Contacts of the helix formed by residues 76 - 89 (chain B) in PDB entry 1PRX
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 VAL 76 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ASN* 3.5 22.2 - - - +
18B THR* 3.9 11.2 - - - +
19B THR* 3.8 28.3 - - + +
75B SER* 1.3 74.9 - - - +
77B GLU* 1.3 59.9 + - + +
79B HIS* 3.0 9.1 + - + +
80B LEU* 2.8 40.2 + - + +
104B ASP* 3.2 31.4 + - + +
106B ARG* 4.5 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B SER* 3.3 7.8 + - - +
76B VAL* 1.3 79.5 - - + +
78B ASP* 1.3 59.1 + - - +
80B LEU* 3.3 28.4 + - - +
81B ALA* 3.0 28.4 + - - +
96B GLU* 5.3 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A LYS* 5.2 2.3 + - - -
42B ASP* 3.1 12.3 - - - +
43B PHE* 3.7 21.0 - - + -
74B ASP* 4.2 16.8 - - + +
75B SER* 3.1 27.0 + - - +
76B VAL 3.2 0.6 - - - -
77B GLU* 1.3 74.6 - - - +
79B HIS* 1.3 56.9 + - - +
81B ALA* 3.2 3.9 + - - +
82B TRP* 2.7 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B THR* 3.6 15.0 - - + -
42B ASP* 2.8 40.1 + - - -
72B SER* 3.5 18.8 + - - -
74B ASP 3.4 25.5 + - - -
75B SER 2.9 14.8 + - - -
76B VAL* 3.0 13.0 + - + +
78B ASP* 1.3 76.1 - - - +
80B LEU* 1.3 59.6 + - - +
82B TRP* 3.3 3.9 + - - +
83B SER* 3.0 28.0 + - - -
102B ILE* 3.5 39.0 - - + +
103B ILE 2.8 23.6 + - - -
104B ASP* 4.0 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B THR* 3.8 31.9 - - + +
76B VAL* 2.8 30.2 + - + +
77B GLU* 3.4 34.3 - - - +
79B HIS* 1.3 73.8 - - - +
81B ALA* 1.3 62.0 + - - +
83B SER* 3.3 19.1 + - - -
84B LYS* 3.7 1.6 + - - +
96B GLU* 3.6 58.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A SER* 5.4 3.1 - - - -
43B PHE* 3.7 19.6 - - + -
77B GLU 3.0 17.1 + - - +
78B ASP* 3.7 5.4 - - - +
80B LEU* 1.3 72.3 - - - +
82B TRP* 1.3 65.9 + - - +
84B LYS* 3.0 30.2 + - - +
85B ASP* 3.6 5.2 + - - +
96B GLU* 4.8 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A TYR* 3.8 11.2 + - - -
39B HIS* 4.6 3.6 - - + -
41B ARG 3.7 12.3 - - - -
42B ASP* 3.2 35.4 - - + +
43B PHE* 3.2 43.2 - + + +
44B THR* 4.1 2.5 - - + -
47B CSO 3.9 16.4 - - + -
48B THR* 2.9 43.2 + - - -
51B LEU* 3.8 26.5 - - + -
72B SER* 4.0 12.8 - - - -
78B ASP 2.7 20.6 + - - +
79B HIS* 3.6 7.2 - - - +
81B ALA* 1.3 72.7 - - - +
83B SER* 1.3 56.0 - - - +
85B ASP* 3.1 3.8 + - + -
86B ILE* 3.0 37.8 + - + +
102B ILE* 4.9 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B THR* 5.1 3.1 - - - +
79B HIS 3.0 16.0 + - - -
80B LEU* 3.4 11.9 - - - -
81B ALA 3.1 0.6 - - - -
82B TRP* 1.3 74.7 - - - +
84B LYS* 1.3 58.3 + - - +
86B ILE* 3.6 10.0 - - - +
87B ASN* 2.9 34.7 + - - +
95B THR 3.5 2.0 - - - -
96B GLU 3.8 23.3 + - - -
98B LEU* 3.9 26.6 - - - +
102B ILE* 4.0 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A PRO* 3.6 30.6 + - + +
213A SER* 6.2 0.4 - - - +
80B LEU 3.8 9.9 - - - +
81B ALA* 3.0 17.2 + - - +
83B SER* 1.3 77.5 - - - +
85B ASP* 1.3 58.2 + - - +
87B ASN* 3.5 1.9 + - - +
88B ALA* 2.9 29.8 + - - +
94B PRO* 3.6 25.5 + - - +
95B THR* 3.3 16.6 - - - +
96B GLU* 3.9 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 3.6 13.8 - - + +
212A PRO* 3.1 14.4 - - - +
213A SER* 2.6 50.9 + - - -
217A TYR* 2.7 30.8 + - - +
43B PHE* 3.5 10.6 - - - -
48B THR* 5.0 1.8 - - + -
81B ALA 3.6 2.5 + - - +
82B TRP* 3.1 12.5 + - + +
84B LYS* 1.3 74.2 - - - +
86B ILE* 1.3 54.7 + - - +
88B ALA* 3.1 2.9 + - - +
89B TYR* 2.7 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B THR* 4.6 10.5 - - + +
51B LEU* 3.9 34.8 - - + +
52B GLY* 3.6 30.3 - - - +
55B ALA* 5.0 1.1 - - + -
82B TRP* 3.0 39.3 + - + +
83B SER* 3.6 16.4 - - - +
85B ASP* 1.3 75.7 - - - +
87B ASN* 1.3 62.0 + - - +
89B TYR* 3.3 8.7 + - - +
90B ASN* 3.1 25.3 + - - +
98B LEU* 4.1 24.9 - - + -
102B ILE* 4.7 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LYS* 6.1 0.8 - - - +
83B SER 2.9 15.4 + - - +
84B LYS 3.6 4.5 - - - +
86B ILE* 1.3 76.4 - - - +
88B ALA* 1.3 59.5 + - - +
90B ASN* 3.1 12.7 + - - +
92B GLU* 2.9 39.2 + - + +
93B GLU 3.3 23.2 + - - +
94B PRO* 3.8 2.9 - - + -
95B THR* 2.6 27.5 + - - +
97B LYS 3.2 22.7 + - - +
98B LEU* 4.1 10.0 - - - +
99B PRO* 5.8 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LYS* 4.5 8.0 + - - -
210A GLU 5.6 0.4 - - - +
211A LEU* 4.5 6.1 - - + -
212A PRO* 3.4 29.8 - - + -
84B LYS 2.9 19.2 + - - +
85B ASP 3.1 2.4 + - - +
87B ASN* 1.3 73.1 - - - +
89B TYR* 1.3 66.8 + - - +
91B SER* 3.0 14.4 + - - +
92B GLU 3.9 9.6 + - - -
94B PRO* 4.4 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A PRO* 5.8 0.2 - - - +
179A VAL* 4.2 8.0 - - - +
209A LYS* 4.3 22.2 - - + +
211A LEU* 4.6 4.0 - - + +
218A LEU* 3.7 23.1 - - + -
220A TYR* 3.4 22.1 + - - -
48B THR* 4.3 12.3 - - + -
49B THR* 3.6 41.5 - - + +
52B GLY* 4.3 8.7 - - - -
53B ARG* 4.9 0.9 - - + -
85B ASP 2.7 20.7 + - - +
86B ILE* 3.3 9.2 + - - +
88B ALA* 1.3 71.7 - - - +
90B ASN* 1.3 76.6 + - - +
91B SER* 3.2 8.7 + - - -
----------------------------------------------------------
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