Contacts of the helix formed by residues 27 - 32 (chain A) in PDB entry 5JTO
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 27 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA 3.4 0.2 - - - -
26A PRO* 1.3 87.3 - - - +
28A ALA* 1.4 54.1 + - - +
29A PRO* 3.4 7.0 - - - -
30A HIS* 3.0 14.2 + - + -
31A VAL* 2.8 35.3 + - - +
71A GLU* 3.3 39.3 - - + +
72A THR* 3.1 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA* 3.2 36.0 + - + +
27A ASN* 1.4 75.4 - - - +
29A PRO* 1.4 68.0 - - + +
30A HIS 3.1 1.2 + - - -
31A VAL* 3.2 12.3 + - - +
32A PHE* 3.0 33.1 + - + -
73A ALA 4.4 3.1 + - - -
121A GLY 5.8 0.2 - - - +
17B TYR* 3.5 24.9 - - + -
19B LYS* 4.3 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PRO 4.9 1.8 - - - +
27A ASN* 3.4 5.8 - - - -
28A ALA* 1.4 93.6 - - + +
30A HIS* 1.3 65.8 + - + +
32A PHE* 4.5 8.0 + - + +
33A GLN* 4.5 8.7 + - - +
17B TYR* 3.2 24.0 - - + +
19B LYS* 3.5 23.3 - - - +
49B SER* 5.5 1.3 - - - +
51B LEU* 3.5 39.2 - - + +
57B GLU* 3.8 6.1 - - + +
83B ILE* 4.3 10.5 - - + +
304E PRO* 5.3 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PRO 5.6 0.2 - - - -
27A ASN* 3.0 16.3 + - + +
29A PRO* 1.3 97.3 - - + +
31A VAL* 1.3 59.9 + - - +
32A PHE 3.5 1.1 - - - -
33A GLN* 3.0 37.8 + - - +
34A LYS* 3.2 8.2 - - - +
71A GLU* 3.1 28.9 + - - +
51B LEU* 4.2 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASN 2.8 12.2 + - - +
28A ALA* 3.2 6.4 + - - +
30A HIS* 1.3 74.5 - - - +
32A PHE* 1.3 78.2 + - + +
33A GLN 3.1 5.2 - - - -
34A LYS* 3.0 24.0 + - + +
36A TRP* 3.9 4.5 - - - -
68A LEU* 3.7 27.2 - - + +
71A GLU* 3.4 19.5 - - + +
72A THR 3.5 27.1 - - - +
73A ALA* 3.6 27.8 - - + -
123A PHE* 4.8 4.9 - - + -
297E TYR* 4.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ALA* 3.0 34.9 + - + -
29A PRO* 4.5 7.6 + - + +
30A HIS 3.5 0.8 - - - -
31A VAL* 1.3 83.4 - - + +
33A GLN* 1.3 55.5 + - - +
36A TRP* 3.2 23.4 - - - -
121A GLY 3.3 21.5 - - - -
122A THR 3.5 9.4 - - - -
123A PHE* 4.2 20.9 - + + -
15B ARG* 3.2 50.7 - - - +
17B TYR* 3.9 15.5 - + - -
83B ILE* 5.5 0.7 - - + -
297E TYR* 4.7 1.3 - - - -
301E ILE* 4.1 14.6 - - + -
302E ASP 4.6 4.6 - - - +
303E LYS* 4.9 1.4 - - - +
304E PRO* 4.1 22.2 - - + +
----------------------------------------------------------
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