Contacts of the helix formed by residues 107 - 124 (chain C) in PDB entry 2WWR
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 LEU 107 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C VAL* 3.7 33.4 - - + +
103C THR* 3.4 23.3 - - - +
104C PRO 4.9 0.4 - - - -
105C ASP 2.7 10.5 + - - +
106C VAL* 1.3 76.3 - - - +
108C THR* 1.3 65.6 + - - +
109C ASP 3.5 2.2 - - - -
110C THR* 4.2 2.4 - - - -
111C THR* 2.7 43.5 + - + +
164C ILE* 4.7 12.3 - - + -
296C SER* 4.2 10.1 - - - +
301C THR* 3.9 17.3 - - + -
305C MET* 3.7 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ASP* 2.7 41.2 + - - -
106C VAL 3.6 0.2 - - - -
107C LEU* 1.3 77.1 - - - +
109C ASP* 1.3 70.8 + - - +
111C THR* 4.0 1.2 - - - -
112C ALA* 3.0 23.2 + - - +
163C ARG* 3.4 41.7 - - + +
164C ILE* 4.2 10.9 - - - +
167C ALA* 4.0 9.6 - - + -
170C ARG* 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ASP 4.7 0.2 + - - -
106C VAL 5.5 0.2 + - - -
107C LEU 3.5 0.4 - - - -
108C THR* 1.3 86.5 - - - +
110C THR* 1.3 54.0 + - - +
112C ALA* 3.2 5.7 + - - +
113C GLU* 2.8 35.3 + - - +
167C ALA* 4.6 1.9 - - - +
170C ARG* 5.5 2.8 + - - -
171C ARG* 3.3 30.6 + - - +
152D THR* 4.1 27.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C VAL 5.1 0.7 + - - -
107C LEU* 3.7 4.3 + - - -
108C THR 3.5 0.6 - - - -
109C ASP* 1.3 77.0 - - - +
111C THR* 1.3 56.2 + - - +
113C GLU* 3.2 9.7 - - - +
114C LEU 3.1 11.6 + - - -
295C GLY 3.1 13.3 - - - +
296C SER* 3.8 13.0 - - - -
298C THR* 3.5 24.9 + - + +
301C THR* 2.6 31.8 + - - +
124D ARG* 3.0 37.3 + - - +
152D THR* 5.1 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C LEU* 2.7 35.5 + - + +
108C THR 4.0 2.2 - - - -
110C THR* 1.3 72.1 - - - +
112C ALA* 1.3 65.9 + - - +
113C GLU 3.1 1.1 - - - -
114C LEU* 3.3 3.2 + - + +
115C ALA* 3.1 21.8 + - - +
164C ILE* 4.4 17.9 - - + -
243C ILE* 3.9 26.2 - - + +
295C GLY* 3.4 28.7 + - - -
296C SER* 4.2 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C THR 3.0 10.2 + - - +
109C ASP 3.3 9.0 - - - +
111C THR* 1.3 75.6 - - - +
113C GLU* 1.3 62.1 + - - +
115C ALA* 3.3 3.1 + - - +
116C VAL* 3.2 28.2 + - - +
164C ILE* 4.3 5.0 - - - +
167C ALA* 3.3 43.7 - - + -
168C ILE* 3.9 13.1 - - + +
171C ARG* 3.9 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C ASP 2.8 13.1 + - - +
110C THR* 3.2 14.3 - - - +
112C ALA* 1.3 77.1 - - - +
114C LEU* 1.3 60.1 - - - +
116C VAL* 3.5 3.3 + - - +
117C SER* 2.9 26.9 + - - +
171C ARG* 4.2 10.4 + - - +
298C THR* 4.6 1.0 - - - +
120D LEU* 4.2 12.3 - - + +
123D CYS* 6.0 0.7 - - - -
124D ARG* 3.1 24.8 + - + +
149D TYR 5.4 0.2 - - - -
150D GLY* 3.5 16.3 - - - -
151D LEU* 2.8 38.5 + - - +
152D THR* 4.0 10.0 + - - -
175D PHE* 4.1 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C THR 3.1 3.1 + - - +
111C THR* 3.3 7.2 + - + +
113C GLU* 1.3 77.1 - - - +
115C ALA* 1.3 57.2 + - - +
117C SER* 3.1 6.4 + - - -
118C LEU* 2.7 35.0 + - + +
243C ILE* 5.1 5.2 - - + -
269C ASP* 3.3 36.3 - - + +
291C LEU* 4.2 9.6 - - + -
294C ILE* 3.4 37.2 - - + +
295C GLY* 3.5 28.7 - - - +
124D ARG* 3.5 18.6 - - + +
126D LEU* 4.3 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C THR 3.1 13.2 + - - +
112C ALA 3.6 8.7 - - - +
113C GLU 3.3 0.2 - - - -
114C LEU* 1.3 77.5 - - - +
116C VAL* 1.3 58.7 + - - +
118C LEU* 3.5 3.2 + - - +
119C LEU* 3.0 28.6 + - - +
168C ILE* 3.9 29.4 - - + -
213C VAL* 4.8 6.8 - - + +
241C ILE* 4.4 5.6 - - + +
243C ILE* 4.2 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ALA 3.2 14.2 + - - +
113C GLU 3.9 5.8 - - - +
