Contacts of the helix formed by residues 56 - 69 (chain F) 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 56 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ALA* 3.9 16.6 - - - +
63B ILE* 4.0 19.5 - - + -
66B ARG* 3.0 36.3 + - - +
53F VAL 3.2 5.7 + - - +
55F PRO* 1.3 84.0 - - - +
57F GLN* 1.3 60.3 + - - +
58F THR* 3.6 12.4 + - - -
59F GLY* 2.8 24.7 + - - -
60F THR* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 57 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ARG* 4.2 4.4 - - - +
13F PRO* 3.7 1.3 - - + +
14F LEU 2.9 29.9 + - - +
15F VAL* 3.7 5.4 - - - +
33F ALA* 3.5 17.7 - - + +
34F VAL 3.0 24.4 + - - +
35F ASN* 3.0 15.3 + - - +
53F VAL* 3.5 19.9 + - + +
56F ASP* 1.3 73.1 + - - +
58F THR* 1.3 58.5 + - - +
60F THR* 3.3 7.7 + - - -
61F ALA* 2.8 32.2 + - - +
372F TYR* 3.3 31.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 58 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ALA* 5.4 6.5 - - + -
56F ASP* 3.3 11.5 + - - -
57F GLN* 1.3 76.8 - - - +
59F GLY* 1.3 59.7 + - - +
61F ALA* 3.3 5.4 + - - +
62F ALA* 3.0 28.5 + - + +
372F TYR* 2.7 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 59 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLY* 3.7 28.1 - - - -
62B ALA* 4.4 3.8 - - - -
63B ILE* 4.7 3.4 - - - -
56F ASP* 2.8 20.6 + - - -
58F THR* 1.3 78.1 - - - +
60F THR* 1.3 57.9 + - - +
62F ALA* 3.3 5.6 + - - +
63F ILE* 3.1 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 60 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 4.6 7.6 - - + -
35F ASN* 3.3 12.4 + - - -
52F THR 4.8 1.3 - - - -
53F VAL* 2.9 33.6 + - - +
54F ALA 3.5 16.6 - - - +
55F PRO* 4.2 7.2 - - + -
56F ASP 2.9 13.2 + - - +
57F GLN 3.3 6.8 + - - -
59F GLY* 1.3 74.4 - - - +
61F ALA* 1.3 59.5 + - - +
63F ILE* 3.8 11.4 - - + +
64F LEU* 3.0 29.8 + - - +
104F GLN* 4.5 4.0 - - - +
105F ILE* 4.3 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F VAL* 4.1 10.8 - - + +
13F PRO* 3.9 21.1 - - + -
35F ASN* 3.3 21.3 - - - +
57F GLN 2.8 19.8 + - - +
58F THR* 3.5 8.1 - - - +
60F THR* 1.3 77.3 + - - +
62F ALA* 1.3 62.1 - - - +
64F LEU* 3.4 3.6 + - - +
65F TYR* 3.1 24.1 + - - +
372F TYR* 5.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ASP* 3.9 19.6 - - - +
58B THR* 5.5 5.8 - - + -
59B GLY* 4.3 6.7 - - - +
58F THR* 3.0 13.6 + - + +
59F GLY* 3.4 11.0 - - - +
61F ALA* 1.3 77.4 - - - +
63F ILE* 1.3 61.0 + - - +
65F TYR* 3.8 5.9 - - - +
66F ARG* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PRO* 3.5 35.4 - - + -
56B ASP* 4.0 20.2 - - + -
59B GLY* 4.7 3.1 - - - -
60B THR* 4.7 7.4 - - + -
63B ILE* 4.6 15.3 - - + -
59F GLY 3.1 17.0 + - - +
60F THR* 3.8 15.7 - - + +
61F ALA 3.3 0.2 - - - -
62F ALA* 1.3 77.0 - - - +
64F LEU* 1.3 63.7 + - - +
66F ARG* 3.1 6.6 + - - +
67F LEU* 3.0 31.0 + - + +
91F TYR* 3.8 13.0 - - - +
105F ILE* 4.2 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F VAL* 3.8 19.3 - - + -
35F ASN* 3.8 35.7 - - + +
37F ILE* 4.0 20.2 - - + -
51F CYS* 3.8 20.2 - - + -
60F THR 3.0 17.7 + - - +
61F ALA 3.7 4.0 - - - +
63F ILE* 1.3 77.0 - - - +
65F TYR* 1.3 57.0 + - - +
67F LEU* 3.5 1.2 + - - +
68F ALA* 2.9 30.8 + - - +
105F ILE* 3.6 27.8 - - + +
109F ILE* 3.8 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 65 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F VAL* 3.7 27.8 + - + +
10F ARG* 4.6 2.7 - - - -
11F VAL* 3.7 28.0 - - + +
61F ALA 3.1 16.2 + - - +
62F ALA* 3.8 7.4 - - - +
64F LEU* 1.3 74.2 - - - +
66F ARG* 1.3 67.7 + - - +
68F ALA* 3.9 1.9 - - + +
69F LYS* 3.0 77.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 66 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PRO 3.1 24.0 + - - -
56B ASP* 2.8 36.5 + - - +
57B GLN* 4.1 4.6 - - - +
62F ALA 3.1 13.1 + - - +
63F ILE* 3.1 9.5 + - - +
65F TYR* 1.3 78.0 - - - +
67F LEU* 1.3 66.1 + - + +
69F LYS* 3.6 25.3 + - - +
70F HIS* 3.3 14.6 + - - +
90F GLU* 3.0 36.8 + - - +
94F HIS* 5.5 4.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PRO* 4.5 4.5 - - + -
63F ILE* 3.0 30.1 + - + +
64F LEU 3.9 3.8 - - - +
66F ARG* 1.3 85.9 - - + +
68F ALA* 1.3 61.4 + - - +
70F HIS* 3.3 25.0 + - - +
86F ILE* 3.6 26.5 - - + +
90F GLU* 4.5 15.7 - - + -
91F TYR* 3.7 26.7 - - + +
105F ILE* 3.8 20.0 - - + -
106F PHE* 3.6 30.3 - - + -
109F ILE* 4.1 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F VAL* 3.7 17.9 - - + +
37F ILE* 3.6 28.7 - - + -
64F LEU 2.9 19.5 + - - +
65F TYR* 3.9 4.7 - - - +
67F LEU* 1.3 75.5 - - - +
69F LYS* 1.3 58.1 + - - +
71F LEU* 2.8 42.3 + - + +
109F ILE* 4.1 9.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 69 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F VAL* 3.9 13.4 - - + +
65F TYR* 3.0 69.2 + - + +
66F ARG* 3.8 19.5 - - - +
67F LEU 3.3 0.6 - - - -
68F ALA* 1.3 74.7 - - - +
70F HIS* 1.3 60.7 + - + +
71F LEU 3.0 1.5 + - - -
72F VAL* 3.3 21.5 + - + +
----------------------------------------------------------
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