Contacts of the helix formed by residues 56 - 65 (chain I) 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 ARG 56 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047A G 3.3 25.0 + - - +
1048A A 6.1 0.9 - - - -
1106A G 2.9 33.6 + - - +
1107A G 3.2 26.5 - - - +
2I ALA* 5.8 1.2 - - - +
3I LEU* 3.2 47.4 + - - +
8I LYS* 3.1 34.6 - - - +
55I VAL* 1.3 77.6 - - - +
57I ASN* 1.3 60.0 + - - +
58I THR 3.6 1.6 - - - +
59I LEU* 3.5 24.7 - - + +
60I LEU* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 57 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1107A G 2.9 43.3 + - - +
1108A U 3.8 6.7 + - - +
55I VAL 3.6 7.8 - - - +
56I ARG* 1.3 71.7 - - - +
58I THR* 1.3 61.5 + - - +
59I LEU 3.2 1.3 - - - -
60I LEU* 3.3 7.5 + - - +
61I ARG* 2.9 42.0 + - - +
76I PHE* 2.3 38.8 + - + +
78I GLY 3.2 17.0 + - - -
80I THR* 3.6 14.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 58 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1046A A 3.5 34.3 - - - +
1047A G 3.7 34.8 + - - +
1110A G 5.7 0.5 + - - -
56I ARG* 4.7 1.2 - - - +
57I ASN* 1.3 76.6 - - - +
59I LEU* 1.3 60.1 + - - +
61I ARG* 3.6 28.5 + - + +
62I ARG* 3.7 26.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 59 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1046A A 5.3 5.3 - - - +
1047A G 5.4 0.4 + - - -
3I LEU* 5.3 1.6 - - + -
8I LYS* 4.3 26.7 - - + +
11I ILE* 3.7 29.8 - - + +
12I VAL* 3.4 41.3 - - + +
15I VAL* 4.9 0.4 - - + -
55I VAL* 3.6 24.0 - - + -
56I ARG* 3.5 31.3 + - + +
58I THR* 1.3 78.0 - - - +
60I LEU* 1.3 56.8 + - - +
61I ARG 3.3 0.7 - - - -
62I ARG* 5.6 0.2 - - - +
63I ALA* 3.0 26.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I VAL* 3.5 31.6 - - + -
55I VAL* 3.6 35.7 - - + +
56I ARG 2.9 20.0 + - - +
57I ASN* 3.3 3.5 + - - +
59I LEU* 1.3 75.6 - - - +
61I ARG* 1.3 58.3 + - - +
63I ALA* 3.9 4.5 - - + -
64I VAL* 3.0 33.7 + - + +
76I PHE* 3.0 27.3 - - + -
80I THR* 3.6 32.1 - - + -
82I ILE* 3.9 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 61 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1108A U 5.6 2.2 + - - -
57I ASN* 2.9 23.1 + - - +
58I THR* 3.6 42.7 + - + +
59I LEU 3.3 0.6 - - - -
60I LEU* 1.3 77.2 - - - +
62I ARG* 1.3 59.4 + - + +
64I VAL* 3.9 2.6 - - - +
65I GLU* 3.0 35.3 + - - +
73I LYS* 3.8 39.4 + - + +
76I PHE* 3.7 24.8 + - + +
77I VAL* 3.6 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 62 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1046A A 3.5 99.2 + - - +
12I VAL* 3.8 22.2 - - + +
16I SER* 4.0 4.5 + - - -
58I THR* 3.7 9.7 + - + +
59I LEU 3.6 2.9 + - - +
60I LEU 3.4 0.2 - - - -
61I ARG* 1.3 76.2 - - + +
63I ALA* 1.3 62.2 + - - +
65I GLU* 4.0 15.6 - - - +
66I GLY* 4.3 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I VAL* 3.9 13.0 - - - +
15I VAL* 3.8 31.6 - - + -
16I SER* 3.0 30.7 + - - +
19I ALA* 4.4 9.0 - - - +
59I LEU* 3.0 19.3 + - + +
60I LEU* 4.2 4.9 - - + -
61I ARG 3.4 0.2 - - - -
62I ARG* 1.3 78.3 - - - +
64I VAL* 1.3 59.2 + - - +
65I GLU 3.5 0.2 - - - -
66I GLY* 3.6 8.5 + - - -
84I TYR* 5.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 64 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60I LEU* 3.0 17.5 + - + +
63I ALA* 1.3 72.0 - - - +
65I GLU* 1.3 59.9 + - - +
66I GLY 2.9 11.6 + - - -
67I THR* 3.0 12.5 + - - -
69I PHE* 3.4 45.6 + - + +
70I GLU* 3.6 16.2 + - - +
72I LEU* 4.5 5.8 - - + -
73I LYS* 3.6 31.6 - - + +
76I PHE* 3.7 22.7 - - + -
84I TYR* 5.2 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 65 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61I ARG* 3.0 20.7 + - - +
62I ARG* 4.0 12.8 - - - +
63I ALA 3.5 0.2 - - - -
64I VAL* 1.3 75.8 - - - +
66I GLY* 1.3 54.8 + - - +
67I THR* 3.2 4.7 + - - -
70I GLU* 3.1 28.8 - - - +
73I LYS* 3.2 33.5 + - - +
----------------------------------------------------------
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