Contacts of the helix formed by residues 28 - 39 (chain T) in PDB entry 5GAG
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 LYS 28 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27T LYS* 1.3 70.8 - - - +
29T VAL* 1.3 54.3 - - - +
30T SER* 2.8 26.2 + - - +
31T GLN* 2.9 35.0 + - + +
32T ALA 3.3 2.7 + - - -
67T ASP 4.8 13.9 - - - +
68T ASP 5.6 0.9 - - - +
69T LEU 3.8 14.4 - - - +
70T LYS* 4.3 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 29 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27T LYS 3.6 0.8 + - - -
28T LYS* 1.3 68.7 - - - +
30T SER* 1.3 58.3 + - - +
32T ALA* 3.4 11.0 - - - +
33T LEU* 2.9 33.6 + - - +
51T LEU* 4.5 3.6 - - + +
55T ILE* 4.2 20.2 - - + -
66T ILE* 3.3 36.6 - - + +
67T ASP* 5.5 0.7 - - - -
69T LEU* 3.6 29.5 + - + +
70T LYS 4.0 5.8 - - - +
71T VAL* 3.9 23.3 - - + -
107T VAL* 4.5 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 30 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28T LYS* 2.8 21.7 + - - +
29T VAL* 1.3 75.7 - - - +
31T GLN* 1.3 68.3 + - - +
33T LEU* 2.9 30.4 + - - +
34T ASP* 3.1 19.6 + - - +
37b LYS* 6.0 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 31 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27T LYS* 3.7 33.7 - - - +
28T LYS* 2.9 28.0 + - + +
30T SER* 1.3 79.2 + - - +
32T ALA* 1.3 57.6 + - - +
34T ASP* 3.2 12.6 + - - +
35T ILE* 2.9 41.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 32 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24T ILE* 4.2 24.4 - - + +
27T LYS* 4.4 9.5 - - + +
28T LYS 3.3 3.3 + - - +
29T VAL* 3.4 18.4 - - - +
30T SER 3.1 0.4 - - - -
31T GLN* 1.3 76.0 - - - +
33T LEU* 1.3 67.8 + - - +
34T ASP 3.1 0.2 + - - -
35T ILE* 3.2 7.9 + - - +
36T LEU* 3.0 26.9 + - - +
51T LEU* 3.8 20.2 - - + -
71T VAL* 4.9 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29T VAL 2.9 15.8 + - - +
30T SER* 2.9 16.0 + - - +
32T ALA* 1.3 71.9 - - - +
34T ASP* 1.3 57.5 + - - +
36T LEU* 3.7 2.3 + - - +
37T THR* 2.6 36.1 + - - -
48T LYS* 3.6 23.2 - - + +
51T LEU* 3.9 20.2 - - + -
52T GLU* 3.7 34.3 - - + +
55T ILE* 4.8 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 34 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30T SER* 3.1 17.2 + - - +
31T GLN* 3.5 12.7 - - - +
32T ALA 3.1 0.2 - - - -
33T LEU* 1.3 80.7 - - - +
35T ILE* 1.3 67.4 + - + +
37T THR* 2.8 19.6 + - - -
38T TYR* 3.0 17.8 + - + -
28b LEU* 3.9 19.7 - - + +
37b LYS* 2.9 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 35 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23T LEU* 4.1 28.0 - - + +
24T ILE* 4.6 5.6 - - + -
27T LYS* 4.1 32.5 - - + +
31T GLN* 2.9 31.3 + - + +
32T ALA* 3.7 7.4 - - - +
34T ASP* 1.3 76.2 - - + +
36T LEU* 1.3 64.8 + - + +
38T TYR* 3.4 1.6 + - - -
39T THR* 3.0 33.5 + - - +
24b ALA* 4.2 25.8 - - + -
25b VAL* 4.1 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20T VAL* 3.6 30.7 - - + -
23T LEU* 6.5 0.2 - - + -
24T ILE* 4.0 16.4 - - + -
32T ALA 3.0 20.4 + - - +
33T LEU* 3.7 4.7 - - - +
35T ILE* 1.3 78.0 - - + +
37T THR* 1.3 64.1 + - - +
39T THR* 3.3 20.5 + - - +
44T ALA* 3.7 26.5 - - + +
47T VAL* 4.0 13.5 - - + -
48T LYS* 3.6 41.4 - - + +
51T LEU* 4.1 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 37 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33T LEU* 2.6 23.2 + - - +
34T ASP* 2.8 18.4 + - - -
36T LEU* 1.3 72.9 - - - +
38T TYR* 1.3 88.5 + - + +
39T THR 3.5 5.2 + - - +
40T ASN* 5.1 1.0 - - - +
48T LYS* 2.6 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 38 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34T ASP* 3.0 13.8 + - + -
35T ILE 3.8 1.3 - - - -
37T THR* 1.3 98.9 - - + +
39T THR* 1.3 60.6 + - - +
40T ASN* 3.6 11.5 + - - +
25b VAL* 4.0 21.2 - - + +
28b LEU* 3.5 44.4 - - + -
37b LYS* 3.5 20.0 + - + +
38b HIS* 3.8 10.4 - - + +
39b LEU* 3.7 34.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 39 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20T VAL* 4.3 11.9 - - + -
23T LEU* 3.9 19.1 - - - +
35T ILE* 3.0 22.0 + - - +
36T LEU* 3.6 16.9 - - - +
37T THR 3.3 5.1 - - - +
38T TYR* 1.3 78.9 - - - +
40T ASN* 1.3 64.0 + - - +
41T LYS* 3.5 21.1 + - + +
44T ALA* 3.6 24.4 - - + +
22b LEU* 4.9 5.6 - - + -
23b THR 5.7 0.3 + - - -
24b ALA* 5.8 0.2 - - - -
25b VAL* 4.9 3.7 + - - +
----------------------------------------------------------
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