Contacts of the helix formed by residues 122 - 128 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ASP 3.8 9.0 - - - +
121A ILE* 1.3 79.0 - - - +
123A PHE* 1.3 65.7 + - - +
124A ASP* 2.9 23.3 + - - +
125A GLU* 2.9 42.9 + - - +
126A LEU* 3.0 11.4 + - - +
209A VAL* 4.3 3.1 - - - -
213A ARG* 4.3 5.2 - - - +
57B VAL* 4.7 4.0 - - + -
84B ALA* 3.8 32.5 - - + +
87B CYS* 3.8 14.6 - - + -
164B TYR* 4.8 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A THR* 1.3 73.1 - - - +
124A ASP* 1.3 60.2 + - - +
126A LEU* 3.4 4.3 + - - +
127A TYR* 3.3 32.0 + + - -
203A HIS* 3.8 28.9 - + - -
205A LEU* 3.5 30.4 - - + +
206A ASN* 3.4 26.9 - - - -
209A VAL* 3.8 16.0 - - + +
213A ARG* 5.2 0.4 - - - +
87B CYS* 4.3 11.6 - - - -
88B TYR 4.7 0.9 - - - +
89B GLY* 3.4 18.8 - - - +
90B ASP* 3.7 16.2 - - + -
166B ILE* 3.5 30.5 - - + -
167B GLY 3.5 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A THR* 2.9 21.9 + - - -
123A PHE* 1.3 77.4 - - - +
125A GLU* 1.3 78.9 + - - +
127A TYR* 3.3 23.3 + - - +
128A ASN* 3.6 6.8 + - - +
87B CYS* 3.9 1.9 - - - -
111B VAL* 4.4 15.5 - - + +
132B TRP* 5.3 3.5 - - - -
134B LEU* 4.6 8.7 - - + +
164B TYR* 4.3 3.8 + - - -
166B ILE* 3.5 34.1 - - + +
225B GLY 5.1 3.8 - - - +
227B ILE* 3.7 27.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ARG* 5.7 0.7 + - - -
116A LEU* 5.5 0.2 - - - +
118A ALA* 5.4 1.4 - - - +
121A ILE* 3.4 16.6 - - + +
122A THR* 2.9 36.9 + - - +
124A ASP* 1.3 82.9 - - - +
126A LEU* 1.3 65.8 + - - +
128A ASN* 3.3 16.8 + - - +
129A ALA* 3.6 10.0 + - - +
55B ARG* 3.1 35.8 + - - -
57B VAL* 3.8 12.3 - - - +
225B GLY 5.5 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 4.7 1.8 - - + -
112A LEU* 5.2 6.7 - - + -
116A LEU* 4.2 24.0 - - + -
121A ILE* 4.0 14.0 - - + +
122A THR 3.0 10.7 + - - +
123A PHE 3.6 8.1 - - - +
124A ASP 3.3 0.2 - - - -
125A GLU* 1.3 74.3 - - - +
127A TYR* 1.3 66.4 + - - +
129A ALA* 2.8 16.0 + - + +
130A ILE* 3.4 15.5 + - + +
205A LEU* 3.8 37.0 - - + +
208A ALA* 3.5 45.8 - - + +
209A VAL* 4.1 8.5 - - + +
212A ALA* 4.4 2.7 - - + -
228A ILE* 5.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PHE* 3.3 26.2 + + - -
124A ASP* 3.3 12.6 + - - +
126A LEU* 1.3 78.5 - - - +
128A ASN* 1.3 61.4 + - - +
129A ALA 3.2 1.4 + - - -
130A ILE* 3.4 26.3 + - + +
173A PRO* 4.6 17.5 - - + +
176A LEU 4.8 1.8 + - - -
178A LEU* 4.3 19.1 + - + +
203A HIS* 4.5 7.4 + - - -
205A LEU* 3.6 24.2 - - + +
132B TRP* 4.4 15.6 - + + +
134B LEU* 3.7 17.7 - - + -
167B GLY 3.5 20.4 - - - -
168B GLY* 3.7 12.3 - - - -
169B PRO* 3.8 3.8 - - - +
170B ALA* 3.6 41.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASN* 3.1 19.4 + - - -
114A ARG* 3.1 33.2 + - - +
124A ASP 3.6 4.0 + - - +
125A GLU* 3.3 12.0 + - - +
126A LEU 3.2 1.0 - - - -
127A TYR* 1.3 79.6 - - - +
129A ALA* 1.3 56.3 + - - +
130A ILE 3.5 1.3 - - - +
111B VAL* 6.0 1.8 - - + -
131B GLU* 2.8 35.0 + - - +
132B TRP* 2.7 39.0 - - + +
172B ARG* 4.7 1.6 - - - +
----------------------------------------------------------
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