Contacts of the helix formed by residues 63 - 77 (chain M) in PDB entry 3G5G
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 SER 63 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43K ARG* 2.6 40.7 - - - +
45K SER* 2.7 30.8 + - - -
57M MET* 5.3 0.7 - - - -
62M VAL* 1.3 78.2 - - - +
64M ASP* 1.3 63.9 + - - +
66M VAL* 3.0 30.6 + - - +
67M PHE* 3.1 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 64 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43K ARG* 4.3 1.0 - - - +
45K SER* 5.0 0.9 - - - -
46K ARG* 5.4 1.4 + - - -
54M GLU* 5.3 2.6 - - - +
57M MET* 3.1 32.2 - - - +
62M VAL 3.9 0.8 + - - -
63M SER* 1.3 69.7 - - - +
65M VAL* 1.3 64.1 - - - +
67M PHE* 3.3 3.5 + - - +
68M PHE* 3.0 34.1 + - + -
4N PHE* 3.9 17.9 - - - -
5N LEU* 4.3 8.2 - - - +
75N ILE* 3.8 41.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 65 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2K GLU* 3.9 17.7 - - - +
45K SER* 3.9 28.9 - - - +
63M SER* 3.4 5.7 + - - +
64M ASP* 1.3 74.4 - - + +
66M VAL* 1.3 53.5 + - + +
68M PHE* 3.2 3.1 + - - +
69M GLU* 2.8 57.3 + - - +
72N ILE* 3.8 39.3 - - + +
75N ILE* 4.5 9.6 - - + -
76N LEU* 4.2 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 66 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2K GLU* 5.6 4.3 - - - +
43K ARG* 4.6 7.4 - - + +
45K SER* 4.5 3.8 - - - +
62M VAL* 3.4 23.3 - - + -
63M SER* 3.0 23.7 + - - +
65M VAL* 1.3 76.5 - - + +
67M PHE* 1.3 61.6 + - - +
69M GLU* 3.3 12.6 + - - +
70M MET* 3.0 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 67 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9M VAL* 4.1 11.7 - - + -
12M VAL* 3.5 23.5 - - + +
13M ILE* 4.0 22.7 - - + -
16M ILE* 3.8 19.7 - - + -
53M LEU* 3.9 31.2 - - + -
57M MET* 3.9 32.5 - - + -
60M LEU* 4.8 3.1 - - + -
62M VAL* 4.3 9.9 - - + -
63M SER 3.1 14.2 + - - +
64M ASP 3.5 7.9 - - - +
65M VAL 3.2 0.2 - - - -
66M VAL* 1.3 78.7 - - - +
68M PHE* 1.3 74.7 + + - +
70M MET* 3.2 8.3 + - - +
71M LEU* 3.0 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 68 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50M ILE* 6.5 0.4 - - + -
53M LEU* 4.4 20.2 - - + -
57M MET* 4.7 5.6 - - - -
64M ASP* 3.0 35.9 + - + +
67M PHE* 1.3 84.8 - + - +
69M GLU* 1.3 65.6 + - - +
70M MET 3.1 0.2 - - - -
71M LEU* 3.4 14.9 - - + +
72M ILE* 3.0 27.7 + - - +
5N LEU* 4.0 21.3 - - + -
9N VAL* 5.8 1.6 - - + -
68N PHE* 3.4 43.9 - + + +
71N LEU* 3.4 27.6 - - + -
72N ILE* 3.8 24.0 - - + -
75N ILE* 4.4 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 69 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2K GLU* 4.2 19.4 - - - +
65M VAL* 2.8 39.4 + - - +
66M VAL* 3.6 10.8 - - - +
67M PHE 3.3 0.2 - - - -
68M PHE* 1.3 76.0 - - - +
70M MET* 1.3 61.8 + - + +
72M ILE* 3.5 11.6 + - + +
73M LYS* 3.2 26.4 + - + +
72N ILE* 4.2 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 70 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M VAL* 4.1 17.1 - - + +
15M LYS* 3.6 39.9 - - + +
16M ILE* 3.7 35.7 - - + -
19M GLU* 4.8 9.0 - - - +
66M VAL* 3.0 24.9 + - + +
67M PHE 3.4 9.6 - - - +
69M GLU* 1.3 75.8 - - + +
71M LEU* 1.3 58.9 + - - +
73M LYS* 3.2 11.6 + - + +
74M GLU* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5M LEU* 4.5 1.3 - - + -
8M LYS* 3.8 41.3 - - + +
9M VAL* 3.8 21.8 - - + +
12M VAL* 4.0 10.9 - - + +
67M PHE* 3.0 19.3 + - + +
68M PHE* 3.2 26.7 + - + +
70M MET* 1.3 76.7 - - - +
72M ILE* 1.3 57.5 + - + +
74M GLU* 3.0 4.2 + - + +
75M ILE* 2.8 42.4 + - + +
68N PHE* 3.8 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68M PHE 3.0 19.8 + - - +
69M GLU* 3.7 11.7 - - + +
71M LEU* 1.3 74.1 - - - +
73M LYS* 1.3 64.2 - - - +
75M ILE* 3.1 9.5 + - + +
76M LEU* 2.9 37.5 + - + +
65N VAL* 3.9 34.5 - - + +
68N PHE* 4.2 26.0 - - + -
69N GLU* 4.3 26.2 - - + +
72N ILE* 4.4 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 73 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69M GLU* 3.2 13.1 + - + +
70M MET* 3.3 16.2 - - + +
72M ILE* 1.3 81.4 - - - +
74M GLU* 1.3 63.4 + - - +
76M LEU* 3.3 9.0 + - - +
77M LYS* 3.3 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 74 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8M LYS* 3.9 31.7 + - + +
11M PHE* 3.2 49.2 - - + -
12M VAL* 4.0 12.2 - - + +
15M LYS* 4.5 12.0 + - - +
70M MET 2.9 12.7 + - - +
71M LEU* 3.0 9.6 + - + +
73M LYS* 1.3 76.5 - - - +
75M ILE* 1.3 64.3 + - - +
77M LYS* 3.2 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 75 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4M PHE* 4.5 16.8 - - + -
5M LEU* 4.3 11.9 - - + -
8M LYS* 3.9 27.7 - - + +
71M LEU* 2.8 44.8 + - + +
72M ILE* 3.1 7.6 + - - +
74M GLU* 1.3 72.0 - - - +
76M LEU* 1.3 63.1 + - + +
77M LYS 3.3 3.3 - - - +
64N ASP* 4.0 34.5 - - + +
65N VAL* 4.2 18.8 - - + -
68N PHE* 4.6 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72M ILE* 2.9 34.6 + - + +
73M LYS* 3.7 8.1 - - - +
74M GLU 3.2 0.2 - - - -
75M ILE* 1.3 77.8 - - + +
77M LYS* 1.3 68.6 + - - +
65N VAL* 4.0 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 77 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8M LYS* 5.8 1.3 - - - +
73M LYS 3.3 10.1 + - - +
74M GLU* 3.2 29.6 + - - +
75M ILE 3.3 3.3 - - - +
76M LEU* 1.3 86.6 - - - +
----------------------------------------------------------
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