Contacts of the helix formed by residues 19 - 29 (chain B) in PDB entry 1JA8
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 ASN 19 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TYR 4.6 0.2 - - - -
15B GLU* 3.4 19.7 - - + +
16B PRO 4.4 0.9 + - - +
18B ILE* 1.3 76.9 - - - +
20B ALA* 1.3 61.8 + - - +
21B GLN* 3.1 14.5 + - - +
22B ILE* 3.0 26.0 + - - +
23B MET* 3.4 17.4 + - - +
167B LEU* 4.8 3.8 + - - +
168B GLN* 2.7 50.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TYR* 3.4 16.2 - - + +
12B GLY* 3.8 13.9 - - - +
15B GLU* 3.2 21.3 + - - +
19B ASN* 1.3 72.1 - - - +
21B GLN* 1.3 67.1 + - - +
23B MET* 3.2 2.4 + - - +
24B GLN* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ASN* 3.1 12.5 + - - +
20B ALA* 1.3 76.7 - - - +
22B ILE* 1.3 63.7 + - - +
24B GLN* 3.4 6.0 + - - +
25B LEU* 2.9 37.0 + - + +
167B LEU* 4.0 34.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ILE* 4.0 12.3 - - + -
19B ASN* 3.0 14.3 + - - +
21B GLN* 1.3 75.4 - - - +
23B MET* 1.3 57.7 + - - +
25B LEU* 3.0 6.5 + - - +
26B HIS* 2.6 43.5 + - + +
163B HIS 3.8 17.0 - - - +
164B ALA* 3.6 19.5 - - - +
165B TYR* 3.9 20.2 - - - -
167B LEU* 4.0 21.1 - - + -
168B GLN* 3.6 45.3 - - + +
169B TYR* 5.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 4.1 16.4 - - + -
9B TYR* 4.1 6.1 - - + +
10B ASP 5.6 0.2 - - - +
11B TYR* 3.2 35.4 - - + +
14B LEU* 3.8 28.5 - - + -
18B ILE* 3.6 31.4 - - + +
19B ASN 3.4 10.3 + - - +
20B ALA 3.2 2.1 + - - +
22B ILE* 1.3 79.7 - - - +
24B GLN* 1.3 58.8 + - - +
26B HIS* 3.6 5.4 - - - +
27B HIS* 2.9 34.0 + - - +
77B PHE* 5.9 0.7 - - - -
78B TRP* 3.6 36.6 - - + -
81B LEU* 5.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TYR* 3.5 43.1 - - + +
20B ALA* 2.9 22.4 + - - +
21B GLN* 3.8 5.3 - - - +
23B MET* 1.3 72.4 - - - +
25B LEU* 1.3 58.1 + - + +
28B SER* 2.4 48.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
21B GLN* 2.9 29.4 + - + +
22B ILE* 3.6 2.7 - - - +
24B GLN* 1.3 76.1 - - + +
26B HIS* 1.3 67.0 + - - +
28B SER* 4.3 1.8 - - - -
29B LYS* 2.9 44.4 + - + +
30B HIS* 3.1 20.8 + - + +
163B HIS 6.1 1.6 - - - +
167B LEU* 3.4 33.0 - - + -
----------------------------------------------------------
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 ILE* 2.6 29.2 + - + +
23B MET* 3.6 8.0 - - - +
25B LEU* 1.3 73.3 - - - +
27B HIS* 1.3 57.0 + - - +
30B HIS* 3.2 14.6 - - + +
31B HIS* 2.8 29.6 + - - +
74B HIS* 2.9 17.5 + + - -
77B PHE* 4.0 15.2 - + - -
78B TRP* 3.4 18.2 - + + -
159B ASP* 2.9 18.6 - - - -
163B HIS* 3.1 17.6 + + - +
164B ALA* 3.8 21.0 - - + -
199B MN 2.2 28.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 3.8 26.8 - - + +
5B PRO 2.7 31.2 + - - -
6B ASP* 4.1 3.8 + - - -
7B LEU* 3.6 35.7 + - + +
11B TYR* 2.8 36.8 - + + -
23B MET 2.9 16.9 + - - +
26B HIS* 1.3 75.6 - - - +
28B SER* 1.3 65.8 + - - +
29B LYS 3.3 0.2 - - - -
31B HIS* 3.5 5.1 - - - +
32B ALA 3.3 19.8 + - - -
78B TRP* 3.9 20.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 4.8 3.6 - - - -
11B TYR* 3.7 15.3 - - - -
24B GLN* 2.4 39.4 + - - +
25B LEU* 5.6 0.2 - - - +
27B HIS* 1.3 78.4 - - - +
29B LYS* 1.3 74.5 + - - +
32B ALA* 3.3 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 2.9 39.0 + - + +
28B SER* 1.3 92.9 - - - +
30B HIS* 1.3 64.5 + - + +
31B HIS 3.5 0.4 - - - -
32B ALA* 3.4 1.4 + - - +
33B ALA* 2.9 32.8 + - - +
----------------------------------------------------------
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