Contacts of the helix formed by residues 56 - 69 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL 3.1 4.9 + - - -
55A PRO* 1.3 84.2 - - - +
57A GLN* 1.3 62.8 + - - +
58A THR* 3.6 11.5 + - - -
59A GLY* 2.9 24.1 + - - -
60A THR* 2.8 31.2 + - - +
62G ALA* 3.8 17.2 - - - +
63G ILE* 4.0 20.4 - - + -
66G ARG* 3.0 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PRO* 3.7 1.7 - - + +
14A LEU 3.0 29.5 + - - +
15A VAL* 3.8 6.8 - - - +
33A ALA* 3.5 20.0 - - + +
34A VAL 3.1 11.7 + - - -
35A ASN* 3.0 27.0 + - - +
53A VAL* 3.4 25.9 + - + +
56A ASP* 1.3 72.9 + - - +
58A THR* 1.3 59.0 + - - +
60A THR* 3.3 0.5 + - - -
61A ALA* 2.8 34.5 + - - +
372A TYR* 3.4 30.5 - - + -
66G ARG* 4.3 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASP* 3.3 12.0 + - - -
57A GLN* 1.3 75.8 - - - +
59A GLY* 1.3 64.2 + - - +
61A ALA* 3.7 3.9 - - - +
62A ALA* 3.1 22.5 + - + +
372A TYR* 2.6 29.3 + - - +
62G ALA* 5.3 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASP* 2.9 21.3 + - - -
58A THR* 1.3 76.2 - - - +
60A THR* 1.3 61.2 + - - +
62A ALA* 3.3 5.9 + - - +
63A ILE* 3.2 28.1 + - - +
59G GLY* 3.7 28.9 - - - -
62G ALA* 4.3 4.2 - - - +
63G ILE* 4.6 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ASN* 3.4 12.2 + - - -
52A THR 4.8 3.6 - - - -
53A VAL* 3.0 32.3 + - - +
54A ALA 3.5 17.0 - - - +
55A PRO* 4.2 8.5 - - + -
56A ASP 2.8 16.2 + - - +
57A GLN 3.3 4.0 + - - -
59A GLY* 1.3 71.0 - - - -
61A ALA* 1.3 61.9 + - - +
63A ILE* 3.6 13.7 - - + +
64A LEU* 2.9 30.1 + - - +
104A GLN* 4.5 5.8 - - - +
105A ILE* 5.0 11.7 - - + +
63G ILE* 4.7 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 3.9 11.1 - - + +
13A PRO* 3.9 18.8 - - + -
35A ASN* 3.3 23.8 - - - +
57A GLN 2.8 20.9 + - - +
58A THR* 3.7 6.3 - - - +
60A THR* 1.3 77.0 + - - +
62A ALA* 1.3 62.4 + - - +
64A LEU* 3.3 4.2 + - - +
65A TYR* 3.0 24.9 + - - +
372A TYR* 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A THR* 3.1 12.0 + - + +
59A GLY* 3.4 11.0 - - - +
61A ALA* 1.3 80.4 - - - +
63A ILE* 1.3 60.9 + - - +
65A TYR* 3.5 7.8 + - - +
66A ARG* 3.0 22.9 + - - +
56G ASP* 3.9 19.2 - - - +
58G THR* 5.6 5.2 - - + -
59G GLY* 4.3 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLY 3.2 18.2 + - - +
60A THR* 3.6 17.5 - - + +
61A ALA 3.2 0.2 - - - -
62A ALA* 1.3 74.6 - - - +
64A LEU* 1.3 64.8 + - - +
66A ARG* 3.1 6.1 + - - +
67A LEU* 3.0 32.0 + - + +
91A TYR* 3.7 13.2 - - - +
105A ILE* 3.8 16.8 - - + -
55G PRO* 3.5 39.5 - - + -
56G ASP* 4.1 15.3 - - + -
59G GLY* 4.7 3.1 - - - -
60G THR* 4.9 6.7 - - + -
63G ILE* 4.6 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 3.8 24.2 - - + -
35A ASN* 3.9 28.5 - - + +
36A LEU 4.1 0.2 - - - +
37A ILE* 4.0 20.4 - - + -
51A CYS* 3.9 19.7 - - + -
60A THR 2.9 17.0 + - - +
61A ALA 3.6 4.7 - - - +
63A ILE* 1.3 77.2 - - - +
65A TYR* 1.3 56.1 + - - +
67A LEU* 3.4 0.7 + - - +
68A ALA* 2.9 31.2 + - - +
105A ILE* 3.4 29.6 - - + +
109A ILE* 3.8 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.9 26.0 + - + -
10A ARG* 4.8 2.5 - - - -
11A VAL* 3.6 28.7 - - + +
61A ALA 3.0 17.2 + - - +
62A ALA* 3.8 7.2 - - - +
64A LEU* 1.3 74.4 - - - +
66A ARG* 1.3 67.6 + - - +
68A ALA* 4.5 0.9 - - - -
69A LYS* 3.1 73.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ALA 3.0 15.8 + - - +
63A ILE* 3.1 8.9 + - - +
65A TYR* 1.3 79.0 - - - +
67A LEU* 1.3 66.2 + - + +
69A LYS* 3.5 17.3 + - - +
70A HIS* 3.3 14.4 + - - +
90A GLU* 2.9 37.3 + - - +
94A HIS* 5.5 5.5 + - - -
55G PRO 3.2 24.5 + - - -
56G ASP* 2.8 35.6 + - - +
57G GLN* 4.2 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 3.0 26.9 + - + +
64A LEU 3.8 3.4 - - - +
66A ARG* 1.3 82.9 - - + +
68A ALA* 1.3 65.6 + - - +
70A HIS* 3.1 28.3 + - - +
86A ILE* 3.7 24.2 - - + +
90A GLU* 4.4 22.9 - - + -
91A TYR* 3.8 27.8 - - + +
105A ILE* 3.5 29.8 - - + -
106A PHE* 4.0 14.8 - - + -
109A ILE* 3.9 12.3 - - + -
55G PRO* 4.5 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.7 21.5 - - + +
11A VAL* 5.1 0.2 - - + -
37A ILE* 3.6 29.4 - - + -
64A LEU 2.9 19.7 + - - +
65A TYR* 3.9 5.4 - - - +
67A LEU* 1.3 76.4 - - - +
69A LYS* 1.3 62.9 + - - +
71A LEU* 3.0 33.9 + - + +
72A VAL 4.1 0.2 + - - -
109A ILE* 4.0 7.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 4.1 10.5 - - + +
65A TYR* 3.1 66.5 + - + +
66A ARG* 3.6 11.4 - - - +
67A LEU 3.1 0.6 - - - -
68A ALA* 1.3 76.2 - - - +
70A HIS* 1.3 57.4 + - + +
71A LEU 3.1 0.4 - - - -
72A VAL* 2.9 31.5 - - + +
----------------------------------------------------------
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