Contacts of the helix formed by residues 57 - 71 (chain A) in PDB entry 2YZA
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 VAL 57 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 4.0 28.9 - - + -
52A ILE* 3.1 15.3 + - + +
55A LEU* 3.4 24.0 - - + +
56A ASP* 1.3 78.3 - - - +
58A VAL* 1.3 63.3 + - - +
59A GLY 3.4 2.7 - - - -
60A LYS* 3.3 15.2 + - + +
61A ILE* 3.1 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ARG* 5.8 1.8 - - - +
52A ILE* 3.4 49.1 + - + +
53A ARG* 3.7 23.1 - - + +
56A ASP* 3.6 2.5 - - - -
57A VAL* 1.3 76.9 - - - +
59A GLY* 1.3 58.7 + - - +
61A ILE* 3.2 4.1 + - - +
62A LYS* 2.8 54.6 + - + +
89A PHE* 4.9 7.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
57A VAL 3.4 0.6 - - - -
58A VAL* 1.3 76.8 - - - +
60A LYS* 1.3 63.1 + - - +
62A LYS* 3.3 12.8 + - - +
63A ARG* 3.0 44.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL* 3.3 19.5 + - + +
59A GLY* 1.3 74.6 - - - +
61A ILE* 1.3 59.6 + - + +
63A ARG* 3.5 16.8 + - - +
64A GLU* 3.0 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 4.6 14.1 - - + -
47A LEU* 3.8 29.2 - - + -
52A ILE* 3.8 39.5 - - + -
57A VAL* 3.1 27.0 + - + +
58A VAL* 3.6 6.5 - - - +
60A LYS* 1.3 74.2 - - + +
62A LYS* 1.3 67.9 + - + +
64A GLU* 3.0 14.1 + - + +
65A ILE* 2.9 36.1 + - + +
89A PHE* 5.7 3.1 - - + -
91A MET* 5.3 0.4 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
49A ARG* 5.3 5.2 - - - +
58A VAL* 2.8 44.6 + - + +
59A GLY* 3.4 9.9 - - - +
61A ILE* 1.3 74.8 - - + +
63A ARG* 1.3 62.8 + - + +
65A ILE* 3.5 12.7 + - + +
66A GLN* 3.2 27.5 + - + +
89A PHE* 4.8 18.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
59A GLY* 3.0 35.8 + - - +
60A LYS* 3.8 12.3 - - - +
62A LYS* 1.3 76.9 - - + +
64A GLU* 1.3 61.5 + - + +
66A GLN* 3.5 7.2 + - - +
67A ASN* 3.1 29.3 + - - +
136A VAL* 6.0 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LYS* 3.0 27.3 + - - +
61A ILE* 3.0 16.3 + - + +
63A ARG* 1.3 75.2 - - + +
65A ILE* 1.3 59.5 + - + +
67A ASN* 3.6 7.8 + - - +
68A LEU* 3.0 30.9 + - - +
91A MET* 6.1 0.2 - - - -
136A VAL* 5.8 8.1 - - + -
138A ARG* 5.7 7.6 - - - -
157A ASP* 5.6 2.1 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
47A LEU* 4.8 2.7 - - + -
61A ILE* 2.9 37.6 + - + +
62A LYS* 3.6 11.9 - - + +
64A GLU* 1.3 75.0 - - + +
66A GLN* 1.3 64.0 + - + +
68A LEU* 3.0 7.7 + - - +
69A LYS* 2.9 33.1 + - + +
79A LEU* 3.9 19.4 - - + +
82A VAL* 4.4 29.2 - - + -
89A PHE* 5.3 10.3 - - + -
91A MET* 3.8 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS 3.2 17.8 + - - +
63A ARG* 3.8 7.2 - - - +
65A ILE* 1.3 82.0 - - - +
67A ASN* 1.3 62.2 + - - +
69A LYS* 3.4 42.6 + - - +
70A LEU* 3.7 13.1 - - - +
82A VAL* 6.0 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ARG 3.1 18.3 + - - +
64A GLU* 3.6 8.8 + - - +
66A GLN* 1.3 78.2 - - - +
68A LEU* 1.3 62.1 + - - +
70A LEU* 3.3 27.1 + - - +
71A PHE* 3.3 33.0 - - - -
133A HIS 3.3 17.1 - - - +
134A MET* 3.5 29.9 - - - +
135A VAL* 3.4 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLU 3.0 18.4 + - - +
65A ILE* 3.0 4.9 + - - +
67A ASN* 1.3 75.3 - - - +
69A LYS* 1.3 66.9 + - - +
71A PHE* 3.1 48.3 + - + +
76A ILE* 4.9 5.8 - - + -
77A ILE* 4.5 22.4 - - + +
79A LEU* 4.2 28.4 + - + +
91A MET* 4.3 20.6 - - + -
93A MET* 4.7 9.6 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
65A ILE* 2.9 17.4 + - - +
66A GLN* 3.4 38.0 + - - +
68A LEU* 1.3 77.5 - - - +
70A LEU* 1.3 62.3 + - + +
71A PHE 4.0 4.3 - - - +
79A LEU* 4.1 24.1 - - + +
81A GLN* 6.0 1.8 - - - +
82A VAL* 4.1 28.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLN 3.7 14.1 - - - +
67A ASN* 3.5 23.8 - - - +
68A LEU 3.2 0.8 - - - -
69A LYS* 1.3 76.8 - - + +
71A PHE* 1.3 69.6 + - + +
72A ARG* 3.7 6.1 + - - +
129A TYR* 4.3 2.6 + - - -
133A HIS* 5.9 1.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASN* 3.3 42.2 - - - -
68A LEU* 3.1 35.9 + - + +
69A LYS 4.0 4.9 - - - +
70A LEU* 1.3 84.7 - - + +
72A ARG* 1.3 62.5 + - - +
73A HIS 5.4 0.7 - - - +
76A ILE* 4.2 17.9 - - + -
77A ILE 5.6 3.1 - - - +
78A LYS* 5.0 8.3 - - + +
129A TYR* 3.6 28.5 - + + -
130A CYS* 4.1 20.6 - - - -
133A HIS* 3.8 23.3 - - + -
134A MET* 4.0 18.8 - - + -
----------------------------------------------------------
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