Contacts of the helix formed by residues 72 - 87 (chain A) in PDB entry 4P5E
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 GLY 72 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLU* 2.9 19.8 + - - -
68A GLU* 3.8 10.5 - - - +
71A GLY* 1.3 79.3 - - - +
73A ASP* 1.3 65.3 + - - -
74A ARG 3.4 2.5 - - - -
75A LEU 3.3 0.9 + - - -
76A ILE* 3.0 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ARG* 6.1 0.4 - - - +
67A GLU* 3.3 25.0 + - - +
72A GLY* 1.3 71.3 - - - -
74A ARG* 1.3 81.4 + - - +
76A ILE* 3.3 11.2 + - + +
77A HIS* 2.9 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLY 3.4 0.6 - - - -
73A ASP* 1.3 85.8 + - - +
75A LEU* 1.3 64.5 + - + +
77A HIS* 3.3 19.1 + - - +
78A GLU* 2.9 66.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ALA 4.7 3.1 - - - +
71A GLY* 3.4 35.2 + - - +
72A GLY 3.3 2.6 + - - +
74A ARG* 1.3 81.4 - - + +
76A ILE* 1.3 65.9 + - - +
78A GLU* 3.9 12.9 - - + +
79A GLN* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLU* 3.7 24.0 - - + -
70A ALA* 3.9 24.9 + - + +
72A GLY 3.0 20.2 + - - +
73A ASP* 3.5 9.6 - - - +
75A LEU* 1.3 76.9 - - - +
77A HIS* 1.3 64.0 + - - +
79A GLN* 3.5 3.9 + - - +
80A ASP* 3.0 27.1 + - - +
201A N6P 3.6 66.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASP 2.9 16.6 + - - +
74A ARG* 3.6 19.7 + - - +
76A ILE* 1.3 80.4 - - - +
78A GLU* 1.3 83.8 + - - +
80A ASP* 3.3 4.7 + - - +
81A LEU* 2.9 48.6 + - + +
103A TYR* 2.7 45.0 + + - -
107A ARG* 4.3 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ARG* 2.9 53.8 + - + +
75A LEU* 3.3 16.5 + - + +
77A HIS* 1.3 106.0 + - - +
79A GLN* 1.3 61.9 + - - +
81A LEU* 3.3 6.1 + - - +
82A GLU* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU 2.9 17.4 + - - +
76A ILE* 4.0 4.7 - - - +
78A GLU* 1.3 75.7 - - - +
80A ASP* 1.3 62.9 + - - +
82A GLU* 3.3 14.8 + - - +
83A TRP* 3.1 69.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.3 26.6 + - - +
56A HIS* 3.4 22.7 - - - -
76A ILE* 3.0 22.4 + - - +
77A HIS* 3.8 5.3 - - - +
79A GLN* 1.3 77.9 - - - +
81A LEU* 1.3 63.7 + - + +
83A TRP* 3.2 14.2 + - - -
84A LEU* 2.8 25.8 + - - +
104A GLU* 3.8 1.9 - - + +
201A N6P 2.8 42.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 5.9 0.2 - - - +
77A HIS* 2.9 46.5 + - + +
78A GLU* 3.8 8.3 - - - +
79A GLN 3.2 0.2 - - - -
80A ASP* 1.3 78.7 - - + +
82A GLU* 1.3 64.7 + - - +
84A LEU* 3.4 11.5 + - + +
85A GLN* 3.0 37.0 + - - +
103A TYR* 4.1 13.5 - - + -
104A GLU* 6.1 2.9 - - + -
107A ARG* 3.6 39.5 - - + +
111A PHE* 3.7 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU 3.1 12.8 + - - +
79A GLN* 3.5 21.1 - - - +
81A LEU* 1.3 76.6 - - - +
83A TRP* 1.3 61.6 + - - +
85A GLN* 3.3 16.3 + - - +
86A GLN* 2.8 58.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.8 12.1 - - + -
53A LEU* 3.4 55.7 - - + +
54A THR* 4.2 6.5 - - + -
56A HIS* 3.8 15.9 - + - -
79A GLN* 3.1 50.8 + - + +
80A ASP* 3.5 31.4 - - - +
82A GLU* 1.3 78.3 - - - +
84A LEU* 1.3 61.4 + - - +
86A GLN* 3.1 23.9 + - - +
87A ALA* 3.0 19.9 + - - +
201A N6P 5.9 0.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.6 29.8 - - + +
80A ASP 2.8 19.5 + - - +
81A LEU* 3.7 14.6 - - + +
82A GLU 3.3 0.4 - - - -
83A TRP* 1.3 70.9 - - - +
85A GLN* 1.3 62.7 + - - +
87A ALA* 3.2 10.8 + - - +
90A VAL* 3.7 31.2 - - + -
104A GLU* 3.7 19.3 - - + +
107A ARG* 3.6 32.3 - - + -
108A ALA* 3.9 11.0 - - + +
111A PHE* 4.2 12.8 - - + -
113A LYS* 3.2 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 3.0 28.8 + - - +
82A GLU* 3.7 15.4 - - - +
83A TRP 3.3 0.2 - - - -
84A LEU* 1.3 75.3 - - - +
86A GLN* 1.3 59.3 + - + +
111A PHE* 3.3 39.0 - - + -
113A LYS* 2.8 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA* 4.0 11.0 - - + +
53A LEU* 4.2 13.3 - - + +
82A GLU* 2.8 53.0 + - - +
83A TRP* 3.1 25.5 + - - +
85A GLN* 1.3 74.3 - - + +
87A ALA* 1.3 64.3 + - - +
88A ASP* 3.5 8.1 + - - +
165A HIS* 5.0 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA* 3.8 8.5 - - - +
23A LEU 4.6 1.3 - - - -
24A TYR* 3.7 21.5 - - + +
53A LEU* 4.5 1.1 - - + -
83A TRP 3.0 11.4 + - - +
84A LEU 3.2 14.5 + - - +
86A GLN* 1.3 78.5 - - - +
88A ASP* 1.3 63.3 + - - +
89A VAL 3.7 19.7 - - - +
90A VAL* 4.5 4.9 - - + -
113A LYS* 2.7 30.7 + - - +
----------------------------------------------------------
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