Contacts of the strand formed by residues 76 - 81 (chain D) in PDB entry 3AQQ
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 HIS 76 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D PHE* 3.5 12.3 - - - -
71D CYS* 3.0 24.8 + - - +
74D LYS* 3.3 43.1 + - + +
75D GLY* 1.3 79.1 - - - +
77D GLY* 1.3 61.7 + - - +
78D PHE* 5.2 7.2 - + - -
89D PHE* 3.5 35.2 - + + -
90D LEU 3.2 16.2 - - - +
91D HIS* 4.2 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D CYS* 3.1 20.2 - - - -
70D PHE* 3.4 11.3 - - - -
76D HIS* 1.3 75.9 - - - +
78D PHE* 1.3 76.4 + - - -
89D PHE* 4.1 3.5 - - - -
90D LEU* 3.1 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D CYS* 3.6 2.1 - - - -
68D LYS* 2.7 44.7 + - + -
69D CYS* 3.0 27.5 + - - +
76D HIS* 5.2 6.1 - + - -
77D GLY* 1.3 80.2 - - - -
79D ILE* 1.3 61.4 + - - +
87D ASP* 3.8 25.8 - - + -
88D ILE 3.5 15.9 - - - -
89D PHE* 4.0 30.7 - + + -
90D LEU* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 79 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D VAL 3.4 18.2 - - - +
67D CYS* 4.7 3.6 - - + -
78D PHE* 1.3 78.3 - - - +
80D THR* 1.3 66.7 + - - +
81D PRO* 3.0 5.3 - - + +
87D ASP* 3.2 3.6 - - - -
88D ILE* 2.6 43.6 + - + +
90D LEU* 3.7 31.6 - - + -
107D VAL* 3.8 25.1 - - + -
109D TYR* 4.0 20.0 - - + -
123D ALA* 3.7 28.7 - - + -
126D VAL* 4.3 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D GLY* 3.4 0.7 - - - -
66D VAL* 2.9 42.1 + - + +
68D LYS* 3.3 27.1 + - - +
79D ILE* 1.3 71.9 - - - +
81D PRO* 1.3 81.0 - - + +
82D ALA* 4.4 0.3 - - - -
85D GLY 5.0 3.4 - - - +
87D ASP* 2.7 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D LYS 4.2 0.9 - - - +
65D GLY* 4.5 0.2 - - - -
79D ILE 3.0 10.5 - - - +
80D THR* 1.3 97.1 - - - +
82D ALA* 1.3 66.4 + - - +
83D ASP* 4.2 10.1 - - - +
84D GLY* 3.6 17.1 + - - +
85D GLY* 3.2 19.3 - - - +
86D PRO 2.8 30.5 - - - +
87D ASP* 3.8 1.6 - - - -
88D ILE* 4.0 11.9 - - + +
109D TYR* 3.8 20.6 - - - +
111D MET* 5.1 4.7 - - + -
----------------------------------------------------------
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