Contacts of the strand formed by residues 59 - 64 (chain A) in PDB entry 2YXD
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 PHE 59 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASP 3.4 1.6 + - - -
38A VAL* 3.3 12.3 - - + +
39A VAL 3.0 23.7 + - - +
57A CYS* 3.6 3.5 - - - -
58A LYS* 1.3 85.8 - - + +
60A VAL* 1.3 85.5 + - - +
61A TYR* 3.5 40.6 - + - -
83A LYS 4.4 6.1 - - - -
84A ASN* 3.1 36.1 - - - +
85A CYS 3.8 2.7 - - - -
86A GLN* 3.5 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL 3.1 9.6 - - - +
41A ASP* 4.0 23.8 - - + -
50A THR* 4.7 10.5 - - + +
53A ILE* 3.6 27.8 - - + -
54A ALA* 3.5 34.1 - - + -
57A CYS* 3.6 5.4 - - - -
59A PHE* 1.3 78.9 - - - +
61A TYR* 1.3 68.3 - - - +
62A ALA 3.9 0.9 - - - +
84A ASN 2.8 7.8 + - - +
85A CYS* 3.2 12.0 - - + -
86A GLN 3.0 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A VAL* 3.5 27.4 - - + +
39A VAL 2.8 18.6 + - - +
40A VAL* 3.6 21.9 - - + -
41A ASP 2.7 28.8 + - - -
59A PHE* 3.5 25.5 - + - -
60A VAL* 1.3 72.6 - - - +
62A ALA* 1.3 61.7 + - - +
63A ILE* 3.4 6.1 + - + +
86A GLN* 3.3 36.3 - - + -
88A ILE* 3.7 21.1 - - + -
99A LEU* 4.1 23.1 - - + -
100A GLU* 4.1 14.3 + - - +
101A PHE* 4.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASP* 3.6 7.9 - - - +
50A THR* 4.0 31.9 - - + +
60A VAL 3.9 2.0 + - - -
61A TYR* 1.3 71.9 - - - +
63A ILE* 1.3 61.9 + - - +
64A ASP* 3.7 13.1 + - - +
73A THR* 4.7 2.5 - - + -
85A CYS* 4.1 8.3 - - - -
86A GLN 2.8 10.4 + - - +
87A ILE* 3.2 17.2 - - + +
88A ILE 2.8 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL* 3.7 26.2 - - + -
41A ASP 3.0 9.9 + - - +
42A VAL* 4.4 7.6 - - + +
43A GLY 3.0 25.6 + - - -
61A TYR 4.2 6.3 - - - +
62A ALA* 1.3 72.7 - - - +
64A ASP* 1.3 62.0 + - - +
88A ILE* 3.4 24.5 - - + +
90A GLY 3.3 23.8 - - - +
91A ARG 4.4 0.4 - - - -
92A ALA* 3.9 19.7 - - + +
95A VAL* 4.0 22.9 - - + -
96A LEU* 3.8 18.8 - - + -
99A LEU* 4.2 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASP* 4.7 1.7 - - - +
43A GLY 4.4 2.8 - - - +
44A CYS* 3.4 21.3 - - + +
45A GLY 3.4 30.0 + - - +
50A THR* 5.1 1.7 + - - -
62A ALA* 3.7 22.5 + - - +
63A ILE* 1.3 79.5 - - - +
65A TYR* 1.3 59.5 + - - +
69A ALA* 3.5 6.6 - - + +
70A ILE* 3.6 24.5 - - + +
73A THR* 3.4 14.1 + - - +
87A ILE* 5.0 2.0 - - + -
88A ILE 3.3 3.6 + - - -
89A LYS* 3.3 9.7 - - - -
90A GLY 3.0 20.2 + - - -
----------------------------------------------------------
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