Contacts of the strand formed by residues 68 - 75 (chain A) in PDB entry 5CYP
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 LYS 68 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A THR* 5.3 6.5 - - + -
66A GLU* 3.3 19.5 + - + +
67A ILE* 1.3 78.6 - - - +
69A SER* 1.3 64.4 + - - +
70A ILE* 3.9 17.8 + - + +
85A VAL 3.6 1.2 - - - +
86A ILE* 3.4 3.5 - - - -
87A ASP* 2.8 47.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ILE 4.3 0.6 + - - -
68A LYS* 1.3 75.0 - - - +
70A ILE* 1.3 63.1 + - - +
71A THR* 4.3 2.5 + - - -
84A THR* 4.0 16.1 - - - +
85A VAL 3.6 3.6 - - - -
86A ILE* 3.5 18.3 - - - +
107A PHE* 3.8 16.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ILE* 4.3 24.5 - - + -
41A ASN* 5.1 6.1 - - - +
44A PHE* 3.6 19.7 - - + -
68A LYS* 4.4 22.9 - - + +
69A SER* 1.3 78.3 - - - +
71A THR* 1.3 63.7 + - - +
72A HIS* 3.6 26.9 - - + -
84A THR* 3.2 1.9 - - - +
85A VAL* 2.7 44.2 + - + +
87A ASP* 5.2 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A SER* 4.2 2.5 - - - -
70A ILE* 1.3 73.0 + - - +
72A HIS* 1.3 81.9 + - - +
73A ASP* 4.6 0.2 - - - +
82A LYS* 3.8 36.6 - - + +
83A LEU 3.2 6.1 - - - +
84A THR* 2.7 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PHE* 3.8 32.3 - + + -
70A ILE* 3.6 29.0 - - + +
71A THR* 1.3 85.5 + - - +
73A ASP* 1.3 68.7 + - - +
74A ILE* 3.6 7.1 + - + +
83A LEU* 3.0 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A THR* 4.6 0.5 - - - +
72A HIS* 1.3 74.1 - - - +
74A ILE* 1.3 63.5 + - - +
80A ARG* 5.9 6.2 + - + -
81A MET 3.5 6.1 - - - +
82A LYS* 3.3 44.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PHE* 5.3 4.7 - - + -
47A LYS* 3.6 47.6 - - + -
72A HIS* 4.2 15.5 - - + +
73A ASP* 1.3 80.5 - - - +
75A GLU* 1.3 59.8 + - - +
76A GLU* 3.7 7.4 + - + +
80A ARG* 4.4 2.9 - - - -
81A MET* 2.7 51.7 + - + +
83A LEU* 3.7 31.2 - - + -
266A ILE* 4.7 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE* 1.3 71.5 - - - +
76A GLU* 1.3 65.3 + - - +
78A GLY 4.4 6.9 + - - +
79A VAL 3.6 9.2 - - - +
80A ARG* 4.2 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