Contacts of the helix formed by residues 59 - 69 (chain A) in PDB entry 6PSI
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 59 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ALA 3.7 2.4 - - - +
56A VAL 4.1 1.6 + - - -
58A SER* 1.3 80.5 + - - +
60A PRO* 1.4 59.9 - - - +
61A GLU* 3.3 2.6 + - + +
62A LYS* 3.0 44.9 + - + +
63A ARG* 2.9 34.4 + - - +
84A ASP* 3.5 0.2 - - - +
143A ARG* 2.9 43.5 + - + -
144A ARG 3.8 7.9 - - - +
145A VAL* 3.3 15.8 - - - +
146A SER 4.0 1.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A SER 4.0 5.4 - - - +
59A ASP* 1.4 80.3 - - - +
61A GLU* 1.3 76.3 + - - +
63A ARG* 3.3 8.3 - - + +
64A ARG* 3.1 36.0 + - + +
137A VAL* 5.5 6.5 - - + -
144A ARG* 3.3 32.5 - - + +
145A VAL 4.9 0.2 - - - -
146A SER* 4.6 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASP* 3.3 2.6 - - + -
60A PRO* 1.3 85.9 - - - +
62A LYS* 1.3 64.3 + - + +
64A ARG* 3.0 11.7 + - - +
65A ILE* 2.9 34.7 + - + +
79A PRO* 4.8 20.6 - - + -
144A ARG* 3.0 54.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ALA* 2.9 30.6 + - - +
56A VAL* 3.1 29.0 - - - +
59A ASP* 3.0 25.3 + - + +
61A GLU* 1.3 75.2 - - + +
63A ARG* 1.3 66.0 + - - +
65A ILE* 3.2 21.4 + - + +
66A TYR 3.2 15.1 + - - -
79A PRO* 6.2 2.9 - - + -
83A TYR* 5.1 6.3 - - + -
84A ASP* 2.8 58.9 + - + +
85A PHE* 4.0 7.3 - - - +
86A SER* 4.7 0.6 + - - +
88A PHE* 5.4 0.6 - - - -
101A PHE* 4.3 14.1 - - + -
143A ARG* 5.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A TYR* 2.8 32.4 + - - -
17A ALA 2.8 29.7 + - - -
18A THR* 4.5 3.4 - - - +
19A GLN* 4.7 16.2 - - + +
22A ILE* 4.3 5.6 - - - +
56A VAL 2.9 7.4 + - - +
57A LEU* 3.4 51.0 + - - +
59A ASP 2.9 20.4 + - - +
60A PRO* 3.3 11.0 - - + +
62A LYS* 1.3 73.8 - - - +
64A ARG* 1.4 83.8 + - - +
66A TYR* 3.1 11.2 + - - +
67A ASP* 2.8 47.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PRO* 3.1 19.4 + - + +
61A GLU* 3.0 11.2 + - - +
63A ARG* 1.4 104.3 - - - +
65A ILE* 1.3 51.3 + - - +
67A ASP* 2.8 42.0 + - - +
68A THR* 2.8 46.8 + - + +
76A PRO* 5.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLU* 2.9 20.2 + - + +
62A LYS* 3.3 25.4 - - + +
63A ARG 3.2 0.2 - - - -
64A ARG* 1.3 72.3 - - - +
66A TYR* 1.4 59.3 + - - +
68A THR* 3.1 7.9 + - - -
69A TYR* 3.0 30.7 + - - +
75A PRO* 5.6 0.2 - - + -
76A PRO* 3.8 36.9 - - + +
77A PRO 5.4 0.9 - - - +
79A PRO* 5.3 4.7 - - + -
83A TYR* 3.5 35.9 - - + +
100A LEU* 4.2 14.1 - - + +
101A PHE* 3.8 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LYS* 3.7 26.7 - - + +
5A LYS 3.0 27.2 + - - -
6A ASP* 3.3 18.4 + - - +
7A TYR* 3.4 27.3 + + + -
8A TYR* 3.4 33.0 - + - -
15A ARG* 5.4 2.8 - - - -
56A VAL* 3.7 18.6 - - + +
57A LEU* 3.6 18.4 - - + -
62A LYS 3.2 4.2 + - - -
63A ARG* 3.1 12.5 + - - +
65A ILE* 1.4 77.6 - - - +
67A ASP* 1.4 59.3 + - - +
69A TYR* 2.9 32.6 + - + +
96A PHE* 4.1 10.3 - + - -
100A LEU* 4.8 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A TYR* 3.2 11.1 + - - -
63A ARG* 2.8 47.5 + - - +
64A ARG* 2.8 43.1 + - - +
66A TYR* 1.4 77.9 - - - +
68A THR* 1.3 61.8 + - + +
69A TYR 4.0 3.3 - - - +
71A THR* 4.0 11.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ARG* 2.8 35.1 + - + +
65A ILE 3.1 8.5 + - - -
67A ASP* 1.3 72.5 - - + +
69A TYR* 1.4 58.8 + - - +
71A THR* 3.0 11.1 + - - -
72A THR* 2.8 44.8 + - - +
76A PRO* 3.2 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ALA* 3.8 21.5 - - + +
4A LYS* 4.0 17.9 + - - -
65A ILE 3.0 17.9 + - - +
66A TYR* 2.9 18.5 + + + +
67A ASP 4.0 3.1 - - - +
68A THR* 1.4 75.7 + - - +
70A GLY* 1.3 62.0 + - - +
72A THR 3.6 4.9 - - - -
73A GLU* 3.4 29.5 + - - -
74A ALA 4.7 4.9 - - - -
75A PRO* 5.0 3.8 - - + -
76A PRO* 5.3 2.5 - - + -
96A PHE* 3.5 37.6 - + - -
100A LEU* 3.6 35.7 - - + -
----------------------------------------------------------
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