Contacts of the helix formed by residues 55 - 67 (chain G) in PDB entry 5DNF
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 55 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G ASN* 3.0 38.7 + - + +
53G PRO 3.9 4.0 - - - +
54G GLU* 1.3 83.5 - - + +
56G LYS* 1.3 64.6 + - - +
57G TRP* 3.5 23.8 - - + +
58G VAL* 3.4 15.0 + - + +
59G ARG* 3.3 20.1 + - - +
102G SO4 3.5 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 56 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G GLU 3.9 1.2 + - - -
55G LYS* 1.3 71.2 - - - +
57G TRP* 1.3 61.8 + - - +
59G ARG* 3.1 41.2 - - - +
60G GLU* 2.9 60.9 + - + +
102G SO4 3.4 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 57 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G ILE* 4.7 11.7 - - + -
16G ALA 4.4 10.2 + - - -
17G ARG 5.1 0.7 - - - -
18G PRO* 3.5 52.3 - - + +
19G LEU* 4.1 13.0 - - + -
41G PHE* 3.9 9.2 - + - -
49G VAL* 6.2 1.8 - - + -
51G ALA* 4.2 14.8 - - + -
52G ASN 5.5 0.7 - - - -
55G LYS* 3.5 28.4 - - + +
56G LYS* 1.3 78.2 - - - +
58G VAL* 1.3 72.6 + - + +
60G GLU* 3.5 15.9 - - - +
61G TYR* 2.9 71.4 + + + -
102G SO4 5.5 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 58 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G VAL* 4.4 4.5 - - + -
41G PHE* 3.8 17.2 - - + -
51G ALA* 3.7 15.3 - - + -
52G ASN 3.1 30.5 - - - +
53G PRO* 4.0 13.7 - - + -
55G LYS* 3.6 9.2 - - + +
56G LYS 3.1 0.8 - - - -
57G TRP* 1.3 112.4 - - + +
59G ARG* 1.3 58.7 + - - +
61G TYR* 3.3 4.2 + - - +
62G ILE* 3.0 42.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 59 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E PRO 3.9 14.6 - - - +
54E GLU* 3.7 25.0 + - - +
55E LYS 4.5 0.4 - - - -
56E LYS* 4.1 32.4 - - - +
59E ARG* 3.3 54.2 - - + +
102E SO4 5.0 3.4 + - - -
53G PRO 4.8 0.4 - - - +
54G GLU* 4.4 12.5 + - - +
55G LYS 3.3 5.3 + - - +
56G LYS* 3.1 48.9 + - - +
58G VAL* 1.3 76.9 - - - +
60G GLU* 1.3 62.6 + - + +
62G ILE* 3.8 5.7 - - - +
63G ASN* 2.9 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E GLU* 6.3 2.9 - - + -
56G LYS* 2.9 52.9 + - + +
57G TRP* 3.5 16.2 - - - +
59G ARG* 1.3 81.3 - - + +
61G TYR* 1.3 63.4 + - + +
63G ASN* 3.6 9.0 - - - +
64G SER* 2.9 30.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 61 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G PRO* 4.2 8.2 - - + +
19G LEU 2.8 29.8 + - - -
20G PRO* 4.3 0.7 - - - +
21G ARG* 3.4 35.8 + - + +
24G ILE* 3.5 27.6 - - + -
41G PHE* 3.6 13.5 - + + -
57G TRP* 2.9 50.8 + + + +
58G VAL 3.4 9.2 - - - +
60G GLU* 1.3 83.2 - - + +
62G ILE* 1.3 55.8 + - - +
64G SER* 3.2 6.7 + - - -
65G LEU* 2.8 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E TYR* 3.7 7.2 - - - +
59E ARG* 3.6 38.6 - - - +
63E ASN* 5.6 0.2 - - - +
27G TYR* 3.4 39.9 - - + +
29G TYR* 3.8 7.2 - - - +
39G VAL* 3.9 24.0 - - + -
41G PHE* 4.2 9.9 - - + -
53G PRO* 5.8 0.4 - - + -
58G VAL* 3.0 28.4 + - + +
59G ARG* 3.8 4.5 - - - +
60G GLU 3.3 0.2 - - - -
61G TYR* 1.3 73.8 - - - +
63G ASN* 1.3 62.9 + - - +
65G LEU* 3.1 9.9 + - - +
66G GLU* 3.0 23.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 63 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E TYR* 3.4 19.0 + - - -
37E PRO* 6.3 0.2 - - + -
53E PRO* 3.2 42.8 + - + +
54E GLU* 4.2 8.9 - - - +
59E ARG* 3.3 19.3 + - - -
59G ARG* 2.9 25.2 + - - +
60G GLU* 3.6 7.9 - - - +
62G ILE* 1.3 76.8 - - - +
64G SER* 1.3 57.5 + - - +
66G GLU* 3.0 2.1 + - - -
67G MET* 2.9 39.7 + - + +
104G CL 4.4 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 64 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ARG* 2.9 33.0 + - - +
60G GLU 2.9 17.2 + - - -
61G TYR* 3.4 6.7 - - - -
63G ASN* 1.3 77.2 - - - +
65G LEU* 1.3 62.6 + - - +
66G GLU 3.3 0.7 + - - -
67G MET 3.7 15.5 + - - +
68G SER* 3.8 4.5 + - - -
104G CL 4.3 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ARG* 3.6 29.4 - - - +
24G ILE* 4.0 26.0 - - + +
25G LYS 4.3 15.3 - - - +
26G GLU* 4.5 1.6 - - - -
27G TYR* 3.8 31.4 - - + -
41G PHE* 3.9 23.1 - - + -
61G TYR* 2.8 22.4 + - + +
62G ILE 3.1 5.1 + - - +
64G SER* 1.3 76.7 - - - +
66G GLU* 1.3 61.5 + - - +
68G SER* 4.0 13.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 66 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E TYR* 3.5 49.3 - - + +
30E THR 5.2 2.3 - - - +
32E GLY 5.0 3.3 + - - -
101E BGC 2.8 32.5 + - - +
27G TYR* 2.7 30.7 + - + +
62G ILE 3.0 19.9 + - - +
63G ASN 3.0 3.8 + - - +
65G LEU* 1.3 77.2 - - - +
67G MET* 1.3 61.0 + - - +
68G SER* 3.0 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 67 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E TYR* 3.4 33.7 - - + -
30E THR* 3.9 20.0 - - - +
31E SER 5.2 0.7 - - - +
32E GLY* 4.0 21.8 - - - +
37E PRO* 3.7 20.6 - - + -
38E ALA 3.5 25.1 - - - +
53E PRO* 3.9 11.7 - - + -
63G ASN* 2.9 18.0 + - + +
64G SER* 3.7 6.9 - - - +
66G GLU* 1.3 73.7 - - - +
68G SER* 1.3 63.4 + - - +
104G CL 3.7 20.4 - - + -
----------------------------------------------------------
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