Contacts of the helix formed by residues 20 - 33 (chain B) in PDB entry 1KO1
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* 3.1 7.1 + - - -
19B SER* 1.3 78.9 - - - +
21B LYS* 1.3 64.3 + - - +
22B SER 3.5 2.7 - - - -
23B ALA* 3.4 10.8 + - - +
24B VAL* 3.0 28.6 + - - +
110B LEU* 4.1 1.3 - - - -
120B ARG* 4.0 18.8 - - - +
124B ARG* 5.7 1.6 - - - -
176B CL 3.4 4.6 - - - +
----------------------------------------------------------
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 LEU* 3.4 23.9 - - + +
14B MET 3.6 18.6 - - - +
15B GLY 3.0 19.8 + - - +
16B VAL 3.2 9.9 + - - -
17B SER* 3.9 3.8 - - - +
19B SER* 3.4 12.3 - - - +
20B GLY* 1.3 76.6 - - - +
22B SER* 1.3 57.8 + - - +
24B VAL* 3.4 1.6 + - - +
25B ALA* 2.9 31.2 + - - +
40B ASP* 6.1 0.7 - - - -
86B VAL* 3.6 29.5 - - + +
88B SER* 3.8 17.5 - - - +
110B LEU* 3.6 18.8 - - + -
176B CL 2.9 30.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
20B GLY 3.5 0.4 - - - -
21B LYS* 1.3 73.4 - - - +
23B ALA* 1.3 61.6 + - - +
25B ALA* 3.8 0.2 - - - +
26B SER* 2.8 38.4 + - - -
36B PHE* 4.2 4.7 - - - -
38B ASP* 2.8 29.7 + - - -
40B ASP* 5.6 1.4 + - - -
86B VAL* 3.9 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLY* 3.4 13.6 + - - +
22B SER* 1.3 78.7 - - - +
24B VAL* 1.3 63.3 + - - +
26B SER* 3.9 4.6 - - - -
27B GLU* 3.2 23.7 + - - +
160B LEU* 4.4 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 3.9 11.0 - - + -
19B SER 5.0 1.3 - - - +
20B GLY* 3.0 19.8 + - - +
21B LYS 3.7 3.6 - - - +
23B ALA* 1.3 73.8 - - + +
25B ALA* 1.3 59.9 + - - +
27B GLU* 3.3 2.6 + - - +
28B VAL* 2.9 36.5 + - + +
110B LEU* 4.1 11.4 - - + -
120B ARG* 6.2 1.6 - - - +
160B LEU* 4.1 16.4 - - + -
163B VAL* 3.7 26.7 - - + -
164B VAL* 4.5 11.0 - - + -
167B THR* 3.6 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 3.8 17.7 - - + +
21B LYS 2.9 21.9 + - - +
24B VAL* 1.3 73.8 - - - +
26B SER* 1.3 58.6 + - - +
29B ALA* 2.8 33.2 + - - +
36B PHE* 3.2 33.7 - - + -
84B LEU* 3.5 12.9 - - + +
86B VAL* 3.7 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A HIS* 4.7 4.9 - - - -
22B SER* 2.8 26.3 + - - -
23B ALA* 3.9 5.1 - - - -
25B ALA* 1.3 73.8 - - - +
27B GLU* 1.3 62.8 + - - +
29B ALA* 3.8 2.4 - - - +
30B HIS* 3.1 23.6 + - - +
36B PHE* 3.2 26.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A HIS* 3.0 31.1 + - - -
23B ALA 3.2 15.6 + - - +
24B VAL 3.9 0.2 - - - +
26B SER* 1.3 76.5 - - - +
28B VAL* 1.3 65.9 + - - +
30B HIS* 3.3 3.5 + - - +
31B GLN* 3.0 54.5 + - - +
160B LEU* 5.7 6.3 - - + -
164B VAL* 3.8 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B VAL* 2.9 26.3 + - + +
27B GLU* 1.3 74.7 - - - +
29B ALA* 1.3 65.0 + - - +
31B GLN* 3.2 2.4 + - - +
32B LEU* 2.9 34.9 + - + +
84B LEU* 3.6 20.6 - - + -
164B VAL* 3.9 19.3 - - + +
167B THR* 3.8 28.7 - - + -
168B ILE* 4.0 12.3 - - + -
171B ILE* 3.8 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA 2.8 23.1 + - - +
26B SER* 3.8 4.0 - - - +
28B VAL* 1.3 74.0 - - - +
30B HIS* 1.3 59.2 + - - +
33B HIS* 2.9 10.4 + - - -
34B ALA* 2.9 46.8 + - - +
35B ALA 4.3 1.6 - - - +
36B PHE* 3.6 27.1 - - + -
84B LEU* 3.8 6.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER* 4.8 8.5 - - - -
27A GLU* 3.3 27.2 + - - -
30A HIS* 3.4 62.8 + + + +
26B SER 3.1 11.2 + - - +
27B GLU* 3.7 7.6 + - - +
28B VAL 3.2 0.2 - - - -
29B ALA* 1.3 81.6 - - - +
31B GLN* 1.3 66.5 + - - +
33B HIS* 3.4 19.7 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLU* 3.0 48.5 + - - +
28B VAL 3.8 3.1 - - - +
30B HIS* 1.3 82.1 - - - +
32B LEU* 1.3 62.9 + - + +
33B HIS* 3.3 14.2 + - - -
164B VAL* 3.5 12.3 - - - +
168B ILE* 3.2 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 2.9 38.2 + - + +
31B GLN* 1.3 80.6 - - + +
33B HIS* 1.3 74.7 + - - +
34B ALA* 3.1 12.1 + - + +
82B VAL* 4.6 13.0 - - + +
168B ILE* 4.1 24.2 - - + -
171B ILE* 3.9 30.5 - - + -
172B LYS* 4.0 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ALA 2.9 7.0 + - - -
30B HIS* 3.4 12.2 + + - +
31B GLN 3.3 15.1 + - - -
32B LEU* 1.3 81.5 - - - +
34B ALA* 1.3 60.9 + - - +
80B ASN* 5.5 1.7 - - - +
----------------------------------------------------------
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