Contacts of the helix formed by residues 61 - 70 (chain A) in PDB entry 3DGR
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 GLY 61 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TYR* 1.3 81.5 - - - +
62A LEU* 1.3 65.2 + - - +
63A GLN 3.3 2.2 - - - -
64A TYR* 3.3 21.4 - - - +
65A ILE* 3.6 13.6 + - - +
121A GLU* 2.9 10.7 + - - -
155A SER* 5.0 1.3 - - - -
158A PRO* 3.8 19.3 - - - +
231A TYR* 3.3 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PHE* 3.9 19.3 - - + -
60A TYR 3.7 1.6 - - - -
61A GLY* 1.3 75.0 - - - +
63A GLN* 1.3 61.2 + - - +
65A ILE* 3.0 13.3 + - + +
66A LEU* 2.9 52.5 + - + +
116A ILE* 4.2 10.8 - - + -
118A ALA* 3.9 28.0 - - + -
121A GLU* 3.0 8.9 + - - +
132A PHE* 4.5 15.0 - - + -
152A LEU* 3.7 23.3 - - + -
155A SER* 4.8 7.6 - - - -
461A VAL* 4.0 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLY 3.3 0.4 - - - -
62A LEU* 1.3 77.3 - - - +
64A TYR* 1.3 60.6 + - - +
66A LEU* 3.4 12.6 + - + +
67A ASN* 2.8 45.1 + - - +
121A GLU* 2.8 10.7 + - + +
230A TYR* 2.9 24.0 + - - +
231A TYR* 3.4 23.6 + - + +
467A VAL* 5.5 4.3 - - + -
469A LYS 4.3 2.3 - - - +
470A SER* 3.4 19.6 + - - +
471A TYR* 2.9 52.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TYR* 6.3 0.2 - - + -
61A GLY* 3.3 12.1 - - - +
63A GLN* 1.3 79.3 - - - +
65A ILE* 1.3 70.0 + - + +
67A ASN* 3.4 1.4 + - - +
68A LYS* 2.9 56.8 + - + +
69A TYR* 4.4 7.4 - + - -
158A PRO* 6.5 0.7 - - + -
202A GLU* 2.8 34.5 + - - +
206A ILE* 3.6 32.4 - - + +
226A LEU* 3.5 25.6 - - + +
230A TYR* 3.6 44.1 - + - -
231A TYR* 3.3 16.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLY 3.9 13.0 - - - +
62A LEU* 3.0 11.2 + - + +
64A TYR* 1.3 88.0 - - + +
66A LEU* 1.3 67.3 + - - +
69A TYR* 3.1 30.0 + - + +
70A LEU* 3.4 11.7 + - + +
151A ILE* 3.7 42.0 - - + +
152A LEU* 4.2 20.2 - - + +
154A GLN* 4.3 5.4 - - + +
155A SER* 3.8 30.7 - - - +
158A PRO* 5.6 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 2.9 43.4 + - + +
63A GLN* 3.8 13.2 - - + +
65A ILE* 1.3 76.7 - - - +
67A ASN* 1.3 58.3 + - - +
70A LEU* 3.1 20.1 + - + +
71A LYS* 2.9 30.3 + - - +
116A ILE* 3.8 25.4 - - + -
461A VAL* 3.8 41.5 - - + +
462A PHE* 4.1 11.2 - - + -
467A VAL* 4.0 20.0 - - + -
469A LYS 5.7 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLN* 2.8 41.3 + - - +
66A LEU* 1.3 77.9 - - - +
68A LYS* 1.3 64.7 + - - +
69A TYR 3.6 0.2 + - - -
71A LYS* 2.9 52.4 + - - +
230A TYR* 3.6 30.5 + - + -
467A VAL* 3.8 19.1 - - - +
470A SER* 5.5 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 5.2 2.4 - - - -
64A TYR* 2.9 50.1 + - + +
67A ASN* 1.3 78.1 - - - +
69A TYR* 1.3 101.2 + - + +
202A GLU* 3.9 4.7 - - - -
229A LYS* 5.2 3.8 - - - +
230A TYR* 3.4 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 3.5 52.7 - + + -
11A ILE* 4.2 4.7 - - - +
64A TYR* 4.4 7.4 - + - -
65A ILE* 3.1 25.2 + - + +
68A LYS* 1.3 115.3 - - + +
70A LEU* 1.3 68.3 + - + +
71A LYS 3.9 1.1 - - - -
74A VAL* 3.8 14.1 - - - +
151A ILE* 3.7 30.5 - - + -
154A GLN* 5.6 1.1 - - - -
202A GLU* 2.5 38.2 + - - -
201B GLN* 3.5 21.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 3.5 29.2 - - + -
65A ILE* 3.4 12.5 + - + +
66A LEU* 3.1 25.4 + - + +
69A TYR* 1.3 82.7 - - + +
71A LYS* 1.3 64.9 + - - +
72A GLY 4.1 1.7 + - - +
74A VAL* 3.5 11.0 - - - +
112A LEU* 3.9 18.3 - - + +
116A ILE* 4.3 9.2 - - + -
148A ILE* 4.3 10.3 - - + -
151A ILE* 4.1 15.9 - - + -
152A LEU* 3.7 32.5 - - + -
462A PHE* 3.5 24.9 - - + -
465A GLY* 4.8 0.3 - - - -
----------------------------------------------------------
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