +
20V GLN 2.8 3.8 + - - -
21V LEU* 1.3 75.0 - - - +
23V GLU* 1.3 51.1 + - - +
25V PHE* 2.7 23.8 + - + -
26V ALA* 2.6 41.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 23 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19V LYS 3.6 15.3 + - - +
20V GLN* 2.8 12.0 + - - +
22V LYS* 1.3 75.6 - - - +
24V VAL* 1.3 54.9 + - + +
25V PHE 2.7 10.9 + - - -
26V ALA* 4.6 6.2 - - - +
27V LEU* 3.5 32.4 + - + +
28V GLY* 3.4 13.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 24 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20V GLN* 2.7 42.9 + - + +
21V LEU* 3.2 13.5 - - + +
22V LYS 3.0 0.6 + - - -
23V GLU* 1.3 71.0 - - + +
25V PHE* 1.3 61.6 + - - +
28V GLY* 3.6 10.7 - - - -
29V ASP* 4.5 1.4 + - - +
453V TYR* 4.0 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 25 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13V TRP* 3.4 40.2 - + - -
16V TYR* 3.4 36.1 - + + -
21V LEU 2.9 23.6 - - - -
22V LYS* 2.7 18.8 + - - -
23V GLU 2.7 2.6 + - - -
24V VAL* 1.3 82.2 - - - +
26V ALA* 1.3 84.2 + - - +
27V LEU 2.8 2.2 - - - -
28V GLY* 2.7 14.7 + - - +
29V ASP* 3.1 17.0 + - + +
30V ARG* 3.2 8.1 + - - +
449V LYS* 3.9 19.2 - - + +
450V ALA 3.9 11.0 - - - -
453V TYR* 3.3 34.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13V TRP* 5.7 3.6 - - + -
22V LYS* 2.6 28.6 + - + +
23V GLU* 4.6 3.8 - - - +
25V PHE* 1.3 85.8 - - + +
27V LEU* 1.3 65.3 + - + +
30V ARG* 3.1 21.8 - - - +
449V LYS* 3.5 18.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23V GLU* 3.5 32.8 + - + +
25V PHE 3.3 1.6 - - - -
26V ALA* 1.3 84.2 - - + +
28V GLY* 1.3 71.3 + - - +
30V ARG* 3.6 17.7 - - - +
31V PHE* 3.0 26.5 - - + +
----------------------------------------------------------
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