Contacts of the helix formed by residues 16 - 22 (chain M) in PDB entry 5GSE
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 THR 16 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224I A 5.1 20.7 - - - -
30J A 4.5 2.1 + - - -
31J T 3.5 17.5 + - - -
15M LYS* 1.3 75.6 - - - +
17M ARG* 1.3 66.5 + - - +
18M SER* 3.5 17.5 + - - +
19M SER* 2.4 49.6 + - - +
20M ARG* 3.3 7.3 + - - +
28M GLY 5.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 17 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J T 2.9 45.7 + - - +
32J T 5.7 2.5 - - - +
15M LYS 3.8 1.3 + - - +
16M THR* 1.3 71.5 - - - +
18M SER* 1.3 63.2 + - - +
20M ARG* 3.2 11.9 + - - +
21M ALA* 2.9 24.1 + - - +
27M VAL* 3.9 22.3 - - + +
28M GLY* 3.5 10.3 + - - -
31M HIS* 3.2 50.4 + - - +
45M ALA* 5.2 7.7 + - - +
48M PRO* 4.8 3.6 - - - +
121N TYR* 3.2 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 18 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16M THR* 3.2 15.6 + - - -
17M ARG* 1.3 78.0 - - - +
19M SER* 1.3 56.4 + - - +
21M ALA* 3.5 1.6 + - - +
22M GLY 2.9 6.1 + - - -
23M LEU* 2.8 39.0 + - - +
24M GLN 4.8 2.2 - - - -
25M PHE 3.1 19.0 + - - -
26M PRO* 3.3 5.9 - - - +
27M VAL* 2.8 35.5 + - - +
28M GLY 4.3 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 19 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M LYS* 4.0 18.1 - - - +
16M THR* 2.4 47.1 + - - +
18M SER* 1.3 74.7 - - - +
20M ARG* 1.3 65.0 + - - +
21M ALA 3.1 1.6 - - - -
22M GLY* 3.1 13.6 + - - +
23M LEU 4.8 2.5 - - - +
120N LYS* 6.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 20 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32J T 3.1 32.3 + - - -
33J G 5.9 0.4 + - - -
15M LYS* 4.5 19.6 + - + +
16M THR 3.3 8.7 + - - +
17M ARG* 3.2 12.1 + - - +
19M SER* 1.3 80.1 + - - +
21M ALA* 1.3 59.3 + - - +
120N LYS* 2.9 30.1 - - - +
121N TYR* 3.8 27.4 - - + -
124N ALA* 3.4 45.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 21 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17M ARG 2.9 15.8 + - - +
18M SER 3.7 2.5 - - - +
20M ARG* 1.3 79.0 - - - +
22M GLY* 1.3 59.7 + - - +
23M LEU* 3.6 17.8 - - + +
27M VAL* 4.3 1.6 - - + -
49M VAL* 3.4 33.0 - - + -
117N ALA* 4.0 15.3 - - + +
120N LYS* 3.8 17.6 - - - +
121N TYR* 4.2 9.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 22 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M SER 2.9 3.8 + - - -
19M SER* 3.1 13.5 + - - -
20M ARG 3.3 0.4 - - - -
21M ALA* 1.3 79.1 - - - +
23M LEU* 1.3 67.4 + - - +
24M GLN* 4.6 7.6 + - - -
56M GLU* 4.9 1.7 - - - +
120N LYS* 4.9 11.9 - - - -
----------------------------------------------------------
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