Contacts of the strand formed by residues 111 - 115 (chain C) in PDB entry 2PY2
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 CYS 111 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ASP* 3.1 24.2 - - - +
88C TRP 4.0 1.8 - - - +
89C CYS* 2.0 51.1 - - - +
104C MET 3.7 0.3 - - - -
105C ASN 3.3 4.3 + - - -
106C VAL* 3.0 30.1 + - - +
109C GLY* 4.0 17.7 - - - +
110C LYS* 1.3 74.7 - - - +
112C TRP* 1.3 69.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ILE* 3.8 31.6 - - + +
48C SER* 5.3 3.0 + - - -
64C ILE* 3.9 9.1 - - + +
77C TRP* 3.8 26.5 - + - -
83C MET* 5.1 2.9 - - - -
85C TYR* 3.5 29.8 - + - -
86C ALA* 3.5 22.0 - - + -
87C ASP* 2.7 44.5 + - + +
88C TRP* 3.5 24.7 - + + -
89C CYS* 2.9 27.9 + - - +
92C GLN* 3.9 1.2 - - - +
102C ILE* 4.0 25.6 - - + -
103C GLN 3.3 5.4 - - - +
104C MET* 3.8 24.7 - - + +
105C ASN 5.0 0.2 - - - -
110C LYS 5.6 0.2 - - - -
111C CYS* 1.3 76.6 - - - +
113C ASN* 1.3 60.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C TRP* 4.3 3.4 - - - -
89C CYS* 4.6 6.7 - - - +
92C GLN* 3.2 30.6 - - - +
103C GLN 3.0 19.2 + - - +
106C VAL* 3.8 32.6 - - + +
112C TRP* 1.3 76.1 - - - +
114C ASP* 1.3 67.5 + - - +
115C THR* 2.9 25.0 - - + +
903C CA 2.6 22.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ASP* 4.7 0.2 - - - +
75C TRP* 3.7 23.9 - - + -
88C TRP* 3.9 6.0 - - + -
92C GLN* 2.9 8.2 + - - +
93C PRO* 3.5 9.7 - - + +
94C ASP* 3.0 12.8 + - - +
95C THR* 2.8 30.8 + - - -
96C THR 4.3 0.2 + - - -
99C GLU* 3.1 27.5 - - - +
100C CYS 4.5 0.7 - - - -
101C CYS 3.3 10.5 - - - +
102C ILE* 4.5 1.6 - - - +
113C ASN* 1.3 73.1 + - - +
115C THR* 1.3 57.5 + - - +
903C CA 2.4 50.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C TRP* 3.4 9.6 - - + -
99C GLU* 3.5 7.9 + - - -
101C CYS* 2.8 29.3 + - - +
103C GLN* 3.0 36.6 + - + +
106C VAL* 5.7 0.2 - - + -
113C ASN* 2.9 29.2 - - + +
114C ASP* 1.3 74.3 - - - +
116C PRO* 1.3 87.3 + - - +
117C CYS 3.1 3.5 + - - -
119C HIS* 4.0 10.5 - - - +
----------------------------------------------------------
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