Contacts of the helix formed by residues 62 - 77 (chain A) in PDB entry 1Y88
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 GLY 62 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TYR* 3.7 3.0 + - - -
61A THR* 1.3 76.9 - - - +
63A LEU* 1.3 65.0 + - - -
65A GLU* 3.3 2.1 + - - +
66A ALA* 3.2 15.4 + - - +
93A SER* 3.6 5.6 - - - -
96A ALA* 3.6 10.1 - - - +
301A SO4 3.4 13.0 - - - -
302A SO4 2.9 34.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLY* 1.3 68.9 - - - -
64A LYS* 1.3 66.9 + - - +
66A ALA* 3.1 2.5 + - - +
67A MET* 2.9 60.4 + - + +
93A SER* 3.9 0.4 + - - -
95A GLU* 4.0 26.5 - - + +
96A ALA* 4.2 7.2 - - - +
99A TYR* 3.4 35.9 - - + -
301A SO4 2.7 26.8 + - - +
302A SO4 3.5 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 1.3 79.6 - - - +
65A GLU* 1.3 63.1 + - - +
67A MET* 3.2 6.8 + - - +
68A TYR* 3.0 25.3 + - + +
301A SO4 5.1 1.2 + - - -
302A SO4 3.0 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLU* 4.7 5.0 - - - +
52A CYS 5.2 0.5 - - - +
53A LYS* 3.5 42.8 + - + +
61A THR* 3.6 26.9 - - + -
62A GLY 3.6 4.0 - - - +
64A LYS* 1.3 74.3 - - - +
66A ALA* 1.3 57.6 + - - +
68A TYR* 3.5 17.8 - - - +
69A THR* 2.9 48.1 + - - +
72A ARG* 3.7 11.9 + - - -
86A ILE* 4.4 11.0 - - + +
302A SO4 2.7 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A THR* 6.4 0.2 - - + -
62A GLY 3.2 8.9 + - - +
63A LEU* 3.1 10.1 + - - +
65A GLU* 1.3 79.8 - - - +
67A MET* 1.3 57.1 + - - +
69A THR* 3.3 1.6 + - - -
70A TYR* 2.9 23.4 + - - +
86A ILE* 3.8 16.4 - - + -
92A PHE* 6.3 0.7 - - + -
96A ALA* 4.3 18.8 - - + +
99A TYR* 3.9 19.5 - - + -
100A ALA* 5.3 1.6 - - + -
105A ILE* 3.4 17.7 - - + +
107A LEU* 5.8 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 2.9 55.8 + - + +
64A LYS* 3.8 6.3 - - - +
66A ALA* 1.3 74.1 - - - +
68A TYR* 1.3 63.0 + - - +
70A TYR* 3.2 4.0 + - - +
71A ALA* 3.0 22.5 + - - +
99A TYR* 3.7 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLN* 5.4 3.0 + - - -
64A LYS* 3.0 19.1 + - + +
65A GLU* 3.5 18.8 - - - +
67A MET* 1.3 75.0 - - - +
69A THR* 1.3 56.9 + - - +
71A ALA* 3.3 8.7 + - + +
72A ARG* 2.9 74.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A MET* 3.9 20.1 - - + +
51A GLU* 4.3 7.7 - - + +
65A GLU* 2.9 29.1 + - - -
66A ALA 3.5 5.4 - - - -
67A MET 3.2 0.2 - - - -
68A TYR* 1.3 75.9 - - - +
70A TYR* 1.3 65.6 + - - +
72A ARG* 3.0 25.5 + - - +
73A PHE* 2.9 21.5 + - - +
84A PRO* 4.2 12.1 - - + -
85A TRP 5.2 1.3 - - - +
86A ILE* 3.7 27.0 - - + +
105A ILE* 4.8 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ALA 2.9 12.8 + - - +
67A MET 3.2 4.0 + - - +
69A THR* 1.3 78.5 - - - +
71A ALA* 1.3 63.0 + - - +
73A PHE* 3.2 22.6 + + - +
74A LEU* 3.0 60.2 + - + +
84A PRO* 4.9 2.7 - - + -
99A TYR* 3.2 28.0 - + - +
103A VAL* 3.7 40.5 + - + +
105A ILE* 4.1 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A MET 3.0 13.1 + - - +
68A TYR* 3.6 11.9 - - + +
70A TYR* 1.3 77.9 - - - +
72A ARG* 1.3 60.9 + - - +
74A LEU* 3.2 12.7 + - - +
75A ASP* 3.1 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLN* 3.6 32.0 - - + +
36A GLU* 4.5 7.7 + - - +
38A ASP* 5.1 1.6 + - - -
49A MET* 4.0 11.4 - - + -
51A GLU* 3.2 41.6 + - - +
52A CYS 5.9 0.4 + - - -
65A GLU* 3.7 8.5 + - - -
68A TYR* 2.9 68.3 + - + +
69A THR* 3.0 33.0 + - - +
71A ALA* 1.3 75.4 - - - +
73A PHE* 1.3 64.6 + - - +
75A ASP* 3.1 13.4 + - - +
76A VAL* 3.1 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A MET* 3.6 14.3 - - + -
69A THR 2.9 13.8 + - - +
70A TYR* 3.4 20.0 - + - +
72A ARG* 1.3 76.5 - - - +
74A LEU* 1.3 76.3 + - + +
76A VAL* 3.1 2.2 + - + +
77A GLU* 2.8 56.8 + - + +
81A PHE* 3.5 40.8 - - + -
82A THR 3.7 12.3 - - - -
83A GLN* 3.7 18.6 - - - -
84A PRO* 3.6 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASN* 5.3 2.8 - - - +
70A TYR* 3.0 57.9 + - + +
71A ALA* 3.2 12.3 + - - +
73A PHE* 1.3 84.0 - - + +
75A ASP* 1.3 62.1 + - - +
77A GLU* 3.6 32.2 + - - +
78A LYS 4.9 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLY* 3.2 2.8 - - - -
31A ASN* 2.8 37.0 + - - +
32A CYS* 2.8 39.7 + - - +
33A VAL* 3.2 25.7 + - - +
35A GLN* 2.9 30.5 + - + +
71A ALA 3.1 10.9 + - - +
72A ARG 3.1 9.6 + - - +
74A LEU* 1.3 78.9 - - - +
76A VAL* 1.3 57.5 + - - +
78A LYS* 4.8 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 3.6 29.6 - - + -
30A GLY* 4.5 1.3 - - - -
35A GLN* 3.6 31.6 - - + -
37A ILE* 4.3 4.7 - - + -
49A MET* 3.5 31.0 - - + -
72A ARG 3.1 6.0 + - - +
73A PHE* 3.1 8.4 + - - +
75A ASP* 1.3 76.6 - - - +
77A GLU* 1.3 60.0 + - - +
78A LYS* 3.2 3.1 - - - -
79A HIS* 2.8 35.3 + - - +
81A PHE* 3.5 23.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PHE* 2.8 42.7 + - + +
74A LEU* 3.6 31.7 + - - +
75A ASP 3.6 1.6 - - - -
76A VAL* 1.3 77.8 - - - +
78A LYS* 1.3 57.5 + - - +
79A HIS 3.1 0.2 - - - -
80A GLY* 2.9 19.2 + - - -
81A PHE* 3.4 20.5 + - - +
82A THR 5.5 0.3 - - - +
----------------------------------------------------------
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