Contacts of the strand formed by residues 106 - 113 (chain A) in PDB entry 1WSQ
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 TYR 106 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ILE* 4.1 7.2 - - + -
94A MET* 4.0 30.1 - - + +
95A ARG* 3.3 44.3 - - + -
98A SER* 3.2 28.5 + - - -
104A VAL 3.6 0.4 + - - -
105A GLY* 1.3 73.1 - - - -
107A ILE* 1.3 69.6 + - - +
108A ASP* 3.4 31.1 + - - -
109A SER* 2.8 35.0 + - - -
124A ILE* 4.3 13.7 - - + -
125A LEU 4.1 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A MET* 3.9 17.7 - - + -
70A LYS 5.6 0.2 - - - +
71A CYS* 3.7 22.0 - - - -
105A GLY 4.5 1.3 - - - +
106A TYR* 1.3 87.7 - - - +
108A ASP* 1.3 66.7 + - + +
125A LEU* 2.8 33.9 + - + +
126A MET* 3.5 31.4 - - - +
127A ASP* 3.7 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 3.4 27.6 - - + +
44A GLN* 4.9 8.1 - - - +
106A TYR* 3.4 17.3 + - - -
107A ILE* 1.3 89.0 - - + +
109A SER* 1.3 79.2 + - - +
125A LEU* 2.8 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 3.6 9.8 - - - +
91A ILE* 3.4 31.9 - - - +
106A TYR* 2.8 25.5 + - - -
108A ASP* 1.3 89.9 + - - +
110A SER* 1.3 63.5 + - - +
123A LEU 3.0 15.0 - - - -
124A ILE* 4.2 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLY 3.3 0.5 + - - -
41A ILE* 3.3 18.0 - - - +
42A GLY* 3.5 20.4 - - - -
91A ILE* 5.6 0.4 - - - -
109A SER* 1.3 77.2 - - - +
111A ILE* 1.3 65.2 + - - +
112A ASN* 3.2 25.0 + - - -
121A GLU 3.6 1.6 - - - +
123A LEU* 2.8 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 3.7 29.8 - - + -
87A CYS* 5.2 0.2 - - + -
88A LYS* 3.8 37.0 - - + +
91A ILE* 4.2 17.3 - - + -
110A SER* 1.3 80.8 - - - +
112A ASN* 1.3 63.9 + - - +
120A TRP* 3.9 26.2 - - + -
121A GLU 3.1 8.5 - - - +
122A VAL* 4.2 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLY 3.1 25.7 + - - +
42A GLY* 4.8 4.5 + - - +
110A SER* 3.2 19.3 + - - -
111A ILE* 1.3 77.9 - - - +
113A ASN* 1.3 63.4 + - - +
120A TRP* 3.2 9.7 - - - -
121A GLU* 2.4 69.2 + - - +
123A LEU* 3.5 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ASN* 1.3 75.7 - - - +
114A VAL* 1.3 61.8 + - - +
115A SER 3.0 12.2 + - - -
116A SER* 2.8 34.4 + - - +
117A GLY 3.1 28.9 + - - +
119A VAL 3.5 5.7 + - - +
120A TRP* 3.3 39.0 - - + -
----------------------------------------------------------
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