Contacts of the helix formed by residues 20 - 30 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLY 3.4 1.4 + - - -
19B THR* 1.3 78.8 - - - +
21B LYS* 1.3 66.3 + - - +
22B SER 3.3 3.1 - - - -
23B CYS* 3.3 1.9 + - - +
24B LEU* 2.9 29.8 + - - +
121B ASN* 3.5 4.6 + - - -
601B GDP 3.0 40.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B VAL* 3.2 50.5 - - + +
14B ILE* 3.3 22.0 - - - +
15B GLY* 3.2 11.4 + - - +
16B SER 2.8 20.8 + - - -
19B THR* 3.4 10.5 - - - +
20B GLY* 1.3 77.9 - - - +
22B SER* 1.3 63.2 + - - +
24B LEU* 3.5 7.1 + - - +
25B LEU* 3.3 19.4 + - - +
63B ASP* 4.6 2.1 - - - +
64B THR* 4.3 10.1 - - - -
68B GLU* 2.8 29.8 + - - -
87B VAL* 4.0 9.2 - - + -
601B GDP 2.6 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LYS* 1.3 74.9 - - - +
23B CYS* 1.3 65.6 + - - +
25B LEU* 3.4 4.6 + - - +
26B HIS* 3.0 22.7 + - - +
43B VAL 6.2 1.6 - - - -
63B ASP* 2.5 30.3 + - - -
601B GDP 3.0 16.2 + - - -
602B MG 2.2 29.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLY 3.3 1.3 + - - +
22B SER* 1.3 77.3 - - - +
24B LEU* 1.3 56.2 + - - +
26B HIS* 3.3 8.1 + - - +
27B GLN* 2.9 30.8 + - - +
152B ALA* 3.6 18.5 - - + +
601B GDP 2.8 47.6 + - + +
603B BME 2.1 45.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B VAL* 4.4 3.8 - - + -
20B GLY 2.9 21.6 + - - +
21B LYS* 3.6 7.4 - - - +
22B SER 3.3 0.2 - - - -
23B CYS* 1.3 72.2 - - - +
25B LEU* 1.3 66.0 - - - +
27B GLN* 3.4 1.9 + - - -
28B PHE* 3.0 24.8 + - - +
85B LEU* 4.6 9.0 - - + -
87B VAL* 3.6 39.7 - - + -
119B CYS* 4.8 2.7 - - + -
121B ASN* 3.7 20.9 - - - +
150B THR* 3.8 13.5 - - + +
152B ALA* 3.6 7.2 - - + +
158B VAL* 3.6 34.8 - - + +
162B PHE* 3.7 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B VAL* 4.9 3.1 - - + -
21B LYS 3.3 10.2 + - - +
22B SER* 3.5 8.7 - - - +
23B CYS 3.4 0.2 - - - -
24B LEU* 1.3 79.1 - - - +
26B HIS* 1.3 63.7 + - - +
28B PHE* 3.3 1.2 + - - +
29B ILE* 2.8 59.7 + - + +
43B VAL* 4.4 13.2 - - + +
46B GLY* 4.4 5.4 - - - +
61B ILE* 3.3 46.9 - - + +
62B TRP 4.8 0.2 - - - +
63B ASP* 3.8 33.7 - - + +
162B PHE* 4.3 7.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B SER 3.0 17.5 + - - +
23B CYS* 3.5 8.3 - - - +
24B LEU 3.3 0.2 - - - -
25B LEU* 1.3 76.2 - - - +
27B GLN* 1.3 66.2 + - + +
29B ILE* 4.4 2.9 - - - +
30B GLU* 2.9 53.4 + - + +
43B VAL* 6.5 1.1 - - - -
603B BME 5.5 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B CYS 2.9 17.9 + - - +
24B LEU* 3.8 4.5 - - - +
26B HIS* 1.3 83.2 - - - +
28B PHE* 1.3 66.8 + - - +
30B GLU* 3.7 15.8 - - - +
152B ALA* 2.7 30.3 + - - +
153B LEU 3.8 11.1 + - - -
154B THR 4.6 1.1 - - - +
155B GLY* 3.9 23.9 - - - +
158B VAL* 4.1 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU 3.0 8.8 + - - +
25B LEU 3.3 3.8 + - - +
27B GLN* 1.3 79.6 - - - +
29B ILE* 1.3 62.8 + - + +
30B GLU 4.2 2.6 - - - +
48B ARG* 3.0 61.6 + - + -
50B VAL* 3.9 8.3 - - + -
59B LEU* 3.8 24.5 - - + -
61B ILE* 3.4 29.2 - - + -
158B VAL* 4.0 5.3 - - + +
159B GLU* 3.6 33.7 - - - -
162B PHE* 3.5 52.3 - + + -
163B LEU* 4.5 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 2.8 47.3 + - + +
26B HIS* 4.4 2.7 - - - +
28B PHE* 1.3 79.9 - - + +
30B GLU* 1.3 62.9 + - + +
46B GLY* 3.3 31.9 - - - -
47B SER 3.9 25.6 - - - +
48B ARG* 3.9 16.4 - - + +
61B ILE* 3.4 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B HIS* 2.9 38.6 + - + +
27B GLN* 3.7 18.0 - - - +
28B PHE 4.2 3.3 - - - +
29B ILE* 1.3 82.9 - - + +
48B ARG* 5.4 1.9 + - - -
----------------------------------------------------------
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