Contacts of the helix formed by residues 61 - 73 (chain D) in PDB entry 3G8T
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 GLU 61 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D HIS* 4.2 4.4 + - - -
39D GLN 6.0 0.6 - - - +
59D PHE* 3.5 7.7 - - - +
60D LYS* 1.3 107.8 + - + +
62D VAL* 1.3 66.3 + - - +
63D SER* 4.2 12.1 - - - +
64D SER* 3.1 27.0 + - - +
65D ALA 3.4 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D PRO* 3.8 29.6 - - + +
9D ASN* 4.1 15.5 - - - +
10D HIS* 3.7 34.7 - - + +
61D GLU* 1.3 72.0 + - - +
63D SER* 1.3 60.1 + - - +
65D ALA* 2.8 23.6 + - + +
66D THR* 2.9 19.9 + - - +
86D TYR* 5.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D GLU* 4.2 10.1 - - - +
62D VAL* 1.3 78.5 - - - +
64D SER* 1.3 58.8 + - - +
66D THR* 3.8 6.0 + - - -
67D ASN* 3.0 37.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D PHE* 3.0 34.8 + - - +
38D GLY* 3.3 10.1 - - - -
39D GLN 4.5 1.3 + - - -
59D PHE* 3.5 23.0 - - - -
61D GLU* 3.1 21.7 + - - +
62D VAL 3.1 0.8 - - - -
63D SER* 1.3 77.3 - - - +
65D ALA* 1.3 64.5 + - - +
66D THR 3.4 0.2 - - - -
67D ASN* 3.8 2.1 + - - +
68D ALA* 3.2 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ASN 3.3 26.5 - - - +
10D HIS 3.9 14.8 - - - +
12D ILE* 3.5 20.1 - - + +
59D PHE* 3.8 13.9 - - + -
61D GLU 3.4 4.2 + - - +
62D VAL* 2.8 10.6 + - - +
64D SER* 1.3 77.6 - - - +
66D THR* 1.3 64.5 + - - +
68D ALA* 3.5 3.5 - - - +
69D LEU* 3.1 18.0 + - - +
86D TYR* 4.3 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D PRO* 4.7 3.3 - - - +
62D VAL* 2.9 23.5 + - - +
63D SER* 4.1 6.9 - - - -
65D ALA* 1.3 73.6 - - - +
67D ASN* 1.3 57.4 + - - +
69D LEU* 2.9 6.1 + - - +
70D ARG* 2.8 73.4 + - + +
86D TYR* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D PHE* 3.6 24.5 + - + -
63D SER* 3.0 27.0 + - - +
64D SER* 4.0 4.4 - - - +
65D ALA 3.5 0.2 - - - -
66D THR* 1.3 76.8 - - - +
68D ALA* 1.3 53.5 + - - +
70D ARG* 3.6 11.1 + - - +
71D SER* 2.8 41.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ILE* 3.9 4.0 - - + -
34D PHE* 3.7 28.0 - - + -
37D PHE* 3.5 15.2 - - + -
59D PHE* 3.9 13.7 - - + -
64D SER 3.2 17.2 + - - +
65D ALA 3.5 7.2 - - - +
66D THR 3.2 0.6 - - - -
67D ASN* 1.3 78.9 - - - +
69D LEU* 1.3 55.7 + - - +
72D MET* 3.1 33.4 + - - +
84D ILE* 3.7 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D ALA 3.1 9.4 + - - +
66D THR* 2.9 11.5 + - - +
68D ALA* 1.3 75.7 - - - +
70D ARG* 1.3 77.3 + - - +
73D GLN* 3.3 34.6 + - - +
84D ILE* 3.5 39.2 - - + +
85D GLN* 3.7 23.3 - - - +
86D TYR* 3.8 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D THR* 2.8 50.8 + - + +
67D ASN* 3.3 11.9 + - - +
69D LEU* 1.3 84.2 - - + +
71D SER* 1.3 63.5 + - - +
73D GLN* 4.3 6.6 - - - +
86D TYR* 5.1 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D ARG* 4.6 7.5 + - - -
37D PHE* 3.5 22.8 - - - -
67D ASN* 2.8 22.7 + - - +
70D ARG* 1.3 76.9 - - - +
72D MET* 1.3 63.6 + - - +
73D GLN 3.1 14.7 + - - +
75D PHE* 5.4 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C PHE* 3.9 9.9 - - + -
33D ILE* 3.4 25.1 - - + -
34D PHE* 3.6 20.2 - - + -
36D ARG* 3.7 15.3 - - - -
37D PHE* 3.6 35.7 - - + -
68D ALA 3.1 10.6 + - - +
71D SER* 1.3 76.1 - - - +
73D GLN* 1.3 65.4 + - - +
74D GLY 3.3 0.7 + - - -
75D PHE* 3.0 61.3 + - + +
82D MET* 4.2 6.6 - - - +
84D ILE* 3.7 16.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D LEU* 3.3 36.6 + - - +
70D ARG 4.3 7.4 - - - +
71D SER 3.1 6.9 + - - +
72D MET* 1.3 76.1 - - - +
74D GLY* 1.3 60.0 + - - +
75D PHE* 3.1 5.5 + - - -
82D MET 3.9 1.9 - - - +
83D ARG* 3.6 13.9 - - - +
84D ILE* 3.0 51.3 + - - +
----------------------------------------------------------
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