Contacts of the helix formed by residues 78 - 91 (chain H) in PDB entry 2PGW
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 ASP 78 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D GLN* 2.9 31.4 + - - +
130D GLY 3.4 4.7 - - - -
131D GLY* 3.8 8.6 - - - -
132D ALA 4.6 3.6 + - - -
352D ARG* 5.0 5.0 + - - -
74H HIS* 5.9 0.6 - - + +
75H SER* 3.1 25.1 + - - +
77H HIS* 1.3 82.5 - - - +
79H VAL* 1.3 64.1 + - - +
80H ALA 3.3 3.1 - - - -
81H PRO* 3.2 11.3 - - + +
82H LEU* 3.1 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D GLY* 3.9 6.1 - - - +
76H PRO 3.7 3.0 + - - +
78H ASP* 1.3 77.7 - - - +
80H ALA* 1.3 67.6 + - - +
82H LEU* 3.7 2.1 - - - +
83H ILE* 3.0 37.3 + - + +
110H ASP* 3.5 20.0 - - - +
113H MSE 3.5 47.3 - - + +
114H TRP* 3.8 32.5 - - + +
117H GLN* 3.9 9.9 - - - +
279H GLN* 4.2 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D LEU 5.3 0.2 - - - +
130D GLY* 3.0 16.9 + - - +
133D HIS* 3.8 19.6 + - + +
79H VAL* 1.3 81.0 - - - +
81H PRO* 1.3 70.1 - - + +
83H ILE* 3.5 4.5 + - - +
84H ALA* 3.2 21.8 + - - +
110H ASP* 6.0 0.2 - - - -
279H GLN* 3.5 22.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 81 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D GLY 3.1 18.2 - - - +
131D GLY* 4.0 7.9 - - - -
132D ALA 3.2 28.9 - - - +
133D HIS* 3.7 28.2 - - + +
78H ASP* 3.2 24.5 - - + +
80H ALA* 1.3 86.4 - - + +
82H LEU* 1.3 60.5 + - + +
84H ALA* 3.5 3.6 + - + +
85H ARG* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H ILE* 5.3 0.4 - - + -
70H HIS 5.0 0.2 - - - +
71H LEU* 3.9 20.6 - - + -
74H HIS* 3.7 42.4 - - + +
75H SER 3.6 23.3 - - - +
78H ASP* 3.1 34.4 + - + +
79H VAL 3.7 3.6 - - - +
81H PRO* 1.3 74.6 - - + +
83H ILE* 1.3 66.7 + - - +
85H ARG* 3.1 20.1 + - - +
86H ILE* 2.9 30.1 + - + +
113H MSE 3.7 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 83 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71H LEU* 5.6 1.3 - - + -
79H VAL* 3.0 35.9 + - + +
80H ALA* 4.0 4.5 - - - +
82H LEU* 1.3 79.9 - - + +
84H ALA* 1.3 60.3 + - - +
86H ILE* 3.3 10.1 + - + +
87H PHE* 2.8 29.4 + - + +
106H PHE* 3.6 44.0 - - + +
109H ILE* 4.1 18.6 - - + -
110H ASP* 4.0 23.6 - - + +
276H GLY 5.1 2.2 - - - +
280H PRO* 6.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D HIS* 5.0 8.7 - - + +
80H ALA 3.2 17.8 + - - +
81H PRO* 3.7 8.5 - - + +
82H LEU 3.2 0.2 - - - -
83H ILE* 1.3 79.7 - - - +
85H ARG* 1.3 56.1 + - - +
87H PHE* 3.3 11.0 + - - +
88H HIS* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 85 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C TYR* 3.7 24.8 - - + +
70H HIS* 3.9 38.6 + - - +
74H HIS* 4.3 13.1 + - - -
81H PRO 3.0 14.1 + - - +
82H LEU* 3.1 19.2 + - - +
84H ALA* 1.3 72.7 - - - +
86H ILE* 1.3 69.7 + - - +
88H HIS* 3.1 3.1 + - - +
89H GLN* 2.7 64.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 86 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67H LEU* 3.6 44.9 - - + +
70H HIS* 3.7 35.4 - - + -
71H LEU* 4.0 24.9 - - + -
82H LEU* 2.9 23.8 + - + +
83H ILE* 3.7 7.9 - - + +
85H ARG* 1.3 85.2 - - - +
87H PHE* 1.3 58.2 + - - +
89H GLN* 4.4 4.9 - - - -
90H GLU* 2.9 30.2 + - + +
91H TYR* 4.4 0.5 - - - -
106H PHE* 3.9 14.4 - - + -
109H ILE* 5.6 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 87 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C TRP* 3.7 37.2 - + - -
83H ILE* 2.8 18.6 + - + +
84H ALA* 3.4 9.2 - - - +
86H ILE* 1.3 75.1 - - - +
88H HIS* 1.3 64.3 + - - +
91H TYR* 3.1 49.2 + + + +
92H LEU* 3.2 21.0 + - + -
96H ALA 5.1 0.2 - - - -
98H ILE 4.7 0.9 - - - -
99H MSE 4.0 28.7 - - + -
102H ALA* 3.4 33.2 - - + -
106H PHE* 3.8 14.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 88 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C SER* 3.6 35.0 + - - -
26C TYR* 3.0 24.0 + + - +
84H ALA 2.9 16.1 + - - +
85H ARG* 3.1 1.1 + - - +
87H PHE* 1.3 76.9 - - - +
89H GLN* 1.3 58.5 + - - +
92H LEU* 3.7 30.5 - - + -
93H GLY* 2.8 34.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 89 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C TRP* 3.5 13.6 - - + -
26C TYR* 3.6 40.7 - - + -
70H HIS* 3.4 26.9 + - - -
85H ARG* 2.7 46.7 + - - +
86H ILE* 3.9 3.4 - - - +
87H PHE 3.3 0.2 - - - -
88H HIS* 1.3 78.6 - - - +
90H GLU* 1.3 65.1 + - + +
94H HIS* 3.1 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ALA* 3.5 4.2 - - - +
55C PRO* 3.5 25.6 - - + +
66H ARG* 2.8 48.1 + - - +
67H LEU* 3.8 23.3 - - + -
70H HIS* 2.7 37.1 + - + +
86H ILE* 2.9 20.9 + - + +
89H GLN* 1.3 82.8 - - + +
91H TYR* 1.3 63.4 + - + +
94H HIS* 3.4 17.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 91 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C PRO* 3.6 36.5 - - + +
63H ILE* 3.8 6.6 - - - +
67H LEU* 3.7 34.7 - - + +
86H ILE 4.4 0.2 - - - -
87H PHE* 3.1 36.2 + + + +
89H GLN 3.5 0.6 - - - -
90H GLU* 1.3 84.4 - - + +
92H LEU* 1.3 69.2 + - - +
93H GLY 3.3 1.3 - - - -
94H HIS* 3.0 14.6 + - - +
96H ALA* 3.0 32.4 + - + +
98H ILE* 3.6 37.7 - - + -
101H ALA 4.5 0.8 + - - -
102H ALA* 3.7 30.0 + - + -
105H ILE* 4.0 5.7 - - - +
106H PHE* 4.3 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