Contacts of the helix formed by residues 56 - 70 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D VAL 3.1 5.3 + - - -
55D PRO* 1.3 83.1 - - - +
57D GLN* 1.3 62.6 + - - +
58D THR* 3.5 12.4 + - - -
59D GLY* 2.9 24.4 + - - -
60D THR* 2.8 31.0 + - - +
62E ALA* 4.3 15.7 - - - +
63E ILE* 4.0 20.0 - - + -
66E ARG* 3.0 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D PRO* 3.6 2.0 - - + +
14D LEU 3.1 29.1 + - - +
15D VAL* 3.8 7.6 - - - +
33D ALA* 3.4 19.1 - - - +
34D VAL 3.1 12.7 + - - +
35D ASN* 3.0 24.0 + - - +
53D VAL* 3.4 25.8 + - + +
56D ASP* 1.3 73.4 + - - +
58D THR* 1.3 59.2 + - - +
60D THR* 3.3 1.0 + - - -
61D ALA* 2.9 32.6 + - - +
372D TYR* 3.4 31.0 - - + -
66E ARG* 4.4 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D ASP* 3.3 12.0 + - - -
57D GLN* 1.3 76.9 - - - +
59D GLY* 1.3 62.8 + - - +
61D ALA* 3.4 4.0 + - - +
62D ALA* 3.1 22.5 + - + +
372D TYR* 2.8 29.3 + - - +
62E ALA* 5.6 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D ASP* 2.9 18.6 + - - -
58D THR* 1.3 77.6 - - - +
60D THR* 1.3 61.0 + - - +
62D ALA* 3.2 6.3 + - - +
63D ILE* 3.1 26.9 + - - +
59E GLY* 3.9 28.0 - - - -
62E ALA* 4.7 4.5 - - - -
63E ILE* 4.6 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D ASN* 3.1 19.4 + - - -
52D THR 4.7 1.8 - - - -
53D VAL* 3.0 33.7 + - - +
54D ALA 3.5 17.0 - - - +
55D PRO* 4.2 7.0 - - + -
56D ASP 2.8 15.8 + - - +
57D GLN 3.3 1.2 + - - -
59D GLY* 1.3 70.1 - - - +
61D ALA* 1.3 60.0 + - - +
63D ILE* 3.3 12.4 + - + +
64D LEU* 2.8 29.8 + - - +
104D GLN* 4.5 3.6 - - - +
105D ILE* 4.2 17.4 - - + +
63E ILE* 4.7 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D VAL* 4.0 12.1 - - + +
13D PRO* 3.8 20.6 - - + -
35D ASN* 3.5 20.4 - - - +
57D GLN 2.9 19.1 + - - +
58D THR* 3.7 6.3 - - - +
60D THR* 1.3 77.1 + - - +
62D ALA* 1.3 58.9 + - - +
64D LEU* 3.3 3.7 + - - +
65D TYR* 2.9 31.2 + - - +
372D TYR* 5.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D THR* 3.1 11.1 + - + +
59D GLY* 3.4 9.9 - - - +
60D THR 3.2 0.2 - - - -
61D ALA* 1.3 80.2 - - - +
63D ILE* 1.3 60.6 + - - +
65D TYR* 3.5 6.3 + - - +
66D ARG* 3.1 24.1 + - - +
56E ASP* 4.1 18.0 - - - +
58E THR* 5.4 6.5 - - + -
59E GLY* 4.5 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D GLY 3.1 15.4 + - - +
60D THR* 3.5 16.6 - - + +
62D ALA* 1.3 74.5 - - - +
64D LEU* 1.3 66.7 + - - +
66D ARG* 3.2 7.2 + - - +
67D LEU* 3.0 28.0 + - + +
91D TYR* 3.8 13.2 - - - +
105D ILE* 4.1 16.2 - - + -
55E PRO* 3.6 38.6 - - + -
56E ASP* 4.1 14.4 - - + -
59E GLY* 4.8 3.1 - - - -
60E THR* 4.7 7.6 - - + -
63E ILE* 4.5 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D VAL* 3.8 17.5 - - + -
35D ASN* 3.8 30.1 - - + +
37D ILE* 4.0 17.0 - - + -
51D CYS* 3.8 25.8 - - + -
60D THR 2.8 21.0 + - - +
61D ALA 3.6 4.0 - - - +
63D ILE* 1.3 74.3 - - - +
65D TYR* 1.3 56.9 + - - +
67D LEU* 3.4 0.5 + - - +
68D ALA* 3.0 26.7 + - - +
105D ILE* 3.7 29.1 - - + +
109D ILE* 3.8 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D VAL* 3.8 24.6 + - + -
10D ARG* 4.8 2.5 - - - -
11D VAL* 3.5 28.9 - - + +
61D ALA 2.9 17.6 + - - +
62D ALA* 3.8 7.2 - - - +
64D LEU* 1.3 76.1 - - - +
66D ARG* 1.3 66.0 + - - +
68D ALA* 3.2 3.1 + - - +
69D LYS* 2.9 69.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ALA 3.1 15.1 + - - +
63D ILE* 3.2 5.6 + - - +
65D TYR* 1.3 83.8 - - + +
67D LEU* 1.3 64.3 + - + +
69D LYS* 3.4 16.3 + - - +
70D HIS* 3.2 16.8 + - + -
90D GLU* 2.9 38.4 + - - +
94D HIS* 5.5 5.3 + - - -
55E PRO 3.1 23.2 + - - -
56E ASP* 2.8 43.6 + - - +
57E GLN 4.3 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ILE* 3.0 24.3 + - + +
64D LEU 3.8 3.6 - - - +
66D ARG* 1.3 83.5 - - + +
68D ALA* 1.3 63.1 + - - +
70D HIS* 3.2 24.2 + - - +
86D ILE* 3.6 26.6 - - + +
90D GLU* 4.1 29.4 - - + -
91D TYR* 3.6 27.8 - - + +
105D ILE* 3.5 30.1 - - + -
106D PHE* 3.9 18.4 - - + -
109D ILE* 5.1 5.6 - - + -
55E PRO* 4.5 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D VAL* 3.5 21.9 - - + +
11D VAL* 5.3 0.2 - - + -
37D ILE* 3.7 19.3 - - + -
64D LEU 3.0 18.6 + - - +
65D TYR* 3.7 4.3 - - - +
67D LEU* 1.3 75.5 - - - +
69D LYS* 1.3 65.5 + - - +
71D LEU* 3.1 24.3 + - + +
109D ILE* 3.4 28.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D VAL* 3.9 11.0 - - + +
65D TYR* 2.9 73.0 + - + +
66D ARG* 3.5 11.4 - - - +
67D LEU 3.2 0.6 - - - -
68D ALA* 1.3 75.0 - - - +
70D HIS* 1.3 63.4 + - - +
71D LEU 3.1 1.2 + - - -
72D VAL* 3.2 26.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D ARG* 3.2 24.5 + - + -
67D LEU* 3.2 13.5 + - - +
68D ALA 3.1 0.8 - - - -
69D LYS* 1.3 80.1 - - + +
71D LEU* 1.3 57.2 + - - +
72D VAL 3.3 2.5 + - - +
74D HIS* 3.0 25.1 + - - -
82D LEU* 4.9 1.1 - - - +
86D ILE* 3.5 26.7 - - + +
89D GLN* 3.6 29.9 + - - -
90D GLU* 2.8 37.4 + - + -
----------------------------------------------------------
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