Contacts of the helix formed by residues 122 - 128 (chain I) in PDB entry 2WQT
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 122 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F VAL* 5.0 2.7 - - + -
84F ALA* 4.0 30.5 - - + +
87F CYS* 3.9 15.0 - - + -
164F TYR* 5.1 1.6 - - - +
120I ASP 3.8 9.4 - - - +
121I ILE* 1.3 79.2 - - - +
123I PHE* 1.3 66.2 + - - +
124I ASP* 2.8 23.0 + - - +
125I GLU* 2.9 44.2 + - - +
126I LEU* 3.0 10.7 + - - +
209I VAL* 4.3 3.6 - - - -
213I ARG* 4.3 3.8 - - - +
1N MET* 4.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 123 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F CYS* 4.4 9.9 - - - -
88F TYR 4.7 0.4 - - - +
89F GLY* 3.5 20.4 - - - +
90F ASP* 3.8 13.5 - - + -
166F ILE* 3.6 25.4 - - + -
167F GLY 3.5 22.4 - - - -
122I THR* 1.3 72.9 - - - +
124I ASP* 1.3 60.4 + - - +
126I LEU* 3.4 4.5 + - - +
127I TYR* 3.3 31.4 + + - -
203I HIS* 3.8 32.8 - + - -
205I LEU* 3.5 31.1 - - + +
206I ASN* 3.4 26.7 - - - -
209I VAL* 3.8 15.6 - - + +
213I ARG* 5.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 124 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F CYS* 3.8 2.9 - - - -
111F VAL* 4.5 16.3 - - + +
132F TRP* 5.3 4.2 - - - -
134F LEU* 4.6 8.5 - - + +
164F TYR* 4.6 3.1 + - - -
166F ILE* 3.6 33.2 - - + +
225F GLY 5.2 3.5 - - - +
227F ILE* 3.9 26.1 - - + +
122I THR* 2.8 22.0 + - - +
123I PHE* 1.3 75.6 - - - +
125I GLU* 1.3 76.0 + - - +
127I TYR* 3.3 25.0 - - - +
128I ASN* 3.6 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 125 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F ARG* 3.3 31.9 + - - -
57F VAL* 4.2 6.9 - - - +
225F GLY 5.7 4.2 - - - +
114I ARG* 5.7 0.3 + - - -
116I LEU* 5.6 0.2 - - - +
118I ALA* 5.5 1.9 - - - +
121I ILE* 3.4 22.0 - - + +
122I THR* 2.9 38.6 + - - +
124I ASP* 1.3 81.8 - - - +
126I LEU* 1.3 66.1 + - - +
128I ASN* 3.3 16.8 + - - +
129I ALA* 3.6 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110I LEU* 4.7 1.8 - - + -
112I LEU* 5.2 6.3 - - + -
116I LEU* 4.2 23.1 - - + -
121I ILE* 4.0 14.2 - - + +
122I THR 3.0 10.9 + - - +
123I PHE 3.6 8.1 - - - +
124I ASP 3.3 0.2 - - - -
125I GLU* 1.3 73.9 - - - +
127I TYR* 1.3 60.8 + - - +
129I ALA* 2.8 25.5 + - + +
130I ILE* 3.4 11.5 + - + +
205I LEU* 3.7 37.0 - - + +
208I ALA* 3.5 47.1 - - + +
209I VAL* 4.1 8.7 - - + +
212I ALA* 4.4 2.9 - - + -
228I ILE* 5.6 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 127 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F TRP* 4.4 13.5 - + + +
134F LEU* 3.9 17.0 - - + -
167F GLY 3.6 19.7 - - - -
168F GLY* 3.7 12.6 - - - -
169F PRO* 3.7 4.4 - - + +
170F ALA* 3.6 39.9 + - + -
123I PHE* 3.3 29.3 + + - -
124I ASP* 3.3 11.7 - - - +
126I LEU* 1.3 79.0 - - - +
128I ASN* 1.3 61.6 + - - +
129I ALA 3.1 1.2 + - - -
130I ILE* 3.3 26.6 + - + +
173I PRO* 4.6 18.8 - - + +
176I LEU 4.8 1.6 + - - -
178I LEU* 4.2 18.5 + - + +
203I HIS* 4.5 7.4 + - - -
205I LEU* 3.6 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 128 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111F VAL* 6.3 0.7 - - + -
131F GLU* 3.0 31.7 + - - +
132F TRP* 2.7 39.4 - - + +
172F ARG* 4.6 2.6 - - - +
113I ASN* 2.6 24.4 + - - -
114I ARG* 3.1 31.9 + - - +
124I ASP 3.6 5.5 + - - +
125I GLU* 3.3 12.7 + - - +
126I LEU 3.2 1.0 - - - -
127I TYR* 1.3 77.5 - - - +
129I ALA* 1.3 50.2 + - - +
130I ILE 3.5 1.5 - - - +
----------------------------------------------------------
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