Contacts of the helix formed by residues 52 - 62 (chain K) in PDB entry 5G04
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 GLN 52 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263J PHE 5.1 0.2 + - - -
265J ALA* 3.6 25.6 - - - +
295J TYR* 4.4 11.4 - - + -
20K GLN* 5.1 2.3 + - - +
23K LEU* 3.6 13.0 - - - +
47K LEU* 2.9 28.7 + - + +
50K THR* 3.4 25.3 - - + +
51K ALA* 1.3 78.2 - - - +
53K TYR* 1.3 64.2 + - - +
54K HIS 3.4 2.5 - - - -
55K ARG* 3.1 39.6 + - + +
56K ALA* 3.1 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 53 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295J TYR* 4.3 3.5 + + - -
48K TYR* 3.2 47.9 + + - -
51K ALA* 3.3 32.0 + - + +
52K GLN* 1.3 73.6 - - - +
54K HIS* 1.3 72.1 + + + +
56K ALA* 3.1 6.8 + - - +
57K ALA* 2.9 26.0 + - - +
79K CYS* 3.7 18.6 - - + +
82K ALA* 3.6 43.0 - - + +
83K ALA* 4.3 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 54 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262J PRO* 5.4 3.5 - - + +
263J PHE* 4.7 11.2 - + + -
294J LEU* 3.4 45.6 + - + +
295J TYR* 2.6 40.6 + + + +
53K TYR* 1.3 79.3 - + + +
55K ARG* 1.3 55.4 + - - +
57K ALA* 3.5 6.9 + - - +
58K HIS* 3.0 29.7 + - - +
80K HIS* 5.9 4.2 + + - -
83K ALA* 3.9 29.7 + - + +
85K GLU* 4.2 16.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 55 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261J ASP* 3.2 27.0 + - - +
262J PRO* 5.9 1.6 - - - -
263J PHE* 3.5 32.5 - - + +
264J HIS* 2.9 42.1 + - - +
265J ALA* 4.4 5.1 - - - +
295J TYR* 3.7 6.4 + - - +
23K LEU* 4.0 18.8 - - - +
27K ASP* 4.6 9.9 + - - -
43K LEU* 6.1 0.2 - - - -
47K LEU* 3.4 34.0 - - + +
52K GLN* 3.1 36.7 + - + +
53K TYR 3.2 0.6 - - - -
54K HIS* 1.3 73.3 - - - +
56K ALA* 1.3 65.0 + - - +
58K HIS* 3.3 6.2 + - - +
59K ALA* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44K ALA* 3.5 23.8 - - + +
47K LEU* 3.5 19.2 - - + +
48K TYR* 3.8 5.4 - - - +
52K GLN 3.1 7.1 + - - +
53K TYR 3.1 5.5 + - - +
55K ARG* 1.3 73.5 - - - +
57K ALA* 1.3 66.9 - - - +
59K ALA* 3.2 5.5 + - - +
60K LEU* 3.2 26.5 + - - +
79K CYS* 3.5 25.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53K TYR 2.9 16.6 + - - +
54K HIS* 3.7 7.0 - - - +
56K ALA* 1.3 78.4 - - - +
58K HIS* 1.3 57.4 + - - +
60K LEU* 3.3 4.5 + - - +
61K ARG* 2.9 33.2 + - - +
76K ALA* 4.9 6.1 - - - +
79K CYS* 4.2 12.6 - - + -
80K HIS* 3.6 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 58 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259J GLU 4.7 5.8 + - - -
260J LYS 3.8 17.4 + - - -
261J ASP* 4.2 5.2 - - - +
262J PRO* 3.2 44.2 - - + +
54K HIS 3.0 18.6 + - - +
55K ARG* 3.8 4.7 - - - +
56K ALA 3.2 0.2 - - - -
57K ALA* 1.3 74.8 - - - +
59K ALA* 1.3 56.5 + - - +
61K ARG* 4.6 2.9 - - - +
62K SER* 2.9 62.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 59 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261J ASP* 5.0 4.8 + - - +
40K ILE* 4.2 13.9 - - + +
43K LEU* 5.1 7.2 - - + -
44K ALA* 4.8 7.4 - - + -
47K LEU* 4.7 9.0 - - + -
55K ARG 3.0 15.9 + - - +
56K ALA* 3.6 8.5 - - - +
58K HIS* 1.3 75.9 - - - +
60K LEU* 1.3 58.2 + - - +
62K SER* 3.0 16.9 - - - +
63K ARG* 3.3 35.8 + - - +
65K LEU* 4.6 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40K ILE* 4.4 6.5 - - + +
41K TYR* 4.9 2.5 - - - -
44K ALA* 3.5 32.5 - - + -
56K ALA 3.2 11.6 + - - +
57K ALA 3.9 2.9 - - - +
59K ALA* 1.3 77.6 - - - +
61K ARG* 1.3 59.8 + - - +
62K SER 3.1 9.9 - - - +
65K LEU* 3.2 41.4 + - + +
66K ASP* 3.7 6.2 + - - +
72K CYS* 3.7 32.5 - - + +
75K LEU* 3.8 13.2 - - + -
76K ALA* 3.7 37.7 - - + +
79K CYS* 5.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 61 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57K ALA 2.9 17.4 + - - +
58K HIS* 4.5 1.8 - - - +
60K LEU* 1.3 73.3 - - - +
62K SER* 1.3 66.2 + - - +
63K ARG 3.5 0.2 + - - -
64K LYS* 3.1 18.5 + - - +
66K ASP* 3.7 25.4 + - + +
67K LYS* 6.1 0.2 - - - -
76K ALA* 5.0 7.6 - - + -
80K HIS* 4.5 18.3 + - + -
88K GLN* 4.1 25.6 + - - +
91K ASP* 4.8 5.9 - - - +
92K VAL* 3.4 35.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 62 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260J LYS 5.6 1.8 - - - -
58K HIS* 2.9 46.7 + - - -
59K ALA* 3.0 16.0 - - - +
60K LEU 3.1 6.4 - - - +
61K ARG* 1.3 79.3 - - - +
63K ARG* 1.3 78.1 + - - +
64K LYS 3.1 0.2 - - - -
----------------------------------------------------------
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