Contacts of the helix formed by residues 124 - 134 (chain B) in PDB entry 2WK6
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 LYS 124 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B GLY 2.7 35.1 + - - +
123B ASP* 1.3 70.8 - - - +
125B VAL* 1.3 62.6 + - - +
126B SER 3.4 2.2 - - - -
127B LEU* 3.4 35.6 + - + +
128B VAL* 3.5 7.7 + - - +
154B THR* 5.9 1.3 - - - -
157B LYS* 3.8 3.8 - - - +
277B LEU* 2.8 13.1 + - + -
280B CYS 2.9 21.7 + - - -
286B GLU* 3.7 37.2 - - + +
289B GLU* 2.7 27.0 + - + -
290B ALA* 4.0 10.3 - - + -
302B LEU* 3.8 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LYS* 4.0 17.5 - - - +
123B ASP* 3.2 23.5 + - - +
124B LYS* 1.3 75.0 - - - +
126B SER* 1.3 57.0 + - - +
128B VAL* 3.2 0.9 + - - +
129B LEU* 2.6 50.4 + - + +
235B LYS* 5.2 0.2 - - - +
277B LEU* 4.6 11.9 - - + -
302B LEU* 4.8 0.7 - - + -
305B LEU* 4.2 26.9 - - + -
306B VAL* 3.7 33.7 - - + +
309B LEU* 4.3 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LYS* 3.0 29.0 + - - +
116B HIS* 5.3 0.7 - - - -
117B SER* 5.2 2.6 + - - -
123B ASP 5.0 1.8 + - - -
124B LYS 3.4 0.4 - - - -
125B VAL* 1.3 77.5 - - - +
127B LEU* 1.3 58.4 + - - +
129B LEU* 4.4 3.4 - - - +
130B ALA* 2.8 36.4 + - - +
142B MET* 3.8 27.8 - - - -
154B THR* 4.0 25.4 - - - +
184B ILE* 4.5 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LYS* 3.4 28.7 + - + +
125B VAL 3.2 0.4 - - - -
126B SER* 1.3 77.5 - - - +
128B VAL* 1.3 56.7 + - - +
131B PRO* 2.9 23.9 - - - +
154B THR* 4.5 16.2 - - - +
157B LYS* 4.1 21.8 - - + -
158B LEU* 3.3 41.7 - - + -
184B ILE* 4.4 9.6 - - + -
286B GLU 4.3 2.5 - - - +
287B VAL* 4.3 15.3 - - + -
290B ALA* 4.1 18.2 - - + -
294B MET* 3.9 8.5 - - + +
343B PHE* 4.1 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LYS 3.5 4.0 + - - +
125B VAL 3.2 3.1 + - - +
127B LEU* 1.3 76.6 - - - +
129B LEU* 1.3 60.8 + - - +
131B PRO* 3.3 5.6 - - - +
132B ALA* 3.1 22.3 + - - +
290B ALA* 3.5 40.8 - - + +
293B CYS* 3.7 20.4 - - + -
294B MET* 4.1 11.6 - - + +
302B LEU* 3.8 16.8 - - + -
306B VAL* 3.6 26.9 - - + -
334B LEU* 3.8 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LYS* 3.6 30.1 - - + -
125B VAL* 2.6 33.6 + - + +
126B SER* 4.3 2.0 - - - +
128B VAL* 1.3 72.3 - - - +
130B ALA* 1.3 66.4 + - - +
132B ALA* 4.0 0.4 - - - -
133B LEU* 2.9 65.2 + - + +
142B MET* 5.5 0.9 - - + -
306B VAL* 3.2 37.2 - - + +
309B LEU* 5.2 2.9 - - + -
310B GLY* 3.7 19.1 - - - +
313B LEU* 4.5 2.0 - - + -
330B VAL* 4.2 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B SER* 2.8 23.8 + - - +
129B LEU* 1.3 77.0 - - - +
131B PRO* 1.3 67.6 - - + +
133B LEU* 3.2 11.4 + - - +
134B ALA* 3.1 19.6 + - - +
140B VAL* 4.1 10.0 - - + +
142B MET* 4.1 18.4 - - + -
182B CYS* 4.1 12.6 - - + +
184B ILE* 4.2 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU 2.9 28.0 - - - +
128B VAL 3.3 7.6 - - - +
130B ALA* 1.3 91.8 - - + +
132B ALA* 1.3 65.4 + - - +
134B ALA* 3.4 0.6 + - + -
135B ALA* 3.1 15.1 + - - +
182B CYS* 4.1 9.2 - - - -
184B ILE* 5.5 1.3 - - + -
294B MET* 3.7 16.4 - - - -
339B ALA* 3.1 24.6 - - - +
342B ARG* 3.3 19.1 - - + +
343B PHE* 3.6 24.2 - - + +
346B MET* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B VAL 3.1 17.3 - - - +
129B LEU* 3.2 9.1 + - - +
130B ALA 3.2 0.4 - - - -
131B PRO* 1.3 78.6 - - - +
133B LEU* 1.3 60.1 + - - +
135B ALA* 2.9 22.2 - - - +
136B CYS* 3.8 4.5 - - - -
306B VAL* 4.7 0.7 - - + -
330B VAL* 4.2 26.6 - - + +
333B ALA* 3.7 6.6 - - - +
334B LEU* 4.2 11.4 - - + -
339B ALA* 3.0 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B VAL* 4.2 2.9 - - + -
114B ASP* 5.1 1.1 - - - -
115B LYS 5.3 0.4 - - - +
129B LEU* 2.9 49.8 + - + +
130B ALA* 3.5 5.2 - - - +
132B ALA* 1.3 73.1 - - - +
134B ALA* 1.3 54.0 + - - +
135B ALA 2.7 5.2 - - - -
136B CYS* 2.7 36.7 + - - +
138B CYS* 3.7 11.2 + - + +
140B VAL* 3.8 27.4 - - + -
142B MET* 6.1 0.2 - - + -
310B GLY* 4.3 6.7 - - - -
313B LEU* 3.2 35.9 - - + -
314B LEU* 4.0 27.4 - - + -
330B VAL* 4.4 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ALA 3.1 12.4 + - - +
131B PRO 3.4 1.7 + - - +
133B LEU* 1.3 77.8 - - - +
135B ALA* 1.3 54.1 + - - +
136B CYS 3.1 3.8 + - - -
137B GLY 3.9 3.8 + - - -
138B CYS 3.4 13.0 - - - +
140B VAL* 4.6 0.6 - - + +
181B GLY* 3.6 27.1 - - - +
182B CYS* 3.8 4.9 - - + -
342B ARG* 2.6 60.8 + - + +
----------------------------------------------------------
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