Contacts of the strand formed by residues 124 - 130 (chain C) in PDB entry 2WZJ
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 THR 124 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ILE* 3.8 20.2 - - + -
84C ILE 3.4 12.6 - - - +
85C ASP* 5.1 3.3 + - + -
86C LYS* 3.8 3.6 - - - +
119C ILE 4.3 0.2 - - - +
120C GLU* 3.6 1.0 - - - -
121C THR* 2.8 46.3 + - - +
122C GLU 3.7 0.4 - - - -
123C LYS* 1.3 86.3 - - - +
125C LEU* 1.3 64.9 + - - +
126C TYR* 3.4 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ARG 3.6 3.1 - - - +
84C ILE* 2.9 41.1 + - + +
86C LYS* 4.0 15.7 - - + +
97C LEU* 3.8 29.2 - - + -
98C PHE* 4.3 15.7 - - + -
101C VAL* 4.7 5.6 - - + -
118C VAL* 3.7 22.7 - - + -
119C ILE 3.4 16.6 - - - +
120C GLU* 3.7 20.9 - - + -
124C THR* 1.3 76.3 - - - +
126C TYR* 1.3 60.2 + - - +
127C LEU* 4.0 23.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ILE* 3.9 48.4 - - + +
55C LEU* 5.6 1.8 - - + -
81C VAL* 4.1 12.3 - - + -
82C ARG 3.5 3.4 - - - -
83C ILE* 3.6 35.0 - - + -
118C VAL* 3.6 5.7 - - - +
119C ILE* 2.8 60.1 + - + +
121C THR* 4.2 10.7 - - + +
124C THR* 3.4 34.5 + - + +
125C LEU* 1.3 74.2 - - - +
127C LEU* 1.3 63.1 + - - +
128C VAL* 3.9 1.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ALA 3.4 3.1 - - - +
81C VAL* 4.3 0.8 - - - +
82C ARG* 2.9 41.1 + - + +
84C ILE* 5.0 2.0 - - + -
97C LEU* 4.9 2.5 - - + -
101C VAL* 3.6 31.0 - - + -
104C MET* 4.4 2.7 - - + -
115C LEU* 4.5 6.1 - - + -
117C GLU 4.1 0.4 - - - -
118C VAL* 3.6 34.1 - - + -
125C LEU* 4.3 17.7 - - + +
126C TYR* 1.3 74.5 - - - +
128C VAL* 1.3 63.3 + - - +
129C MET* 3.4 17.4 + - + +
196C PHE* 3.7 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ILE* 6.3 0.2 - - + -
53C TYR* 3.4 53.2 - - + +
79C VAL* 3.9 21.3 - - + -
80C ALA 3.6 3.1 - - - +
81C VAL* 4.2 19.1 - - + +
115C LEU* 3.6 3.3 - - - +
116C PHE* 2.8 32.7 + - + -
117C GLU* 3.0 23.4 + - + +
119C ILE* 4.6 10.3 - - + -
126C TYR* 4.8 2.7 - - + +
127C LEU* 1.3 70.8 - - - +
129C MET* 1.3 60.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C VAL* 6.2 0.7 - - - -
79C VAL* 3.5 9.0 - - - +
80C ALA* 2.7 54.9 + - + +
82C ARG* 4.5 2.7 - - + +
104C MET* 4.1 17.9 - - + +
113C VAL* 4.4 14.1 - - + -
114C LYS 3.3 13.7 - - - +
115C LEU* 4.6 5.2 - - + -
116C PHE* 3.8 6.3 - - - -
127C LEU* 3.7 26.2 - - + +
128C VAL* 1.3 73.9 - - - +
130C GLU* 1.3 66.4 + - - +
131C TYR 3.5 0.5 + - - -
196C PHE* 3.7 24.0 - - + -
198C ASN* 3.6 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ALA* 4.0 7.7 - - - +
112C ILE 3.8 1.9 - - - +
113C VAL* 3.4 23.8 - - + +
114C LYS* 2.9 41.3 + - - +
116C PHE* 3.6 26.1 - - + -
129C MET* 1.3 78.3 - - - +
131C TYR* 1.3 63.6 + - - +
132C ALA* 4.0 1.9 + - - +
182C LEU* 6.2 0.3 - - - +
184C ASP* 5.6 0.9 - - - +
190C LYS* 2.7 43.6 + - - +
363C TYR* 3.9 20.7 + - + +
----------------------------------------------------------
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