Contacts of the helix formed by residues 75 - 90 (chain E) in PDB entry 4P5K
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 ARG 75 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-22E ASP* 4.5 6.1 - - - +
68E GLU* 5.0 8.5 + - - +
71E ALA* 3.1 44.0 + - - +
72E VAL* 3.4 2.6 + - + +
74E ASP* 1.3 79.3 - - + +
76E MET* 1.3 58.6 + - + +
77E CYS 3.4 1.3 - - - -
78E ARG 3.2 1.9 + - - -
79E HIS* 2.8 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 76 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D TYR* 4.3 13.9 - - + -
-22E ASP* 3.8 27.5 + - + +
-21E THR* 3.8 30.7 - - - +
-20E GLN* 3.9 10.3 - - + -
13E GLN* 4.4 11.7 - - + +
15E CYS* 4.0 13.2 - - - -
24E PHE* 3.7 21.3 - - + -
72E VAL* 3.5 30.5 + - + +
75E ARG* 1.3 77.4 - - + +
77E CYS* 1.3 62.6 + - - +
79E HIS* 4.3 0.2 - - - -
80E ASN* 2.9 46.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 77 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E CYS* 2.1 52.8 - - + +
22E GLN* 2.9 31.0 - - + +
24E PHE* 3.9 13.2 - - - -
72E VAL* 3.3 29.7 + - - +
73E PRO* 4.0 2.7 - - - +
76E MET* 1.3 76.6 - - - +
78E ARG* 1.3 62.2 + - - +
80E ASN* 4.2 2.6 - - - +
81E TYR* 3.1 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 78 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E GLY 4.3 14.0 + - - -
21E THR* 3.9 9.6 + - - +
22E GLN* 3.2 53.0 + - - +
73E PRO 3.3 12.9 + - - +
74E ASP* 3.6 38.0 + - - +
75E ARG 3.2 1.8 + - - -
77E CYS* 1.3 75.9 - - - +
79E HIS* 1.3 64.9 + - - +
81E TYR* 3.1 10.9 + - - +
82E GLU* 3.0 49.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 79 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-25E ASN 6.0 0.2 + - - -
-24E LYS* 2.7 30.4 + - + -
-22E ASP* 3.2 33.8 + - - +
75E ARG 2.8 22.3 + - - +
76E MET 3.6 3.8 - - - +
78E ARG* 1.3 73.1 - - - +
80E ASN* 1.3 74.5 + - - +
82E GLU* 3.8 2.5 - - - +
83E LEU* 3.0 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 80 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D SER* 5.8 4.0 - - - -
9D TYR* 4.3 9.3 - - - -
24D PHE* 4.4 10.9 - - + -
-23E PHE* 3.6 30.3 - - + -
-22E ASP* 2.9 45.6 + - - +
15E CYS* 5.5 3.0 - - - -
76E MET* 2.9 33.3 + - - +
77E CYS* 4.3 3.0 - - - +
79E HIS* 1.3 74.2 - - - +
81E TYR* 1.3 58.1 + - - +
83E LEU* 3.5 5.8 - - - +
84E GLY* 2.9 28.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 81 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ASP* 5.4 2.1 + - - +
5D HIS* 4.2 16.5 - + + -
7D SER* 5.4 7.6 - - - -
26D PHE* 5.7 1.8 - + - -
17E ALA* 3.3 32.5 - - + +
22E GLN* 3.9 18.2 - - - +
77E CYS 3.1 19.2 + - - +
78E ARG* 3.1 10.1 + - - +
80E ASN* 1.3 76.8 - - - +
82E GLU* 1.3 68.8 + - + +
85E GLY* 3.1 25.6 + - - -
89E LEU* 3.2 42.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 82 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E ARG* 3.0 43.2 + - + +
79E HIS* 3.8 2.7 - - - +
81E TYR* 1.3 83.5 - - + +
83E LEU* 1.3 59.9 + - - +
85E GLY* 4.2 7.6 - - - +
86E PRO* 5.0 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D PHE* 3.4 22.9 - - + -
-25E ASN* 4.0 22.2 - - - +
-24E LYS 3.6 24.7 - - - +
-23E PHE* 3.5 44.2 - - + -
79E HIS* 3.0 26.3 + - + +
80E ASN 3.5 3.4 - - - +
81E TYR 3.1 0.2 - - - -
82E GLU* 1.3 78.8 - - - +
84E GLY* 1.3 67.0 + - - +
85E GLY 3.3 0.8 + - - -
86E PRO* 4.2 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 84 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D PHE* 3.8 12.4 - - - -
-23E PHE* 4.4 10.5 - - - -
80E ASN 2.9 14.1 + - - -
83E LEU* 1.3 76.6 - - - +
85E GLY* 1.3 64.6 + - - +
86E PRO* 3.1 7.6 - - - +
87E MET* 3.5 8.0 + - - +
88E THR* 2.6 35.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 85 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E TYR 3.1 20.6 + - - -
82E GLU* 4.4 5.4 - - - -
83E LEU 4.2 1.8 - - - -
84E GLY* 1.3 72.0 - - - +
86E PRO* 1.3 69.7 - - - +
88E THR* 3.1 8.9 + - - -
89E LEU* 3.1 21.8 + - - +
90E GLN* 2.9 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 86 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D PHE* 5.9 1.1 - - + -
82E GLU 5.0 3.8 - - - +
83E LEU 4.2 7.4 - - - +
84E GLY 3.2 7.0 - - - +
85E GLY* 1.3 79.8 - - - +
87E MET* 1.3 71.7 + - + +
88E THR 2.9 4.7 + - - -
90E GLN* 2.6 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 87 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D GLU* 4.2 33.2 - - + +
48D PHE* 4.5 14.4 - - + -
51D ALA* 3.8 27.4 - - + -
52D PHE* 3.9 21.3 - - + -
84E GLY 3.8 6.1 - - - +
86E PRO* 1.3 86.8 - - + +
88E THR* 1.3 61.8 + - - +
91E ARG* 3.7 21.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 88 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D PHE* 3.6 46.0 - - + -
31D MET* 4.1 17.7 - - + +
48D PHE* 5.7 3.5 - - + -
52D PHE* 4.4 4.3 - - - -
84E GLY* 2.6 41.5 + - - -
85E GLY 3.1 0.6 + - - -
86E PRO 2.9 4.9 + - - -
87E MET* 1.3 80.9 - - - +
89E LEU* 1.3 69.7 + - + +
90E GLN 3.4 0.6 + - - -
91E ARG* 3.5 17.5 + - - +
121E TYR* 4.9 3.5 + - - -
151E TRP* 5.4 3.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D HIS* 4.1 36.7 + - + +
26D PHE* 4.4 7.0 - - + -
81E TYR* 3.2 51.8 - - + +
85E GLY* 3.1 27.2 + - - +
88E THR* 1.3 89.5 - - + +
90E GLN* 1.3 70.2 - - + +
91E ARG 3.3 4.3 + - - +
92E ARG* 4.4 7.6 + - - -
121E TYR* 5.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 90 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E GLY 2.9 13.6 + - - +
86E PRO* 2.6 42.4 + - - +
88E THR 3.4 0.4 - - - -
89E LEU* 1.3 82.8 - - + +
91E ARG* 1.3 60.3 + - - +
92E ARG* 3.6 33.8 + - - +
----------------------------------------------------------
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