Contacts of the strand formed by residues 60 - 65 (chain A) in PDB entry 2YUZ
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 ILE 60 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LYS* 3.3 48.9 - - + +
29A CYS 3.3 13.5 - - - +
30A GLU* 3.8 23.8 - - + +
56A GLN* 3.2 6.2 - - - +
57A LYS* 2.8 47.9 + - + +
58A GLY 3.4 2.2 + - - -
59A ARG* 1.3 90.1 - - + +
61A HIS* 1.3 72.0 + - - +
62A LYS* 4.9 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU 3.4 5.0 - - - +
28A LYS* 3.4 0.2 - - - -
29A CYS* 2.9 50.7 + - - -
31A ILE* 3.9 18.0 - - + +
35A ILE 3.2 19.9 + - - -
36A PRO* 3.8 3.1 - - + -
37A GLY* 3.2 32.6 + - - -
39A TRP* 3.8 16.9 + - + +
54A VAL* 5.7 3.3 - - + +
55A VAL 3.9 3.1 - - - +
56A GLN* 3.8 20.6 + - + +
58A GLY 5.4 0.2 + - - -
59A ARG* 5.3 0.4 - - - -
60A ILE* 1.3 83.2 + - - +
62A LYS* 1.3 60.0 + - - +
78A PHE* 3.4 27.9 - + + -
----------------------------------------------------------
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
----------------------------------------------------------
26A CYS* 6.2 0.2 - - + -
27A LEU 3.3 8.1 - - - +
28A LYS* 4.4 29.9 - - + +
39A TRP* 4.3 0.4 - - - -
53A LYS 5.1 0.2 - - - -
54A VAL* 3.7 6.2 - - - +
55A VAL* 2.7 57.2 + - + +
57A LYS* 6.2 4.3 - - - -
60A ILE* 4.2 3.5 - - + -
61A HIS* 1.3 73.7 - - - +
63A LEU* 1.3 66.1 + - - +
64A VAL* 4.2 22.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
25A ILE* 4.9 2.2 - - + -
26A CYS* 3.3 2.1 - - - -
27A LEU* 2.7 51.0 + - + +
39A TRP* 3.5 56.3 - - + +
46A VAL* 5.4 6.5 - - + -
52A LEU* 4.9 12.1 - - + -
53A LYS 4.3 4.7 - - - +
54A VAL* 4.1 16.8 - - + -
62A LYS* 1.3 77.5 - - - +
64A VAL* 1.3 69.2 + - - +
65A ILE* 4.3 20.6 - - + -
76A TYR* 5.1 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLU* 4.4 19.7 - - + +
25A ILE 2.9 18.8 - - - +
26A CYS* 3.7 14.4 - - + -
51A ARG 4.0 9.9 - - - +
52A LEU* 4.6 1.0 - - - +
53A LYS* 4.0 21.1 + - + +
55A VAL* 6.3 2.7 - - + -
62A LYS* 4.2 22.9 - - + -
63A LEU* 1.3 82.3 - - - +
65A ILE* 1.3 63.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
24A GLU* 3.1 20.6 - - - +
25A ILE* 3.1 42.6 + - + +
51A ARG* 3.7 31.6 - - - +
52A LEU* 4.9 15.9 - - + -
63A LEU* 4.3 14.4 - - + -
64A VAL* 1.3 77.1 - - - +
66A ALA* 1.3 68.5 + - - +
67A ASN 3.4 25.5 + - - +
69A LEU 5.7 0.7 - - - +
71A GLU* 6.0 0.9 - - - +
72A ASP* 4.9 6.3 - - + -
76A TYR* 3.9 21.5 - - + +
----------------------------------------------------------
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