Contacts of the helix formed by residues 105 - 112 (chain A) in PDB entry 2WSC
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 ASN 105 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A SER* 1.3 75.8 - - - +
106A TYR* 1.3 56.7 + - - -
107A GLU 3.6 0.9 - - - -
108A ALA* 4.0 7.5 - - - +
109A TRP* 2.9 32.3 + - - +
116A ILE* 3.5 6.7 - - - +
118A PRO* 3.1 12.5 - - - +
119A SER 2.9 36.3 + - - +
136A VAL* 3.1 15.8 - - - +
137A GLY 4.3 0.4 - - - +
138A GLY* 3.7 23.2 - - - +
140A PHE* 3.0 39.7 - - + -
150A PHE* 3.2 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLY 3.8 16.8 - - - +
101A ALA* 5.7 0.7 - - - +
104A SER* 2.6 11.1 + - - +
105A ASN* 1.3 71.0 - - - +
107A GLU* 1.3 82.2 + - - +
109A TRP* 3.4 24.5 + + - -
110A LEU* 3.1 45.2 + - + +
150A PHE* 3.2 30.7 - - + -
153A TRP* 2.7 42.2 + + + -
154A ARG* 4.0 7.6 + - - -
156A SER* 2.9 14.8 + - - -
159A THR* 3.7 12.8 - - + +
160A SER 5.3 2.2 - - - -
161A GLU* 5.9 0.7 - - + -
164A LEU* 4.1 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A SER* 4.0 3.6 + - - +
106A TYR* 1.3 87.9 - - - +
108A ALA* 1.3 65.9 + - - +
110A LEU* 3.1 27.2 + - + +
111A ASN* 3.8 5.9 + - - +
159A THR* 5.7 1.3 - - - -
160A SER* 3.2 17.1 + - - -
161A GLU* 2.4 69.7 + - + +
239A PRO* 6.3 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A SER* 4.9 0.8 + - - +
105A ASN* 3.9 16.2 + - - +
106A TYR 3.3 0.4 - - - -
107A GLU* 1.3 79.5 - - - +
109A TRP* 1.3 61.0 + - - +
110A LEU 3.4 0.7 + - - -
111A ASN* 4.1 1.3 + - - +
112A ASP* 3.3 28.7 + - - +
116A ILE* 3.9 3.6 - - - +
138A GLY* 3.4 36.2 - - - +
140A PHE* 5.4 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASN 2.9 21.7 + - - +
106A TYR* 3.4 15.7 + + - +
107A GLU 3.3 0.4 - - - -
108A ALA* 1.3 76.9 - - - +
110A LEU* 1.3 63.3 + - + +
112A ASP 2.8 1.5 - - - -
113A PRO* 2.7 44.0 - - + +
114A THR 5.6 0.4 - - - +
116A ILE* 3.4 38.1 - - + +
117A GLY 4.2 3.1 - - - +
118A PRO* 3.7 26.6 - - + +
150A PHE* 2.9 37.0 - + + -
151A GLN* 4.0 10.9 + - - -
154A ARG* 3.0 44.6 - - - -
384A TYR* 3.4 24.7 - + + -
388A ASP* 5.8 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TYR* 3.1 56.8 + - + +
107A GLU* 3.1 23.8 + - + +
109A TRP* 1.3 83.1 - - + +
111A ASN* 1.3 73.6 + - + +
112A ASP 2.9 1.3 - - - -
113A PRO* 2.8 21.0 - - - +
154A ARG* 3.4 30.5 + - - +
159A THR* 3.9 12.1 - - + -
233A LEU* 4.6 11.5 - - + +
239A PRO* 3.1 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLU 3.8 4.2 + - - +
108A ALA* 4.5 2.9 - - - +
110A LEU* 1.3 84.9 - - + +
112A ASP* 1.4 79.0 + - - +
113A PRO* 3.4 4.6 - - - +
115A HIS* 5.1 1.4 + - - -
233A LEU* 5.7 1.8 - - - -
236A GLY 5.4 5.2 + - - +
237A VAL 3.1 26.0 + - - +
238A ASP* 3.1 25.1 + - - +
239A PRO* 4.6 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ALA* 3.3 19.9 + - - +
109A TRP 2.8 8.2 + - - -
110A LEU 2.9 1.2 - - - -
111A ASN* 1.4 102.1 + - - +
113A PRO* 1.4 63.4 - - - +
115A HIS* 3.2 23.2 - - + +
116A ILE* 3.0 30.4 + - + +
138A GLY* 6.0 1.4 - - - -
----------------------------------------------------------
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