Contacts of the helix formed by residues 20 - 30 (chain A) in PDB entry 2O52
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 GLY 20 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLY 3.4 1.6 + - - -
19A THR* 1.3 79.1 - - - +
21A LYS* 1.3 58.5 + - - +
22A SER 3.4 2.5 - - - -
23A CYS* 3.2 2.8 + - - +
24A LEU* 2.9 36.6 + - - +
121A ASN* 3.4 5.5 + - - -
122A LYS* 4.2 0.2 - - - +
601A GDP 3.1 39.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 3.4 41.6 - - + +
14A ILE 3.4 29.4 - - - -
15A GLY* 3.4 11.5 + - - +
16A SER 2.8 17.8 + - - -
19A THR* 3.5 9.9 - - - +
20A GLY* 1.3 76.4 - - - +
22A SER* 1.3 62.3 + - - +
24A LEU* 3.4 7.6 + - - +
25A LEU* 3.3 20.1 + - - +
63A ASP* 4.6 2.2 - - - +
64A THR* 4.2 10.3 - - - -
68A GLU* 2.7 31.1 + - - -
87A VAL* 4.0 8.7 - - + -
601A GDP 2.4 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 1.3 76.1 - - - +
23A CYS* 1.3 58.2 + - - +
25A LEU* 3.5 4.0 + - - +
26A HIS* 3.0 28.8 + - - +
43A VAL* 4.8 9.8 - - - +
63A ASP* 2.7 27.3 + - - -
601A GDP 3.0 15.5 + - - -
602A MG 2.2 31.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLY 3.2 1.3 + - - +
22A SER* 1.3 75.5 - - - +
24A LEU* 1.3 58.8 + - - +
26A HIS* 4.0 5.2 + - - +
27A GLN* 2.9 31.2 + - - +
152A ALA* 3.5 19.5 - - + +
601A GDP 2.8 51.7 + - + +
603A BME 2.4 42.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 4.7 2.0 - - + -
20A GLY 2.9 20.7 + - - +
21A LYS* 3.7 6.1 - - - +
22A SER 3.3 0.2 - - - -
23A CYS* 1.3 77.6 - - - +
25A LEU* 1.3 56.0 + - - +
27A GLN* 3.4 1.3 + - - -
28A PHE* 3.0 30.5 + - - +
85A LEU* 4.6 12.1 - - + -
87A VAL* 3.5 39.7 - - + -
119A CYS* 4.8 2.9 - - + -
121A ASN* 3.5 23.8 - - - +
150A THR* 3.8 12.8 - - + +
152A ALA* 3.6 13.2 - - + -
158A VAL* 3.6 27.5 - - + +
162A PHE* 4.3 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 5.2 3.1 - - + +
21A LYS 3.3 10.7 + - - +
22A SER* 3.6 9.4 - - - +
24A LEU* 1.3 78.7 - - - +
26A HIS* 1.3 62.8 + - - +
28A PHE* 3.2 2.4 + - + +
29A ILE* 3.1 50.8 + - + +
43A VAL* 4.2 17.7 - - + -
46A GLY 4.1 7.9 - - - +
61A ILE* 3.5 54.3 - - + +
63A ASP* 4.0 28.7 - - + +
162A PHE* 4.4 10.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A SER 3.0 17.3 + - - +
23A CYS* 4.0 6.5 - - - +
25A LEU* 1.3 75.8 - - - +
27A GLN* 1.3 58.6 + - - +
29A ILE* 4.7 1.8 - - - +
30A GLU* 2.8 66.2 + - + +
43A VAL* 5.4 11.2 - - + +
603A BME 5.6 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A CYS 2.9 19.3 + - - +
24A LEU* 3.6 4.9 - - - +
26A HIS* 1.3 82.9 + - - +
28A PHE* 1.3 60.8 + - - +
29A ILE 3.4 0.2 + - - -
30A GLU 3.9 12.4 + - - -
152A ALA* 2.8 28.5 + - - +
153A LEU 3.9 11.1 + - - -
154A THR 4.6 1.7 + - - -
155A GLY* 3.9 23.6 - - - +
158A VAL* 3.9 15.3 - - + -
603A BME 5.4 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU 3.0 18.2 + - - +
25A LEU 3.2 3.8 + - - +
27A GLN* 1.3 77.6 - - - +
29A ILE* 1.3 64.4 + - + +
48A ARG* 3.0 66.0 + - + +
50A VAL* 3.8 25.4 - - + -
59A LEU* 4.1 6.1 - - + -
61A ILE* 3.6 31.6 - - + -
158A VAL* 3.9 6.0 - - + +
159A GLU* 3.9 23.6 - - + -
162A PHE* 3.4 48.7 - + + -
163A LEU* 5.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.1 44.9 + - + +
26A HIS* 4.5 1.6 - - - +
27A GLN 4.4 0.4 - - - -
28A PHE* 1.3 88.3 - - + +
30A GLU* 1.3 65.7 + - + +
43A VAL* 5.8 1.8 - - + -
46A GLY* 3.3 32.1 - - - +
47A SER 4.2 17.7 - - - +
48A ARG* 4.4 12.7 - - + +
61A ILE* 4.5 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A HIS* 2.8 56.0 + - + +
27A GLN* 4.2 11.2 - - - -
28A PHE 3.8 0.4 - - - -
29A ILE* 1.3 79.7 - - + +
----------------------------------------------------------
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