Contacts of the strand formed by residues 63 - 70 (chain D) in PDB entry 1AGQ
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 63 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ARG* 5.3 9.4 + - - -
47B ILE* 5.9 2.1 - - - +
48D HIS* 5.4 9.5 + - + +
49D LEU 3.3 12.9 - - - +
50D ASN* 3.1 27.2 + - - +
51D VAL* 4.2 2.3 - - - +
61D LYS 3.7 6.5 - - - +
62D GLU* 1.3 90.4 - - - +
64D LEU* 1.3 67.8 + - - +
112D LEU* 4.7 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D HIS* 3.6 5.0 + - - +
49D LEU* 2.9 52.5 + - + +
50D ASN 3.8 2.0 - - - +
51D VAL* 3.8 18.4 - - + +
54D LEU* 4.4 14.8 - - + -
63D GLU* 1.3 79.9 - - - +
65D ILE* 1.3 79.3 + - - +
66D PHE* 4.1 14.6 - - + +
112D LEU* 3.8 29.8 - - + -
127D HIS* 4.2 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B THR* 4.3 9.2 - - + +
68B TYR* 4.1 7.0 - - - +
46D ALA* 3.8 26.7 - - + -
47D ILE 3.5 7.0 - - - +
48D HIS* 3.6 36.6 - - + +
64D LEU* 1.3 82.4 - - - +
66D PHE* 1.3 61.2 + - - +
67D ARG* 3.9 12.1 + - + +
109D ASP* 4.8 1.7 - - - +
127D HIS* 5.0 2.1 + - - -
128D SER* 3.9 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C TYR* 3.8 28.5 - + - -
83C ILE* 3.7 27.8 - - + -
84C LEU* 4.0 14.6 - - + -
87C LEU* 3.9 25.1 - - + -
93C LEU* 4.4 0.7 - - + -
46D ALA* 3.3 1.0 - - - -
47D ILE* 2.8 42.2 + - + +
49D LEU* 3.7 21.5 - - + -
54D LEU* 5.4 0.2 - - + -
64D LEU* 3.9 13.5 - - + -
65D ILE* 1.3 73.8 - - - +
67D ARG* 1.3 64.9 + - - +
68D TYR* 3.7 27.0 - + + -
127D HIS 3.0 29.2 - - - -
128D SER* 3.9 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLY* 4.9 5.5 + - - -
43B VAL* 4.2 16.4 - - - +
80C TYR* 3.6 6.4 - - - -
44D LEU* 3.5 27.8 - - + +
45D THR 3.3 10.1 - - - +
46D ALA* 3.8 17.2 - - + +
65D ILE* 4.2 11.8 - - + +
66D PHE* 1.3 81.0 - - - +
68D TYR* 1.3 62.8 + - - +
109D ASP* 2.7 45.0 + - - +
128D SER* 2.9 8.3 + - - +
129D ALA* 2.9 38.9 + - - +
130D LYS* 4.0 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C TYR* 3.5 14.4 - - + +
84C LEU* 4.4 4.5 - - + -
93C LEU* 3.6 21.2 - - + +
98C VAL* 3.4 40.1 - - + +
43D VAL 3.7 0.5 - - - +
44D LEU* 3.4 4.8 - - - -
45D THR* 3.0 71.4 + - + +
46D ALA* 4.4 2.8 + - - -
47D ILE* 3.9 22.4 - - + +
66D PHE* 3.7 30.3 - + + -
67D ARG* 1.3 78.3 - - - +
69D CYS* 1.3 68.2 + - - +
70D SER* 4.2 4.3 - - - -
129D ALA* 4.3 1.3 - - - -
132D CYS* 4.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C TYR* 3.0 12.6 + - - +
98C VAL 3.5 13.7 + - - -
99C GLY* 3.7 7.8 + - - -
43D VAL 3.6 0.2 - - - -
68D TYR* 1.3 71.6 - - - +
70D SER* 1.3 63.7 + - - +
103D CYS* 3.8 12.4 - - - +
104D ARG* 3.8 15.9 - - - -
105D PRO* 3.5 22.4 - - - -
129D ALA* 3.7 11.4 - - - -
132D CYS* 2.0 57.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C VAL* 3.4 34.3 - - - -
99C GLY* 5.1 0.9 - - - +
41D GLY 3.3 1.6 - - - +
43D VAL* 2.9 39.1 + - - +
45D THR* 4.2 12.8 - - - +
68D TYR* 4.2 4.1 + - - -
69D CYS* 1.3 75.9 - - - +
71D GLY* 1.3 59.0 + - - +
103D CYS* 3.3 12.2 - - - -
----------------------------------------------------------
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