Contacts of the helix formed by residues 65 - 74 (chain R) in PDB entry 1BKD
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 SER 65 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62R GLU 4.1 6.1 - - - -
63R GLU* 2.8 13.2 + - - -
64R TYR* 1.3 67.0 - - - +
66R ALA* 1.3 59.1 + - - +
67R MET 3.0 10.4 + - - -
68R ARG* 3.2 48.5 + - - +
69R ASP 4.9 0.2 + - - -
99R GLN* 4.7 1.7 + - - -
829S THR* 3.5 19.3 + - - +
833S LEU* 5.7 0.5 - - - +
1002S GLU* 4.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 66 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64R TYR 3.3 0.8 - - - -
65R SER* 1.3 78.8 + - - +
67R MET* 1.3 57.6 + - - +
68R ARG 3.5 0.8 + - - -
69R ASP* 4.8 5.6 + - - +
70R GLN 5.3 1.2 + - - -
829S THR* 4.1 16.9 - - + +
832S THR* 3.6 40.1 - - + +
833S LEU* 4.0 20.9 - - + -
836S GLU* 4.7 4.1 - - - +
876S SER* 4.1 10.7 - - - +
880S SER* 5.3 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 67 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64R TYR* 3.3 34.5 - - + +
65R SER 3.0 1.0 + - - -
66R ALA* 1.3 78.1 - - - +
68R ARG* 1.3 63.8 + - - +
69R ASP 3.5 1.8 - - - -
70R GLN* 3.4 12.8 + - - +
71R TYR* 3.2 47.5 + - + -
828S THR* 4.4 13.5 - - + -
832S THR* 5.5 1.1 - - - +
872S LEU* 4.1 16.4 - - + +
873S GLU* 5.4 0.2 - - - -
876S SER* 3.2 28.0 - - - +
912S TYR* 4.4 4.0 - - - -
929S PHE* 3.6 41.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 68 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9R VAL* 6.1 0.7 - - + -
62R GLU* 4.7 8.9 + - - +
64R TYR 3.9 3.6 + - - +
65R SER* 3.2 38.8 + - - +
66R ALA 3.5 0.2 - - - -
67R MET* 1.3 75.5 - - - +
69R ASP* 1.3 60.9 + - - +
71R TYR* 3.3 7.7 + - + +
72R MET* 2.8 51.8 + - + +
95R GLN* 5.7 5.9 - - - +
96R TYR* 4.3 26.5 + - - -
99R GLN* 3.0 40.0 + - - +
1002S GLU* 2.8 27.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 69 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65R SER 4.9 0.2 + - - -
66R ALA 4.8 4.6 + - - +
67R MET 3.5 0.4 - - - -
68R ARG* 1.3 76.6 - - - +
70R GLN* 1.3 65.2 + - - +
72R MET* 3.3 1.9 + - - +
73R ARG* 2.9 25.6 + - - +
99R GLN* 3.2 23.6 + - - +
103R VAL* 3.2 25.5 - - + +
879S ASN 4.0 4.7 - - - +
880S SER* 3.8 23.3 - - - -
881S SER* 3.1 33.1 + - - +
882S PRO* 4.5 2.4 - - - +
1006S THR* 5.7 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 70 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66R ALA 5.3 0.6 + - - -
67R MET* 3.4 17.1 + - - +
68R ARG 3.2 0.6 - - - -
69R ASP* 1.3 81.0 - - - +
71R TYR* 1.3 73.6 + - - +
73R ARG* 3.3 15.2 + - - +
74R THR* 3.6 12.1 - - + +
872S LEU* 4.5 3.4 - - - +
875S VAL* 3.5 24.7 - - - +
876S SER* 3.0 32.8 + - - +
879S ASN* 3.9 33.4 + - + +
905S HIS* 5.2 4.9 - - + -
908S SER* 3.7 27.2 + - - -
912S TYR* 4.5 11.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 71 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7R VAL* 4.2 4.6 - - + +
56R LEU* 3.7 25.2 - - + +
58R THR* 3.6 35.9 - - + +
61R GLN* 2.5 35.7 + - + -
64R TYR* 5.7 1.3 - - + -
67R MET* 3.2 39.6 + - + -
68R ARG* 3.7 9.4 - - + +
70R GLN* 1.3 86.8 - - + +
72R MET* 1.3 60.7 + - + +
74R THR* 2.7 32.3 + - + -
908S SER* 6.4 0.2 - - - -
912S TYR* 2.8 41.7 + + - -
929S PHE* 3.9 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 72 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7R VAL* 4.7 3.8 - - + -
9R VAL* 3.9 29.2 - - + -
68R ARG* 2.8 43.3 + - + +
69R ASP 3.7 3.6 - - - +
71R TYR* 1.3 75.2 - - + +
73R ARG* 1.3 63.3 + - - +
74R THR 3.2 0.9 + - - -
75R GLY 3.3 4.9 + - - +
78R PHE* 3.1 42.0 - - + -
96R TYR* 4.3 10.1 - - + +
99R GLN* 4.0 37.0 - - + +
100R ILE* 3.9 24.5 - - + -
103R VAL* 3.9 14.6 - - + -
104R LYS* 4.4 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 73 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69R ASP 2.9 14.1 + - - +
70R GLN* 3.4 12.1 - - - +
71R TYR 3.2 0.4 - - - -
72R MET* 1.3 77.8 - - - +
74R THR* 1.3 62.5 + - + +
75R GLY 3.2 1.2 + - - -
103R VAL* 3.4 45.1 + - + +
104R LYS* 3.5 22.9 + - - +
879S ASN* 2.4 44.8 + - - +
881S SER* 4.4 9.3 + - - +
884S TYR* 3.4 59.0 - - - +
905S HIS* 6.1 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 74 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5R LYS* 3.7 25.6 - - - +
7R VAL* 3.9 3.5 - - - +
56R LEU* 3.6 17.0 - - + +
70R GLN* 3.6 13.0 - - + +
71R TYR* 2.7 26.8 + - + +
73R ARG* 1.3 77.3 - - + +
75R GLY* 1.3 57.3 + - - +
104R LYS* 5.2 0.2 - - - -
905S HIS* 6.3 3.4 - - + +
----------------------------------------------------------
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