Contacts of the helix formed by residues 25 - 35 (chain J) in PDB entry 5GJQ
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 LEU 25 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J TYR* 1.3 89.6 - - - +
26J SER* 1.3 70.4 + - - +
27J LYS* 4.8 0.2 - - - +
28J ILE* 4.6 2.3 - - - +
29J GLU* 3.2 32.6 + - - +
40K LEU* 4.8 7.0 - - + +
102N ALA* 2.7 59.7 - - + +
105N ILE* 3.3 35.4 - - + -
106N ASP* 4.7 0.9 - - - +
153N ILE* 5.8 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 26 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25J LEU* 1.3 87.7 - - - +
27J LYS* 1.4 68.8 + - - +
29J GLU* 2.9 35.9 - - - +
30J GLU 3.5 2.8 + - - -
40K LEU* 1.9 61.8 - - - +
41K TYR* 4.3 0.4 + - - -
44K TYR* 3.8 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 27 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J TYR* 2.7 35.9 + - + +
26J SER* 1.4 81.6 - - - +
28J ILE* 1.3 63.5 + - - +
29J GLU 2.8 0.3 + - - -
30J GLU* 3.0 19.9 + - - +
31J LEU* 5.3 0.5 - - - +
39K ASP* 5.0 14.8 - - + +
40K LEU* 3.2 39.8 - - + +
43K ARG* 5.2 11.2 - - - +
201S ARG* 6.3 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 28 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J TYR* 3.2 39.5 + - + +
25J LEU 4.6 1.8 - - - +
27J LYS* 1.3 79.1 - - + +
29J GLU* 1.3 56.8 + - + +
31J LEU* 2.6 39.4 + - + +
32J GLN* 3.5 3.2 + - + +
201S ARG* 5.0 2.9 - - - +
240S LEU* 1.6 59.5 - - + +
241S ARG* 3.1 14.4 - - + +
242S HIS* 2.3 53.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 29 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25J LEU* 3.2 34.5 + - - +
26J SER* 2.9 21.8 + - - +
27J LYS 2.8 1.2 + - - -
28J ILE* 1.3 79.1 - - - +
30J GLU* 1.3 60.8 + - - +
31J LEU 3.1 0.7 + - - -
32J GLN* 3.2 29.6 + - - +
33J LEU* 3.5 9.0 + - - +
44K TYR* 2.7 61.4 + - + -
106N ASP* 3.7 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 30 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26J SER 3.5 1.4 + - - -
27J LYS 3.0 14.3 + - - +
29J GLU* 1.3 76.3 - - - +
31J LEU* 1.3 49.8 - - - +
33J LEU* 3.6 1.5 + - - -
34J ILE* 1.9 54.4 + - + +
40K LEU* 5.6 1.3 - - - -
43K ARG* 2.9 48.2 + - + +
44K TYR* 3.5 31.6 - - + +
47K LEU* 3.6 27.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J LYS 5.3 0.4 - - - +
28J ILE* 2.6 29.4 + - + +
30J GLU* 1.3 69.5 - - + +
32J GLN* 1.3 65.5 + - - +
34J ILE* 2.9 20.5 - - + +
35J VAL* 3.0 38.8 + - + +
201S ARG* 3.3 29.8 - - - +
241S ARG 3.5 14.1 - - - +
242S HIS* 4.0 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 32 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J ILE* 3.5 1.7 + - - +
29J GLU* 3.2 24.7 + - - +
31J LEU* 1.3 80.5 - - - +
33J LEU* 1.3 60.7 + - + +
35J VAL* 3.9 12.6 + - - +
36J ASN* 3.9 10.7 - - - +
44K TYR* 5.5 1.9 - - - -
242S HIS* 4.0 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J GLU 3.5 9.7 + - - +
30J GLU* 4.1 2.5 - - - +
31J LEU 3.1 0.2 - - - -
32J GLN* 1.3 76.4 - - + +
34J ILE* 1.3 61.2 + - - +
35J VAL 3.2 2.2 - - - -
36J ASN* 2.9 44.5 + - - +
37J ASP* 4.5 0.5 + - - +
44K TYR* 4.7 13.5 - - + +
47K LEU* 2.8 51.6 - - + +
48K GLN* 3.9 34.3 - - + +
50K GLU* 5.3 2.5 - - + +
51K LEU* 4.8 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 34 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J GLU* 1.9 68.3 + - + +
31J LEU* 2.9 29.8 - - + +
33J LEU* 1.3 76.8 - - - +
35J VAL* 1.3 57.7 + - + +
36J ASN 3.0 0.4 - - - -
37J ASP* 2.6 38.1 - - - +
47K LEU* 3.4 18.8 - - + -
50K GLU* 5.7 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 35 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J LEU* 3.0 26.0 + - + +
32J GLN* 4.0 8.1 - - - +
33J LEU 3.2 0.2 - - - -
34J ILE* 1.3 72.8 - - + +
36J ASN* 1.3 52.9 + - - +
37J ASP* 2.7 18.0 + - - -
38J LYS* 2.8 47.7 - - + +
278S GLU* 5.0 19.3 - - + -
279S GLN* 5.7 8.5 - - + -
----------------------------------------------------------
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