Contacts of the helix formed by residues 69 - 81 (chain A) in PDB entry 5F02
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 LEU 69 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TRP* 4.1 4.7 - - - -
62A ASN* 2.8 11.3 + - - +
68A GLY* 1.3 73.6 - - - -
70A MET* 1.3 66.3 + - - +
71A ASP* 4.1 6.3 - - + +
72A TYR* 3.1 49.1 + - + +
73A ALA* 3.1 19.2 + - - +
302A 5T9 3.5 73.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TRP* 3.4 33.2 - - - +
29A SER* 3.3 25.8 - - - +
30A ALA* 4.0 2.5 - - + +
69A LEU* 1.3 73.4 - - - +
71A ASP* 1.3 57.1 + - - +
73A ALA* 3.1 11.5 + - - +
74A PHE* 2.9 41.8 + - + -
133A SER* 3.9 15.3 - - - +
134A VAL* 3.5 38.1 - - - +
135A ALA 4.0 0.4 - - - +
164A GLY* 4.0 6.1 - - - -
214A ALA 4.5 3.1 - - - +
216A SER* 4.6 4.5 - - - +
302A 5T9 3.3 34.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 3.2 7.2 - - + +
70A MET* 1.3 78.8 - - - +
72A TYR* 1.3 61.7 + - + +
74A PHE* 3.3 9.3 + - - +
75A GLN* 2.9 28.1 + - - +
112A PHE* 3.4 34.4 - - + -
114A ASP* 2.6 27.7 - - - +
216A SER* 2.7 29.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLN* 3.2 30.7 - - - +
61A GLY* 3.5 29.2 - - - -
62A ASN* 3.3 31.9 - - - +
69A LEU* 3.1 39.3 + - + +
71A ASP* 1.3 80.9 - - + +
73A ALA* 1.3 57.9 + - - +
75A GLN* 3.3 6.5 + - + +
76A TYR* 2.9 24.9 + - - +
302A 5T9 4.1 8.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TRP* 4.2 5.4 - - + -
30A ALA* 3.6 24.2 - - + -
53A LEU* 4.1 19.4 - - + +
62A ASN* 3.4 12.4 - - - +
69A LEU 3.1 10.9 + - - +
70A MET* 3.1 10.0 + - - +
72A TYR* 1.3 73.6 - - - +
74A PHE* 1.3 66.2 + - - +
76A TYR* 3.2 8.6 + - - +
77A VAL* 3.1 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA* 3.5 33.2 - - + -
33A ALA* 3.9 1.3 - - + -
34A LEU* 4.7 4.5 - - + -
70A MET* 2.9 23.8 + - + -
71A ASP* 3.3 17.5 + - - +
73A ALA* 1.3 76.4 - - - +
75A GLN* 1.3 62.6 + - - +
77A VAL* 3.3 1.7 + - + -
78A GLN* 3.2 8.5 + - - +
109A ASP* 2.8 38.0 - - - +
111A GLY* 4.4 0.4 - - - +
112A PHE* 3.7 26.5 - - + -
133A SER* 3.6 22.2 - - - -
216A SER* 3.7 20.4 - - - -
217A TYR* 4.0 2.9 - - - -
218A PRO* 3.6 40.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLN* 4.1 8.5 - - + -
71A ASP 2.9 16.7 + - - +
72A TYR* 3.5 9.9 - - + +
73A ALA 3.2 0.2 - - - -
74A PHE* 1.3 74.3 - - - +
76A TYR* 1.3 59.0 + - - +
78A GLN* 3.3 29.1 + - - +
79A ASP* 2.9 64.8 + - - +
112A PHE* 3.7 20.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASN* 2.9 29.1 + - - -
53A LEU* 3.7 19.1 - - + -
56A CYS* 3.3 36.2 - - + +
57A SER* 3.6 21.5 - - - -
60A GLN* 3.4 31.8 - - - +
72A TYR 2.9 9.4 + - - +
73A ALA 3.4 7.4 - - - +
75A GLN* 1.3 77.2 - - - +
77A VAL* 1.3 60.2 + - + +
79A ASP* 3.2 0.6 + - + +
80A ASN* 2.8 73.8 + - + +
82A GLY 4.3 1.3 - - - -
83A LEU* 4.2 11.4 - - + -
98A CYS* 4.6 0.5 - - - -
100A TYR* 3.9 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 4.2 12.1 - - + -
53A LEU* 4.2 4.9 - - + -
73A ALA 3.1 15.8 + - - +
74A PHE* 3.8 1.3 - - + +
75A GLN 3.3 0.2 - - - -
76A TYR* 1.3 86.2 - - + +
78A GLN* 1.3 58.7 + - - +
81A GLY* 3.0 24.6 + - - -
82A GLY 3.2 26.0 + - - +
83A LEU* 4.1 26.9 - - + -
108A ASN* 3.8 12.3 - - - -
109A ASP* 3.5 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PHE 3.2 4.4 + - - +
75A GLN* 3.3 29.1 + - - +
77A VAL* 1.3 76.2 - - - +
79A ASP* 1.3 66.7 + - - +
80A ASN 3.3 0.3 + - - -
81A GLY* 3.4 10.6 + - - -
109A ASP* 3.4 29.2 + - - +
110A THR* 3.2 28.9 + - - +
111A GLY* 3.6 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLN* 2.9 36.2 + - - +
75A GLN* 2.9 46.9 + - - +
76A TYR 3.7 1.1 - - - +
78A GLN* 1.3 75.5 - - - +
80A ASN* 1.3 62.4 + - + +
81A GLY* 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A TYR* 2.8 55.0 + - + +
79A ASP* 1.3 77.3 - - - +
81A GLY* 1.3 60.4 + - - +
82A GLY 2.9 23.9 + - - +
100A TYR* 3.2 40.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL 3.0 8.2 + - - -
78A GLN 3.4 6.7 + - - -
79A ASP 3.3 3.2 - - - -
80A ASN* 1.3 78.8 - - - +
82A GLY* 1.3 52.4 + - - +
100A TYR* 4.4 3.8 + - - -
105A SER* 4.3 1.9 + - - -
108A ASN* 2.7 25.5 + - - -
----------------------------------------------------------
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