115C ALA* 1.3 72.4 - - - +
117C SER* 1.3 56.6 + - - +
119C LEU* 3.3 6.8 + - - +
120C LEU* 2.8 50.8 + - + +
168C ILE* 4.2 19.3 - - + +
171C ARG* 4.0 24.5 - - + -
172C LEU* 3.8 24.5 - - + -
175C PHE* 4.7 3.6 - - + -
120D LEU* 4.3 0.4 - - + -
175D PHE* 4.0 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C GLU 2.9 20.0 + - - -
114C LEU* 3.2 13.9 - - - -
116C VAL* 1.3 76.5 - - - +
118C LEU* 1.3 62.1 + - - +
120C LEU* 3.9 2.2 - - - +
121C THR* 3.0 26.3 + - - -
117D SER 5.6 0.9 - - - +
120D LEU* 3.4 40.6 - - - +
121D THR 5.7 0.7 + - - -
124D ARG* 4.0 9.1 - - - +
126D LEU* 3.8 21.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C LEU* 2.7 19.7 + - + +
115C ALA* 3.7 5.2 - - - +
117C SER* 1.3 72.0 - - - +
119C LEU* 1.3 60.4 + - - +
121C THR* 3.2 9.2 + - + +
122C THR* 2.7 41.0 + - - +
241C ILE* 4.1 13.0 - - + -
243C ILE* 4.4 5.6 - - + -
267C GLY* 3.7 24.5 - - - +
268C LEU 3.7 28.9 - - - +
269C ASP* 3.9 9.9 - - + +
289C VAL* 4.0 17.5 - - + +
291C LEU* 3.8 26.0 - - + +
126D LEU* 4.3 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ALA 3.0 18.5 + - - +
116C VAL* 3.5 6.7 - - - +
118C LEU* 1.3 76.9 - - - +
120C LEU* 1.3 58.2 + - + +
122C THR* 3.2 1.0 + - - -
123C CYS* 2.9 34.0 + - - +
151C LEU* 4.5 15.9 - - + -
156C VAL* 5.6 0.2 - - + -
168C ILE* 5.9 0.2 - - + -
172C LEU* 4.0 36.6 - - + -
211C PHE* 3.5 37.9 - - + -
212C ILE 5.6 0.2 - - - +
213C VAL* 4.4 14.4 - - + -
239C VAL* 4.4 5.8 - - + +
241C ILE* 3.7 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C VAL* 2.8 24.6 + - + +
117C SER* 3.9 3.6 - - - +
119C LEU* 1.3 74.2 - - + +
121C THR* 1.3 61.7 + - - +
123C CYS* 3.6 5.1 - - - -
124C ARG* 3.2 24.8 + - - +
151C LEU* 3.7 29.6 - - + -
175C PHE* 3.9 22.7 - - + -
113D GLU* 4.1 26.0 - - + +
116D VAL* 4.4 0.2 - - + -
117D SER* 3.2 35.0 + - - +
120D LEU* 3.7 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C SER 3.0 11.7 + - - -
118C LEU* 3.2 20.0 - - + +
120C LEU* 1.3 76.7 - - - +
122C THR* 1.3 66.8 + - - +
125C ARG 3.4 1.0 + - - -
126C LEU* 3.0 49.4 + - - +
127C PRO* 3.2 17.2 - - + +
289C VAL* 4.5 11.2 - - + -
117D SER* 4.1 5.6 - - - -
121D THR* 3.0 25.6 + - - -
126D LEU* 3.7 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LEU* 2.7 37.2 + - - +
119C LEU 3.6 3.6 - - - -
121C THR* 1.3 79.5 - - - +
123C CYS* 1.3 62.8 + - - +
124C ARG 3.3 0.2 - - - -
125C ARG* 3.3 18.9 + - - +
127C PRO* 5.3 0.2 - - - -
239C VAL* 3.8 24.5 - - + -
241C ILE* 4.0 4.5 - - - +
265C ALA* 3.8 19.2 - - + +
266C ALA 3.8 22.9 - - - +
267C GLY* 4.0 2.0 - - - +
287C ASN 4.9 1.1 - - - +
289C VAL* 4.1 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C LEU* 2.9 26.9 + - - +
120C LEU* 3.6 21.3 - - - -
122C THR* 1.3 77.5 - - - +
124C ARG* 1.3 69.3 + - - +
125C ARG* 3.3 2.6 - - - +
148C GLY* 3.1 7.3 - - - -
149C TYR* 2.9 49.1 + - - +
151C LEU* 5.2 3.1 - - - -
211C PHE* 3.7 22.9 - - + -
239C VAL* 4.1 14.1 - - + -
265C ALA* 5.8 0.7 - - - -
113D GLU* 4.5 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C LEU* 3.2 20.9 + - + +
123C CYS* 1.3 82.5 - - - +
125C ARG* 1.3 71.4 + - - +
126C LEU* 3.3 20.3 + - + +
146C LEU 4.5 5.2 - - - +
148C GLY* 4.6 3.1 + - - -
149C TYR 4.6 3.6 - - - +
110D THR* 2.9 36.4 + - - +
113D GLU* 3.3 33.7 + - - +
114D LEU* 3.5 19.3 - - + +
117D SER* 4.5 6.3 - - - +
294D ILE* 2.7 41.7 + - - +
295D GLY 2.8 17.0 + - - -
297D ALA* 3.5 14.3 + - - +
298D THR* 3.6 18.9 - - - +
----------------------------------------------------------
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