Contacts of the helix formed by residues 125 - 135 (chain D) 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 ARG 125 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C HIS* 5.9 0.8 - - - -
121D THR 3.3 2.7 + - - -
122D THR 3.1 16.7 + - - +
123D CYS 3.8 9.2 - - - +
124D ARG* 1.3 79.3 - - - +
126D LEU* 1.3 63.3 + - - +
127D PRO* 3.4 6.1 - - - -
128D GLU* 3.0 46.5 + - + +
129D ALA* 3.0 21.2 + - - +
146D LEU* 3.5 22.7 - - + +
147D CYS* 2.8 57.0 + - - +
148D GLY* 4.0 2.5 - - - -
149D TYR* 6.2 2.5 - - + -
286D LYS* 5.0 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C LEU* 4.3 4.7 - - + -
117C SER* 3.8 22.0 - - - +
118C LEU* 4.3 3.8 - - - +
121C THR* 3.7 25.4 - - + +
291C LEU* 3.6 29.1 - - + +
294C ILE* 4.2 5.8 - - + -
121D THR* 3.0 33.9 + - - +
124D ARG* 3.2 30.4 + - + +
125D ARG* 1.3 74.5 - - - +
127D PRO* 1.3 65.0 - - - +
129D ALA* 3.1 5.7 + - - +
130D ILE* 2.8 38.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ILE* 4.2 26.5 - - + -
134C LYS* 6.3 0.9 - - - +
121D THR* 3.5 16.6 - - + +
122D THR* 5.4 0.2 - - - -
125D ARG* 3.4 6.5 - - - -
126D LEU* 1.3 90.3 - - + +
128D GLU* 1.3 61.4 + - - +
130D ILE* 3.1 15.8 + - + +
131D GLU* 3.0 22.5 + - - +
289D VAL* 4.0 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 128 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D ARG* 3.0 51.1 + - - +
127D PRO* 1.3 79.5 - - - +
129D ALA* 1.3 56.0 + - - +
131D GLU* 3.3 7.3 + - + +
132D GLU* 3.1 40.2 + - + +
146D LEU* 4.0 14.1 - - + +
286D LYS* 3.2 50.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C LEU* 3.9 4.5 - - + -
292C PRO* 3.7 24.7 - - + +
294C ILE* 3.9 17.5 - - + -
125D ARG 3.0 13.9 + - - +
126D LEU 3.1 8.0 + - - +
128D GLU* 1.3 75.1 - - - +
130D ILE* 1.3 66.1 + - - +
132D GLU* 3.5 1.4 + - - +
133D VAL* 3.3 26.3 + - - +
146D LEU* 3.7 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 130 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C THR* 5.6 1.6 - - + +
127C PRO* 3.7 28.5 - - + -
289C VAL* 3.7 31.9 - - + -
290C ILE 3.9 17.4 + - - +
291C LEU* 4.2 5.4 - - + -
126D LEU* 2.8 29.3 + - + +
127D PRO* 3.1 12.3 + - + +
129D ALA* 1.3 74.2 - - - +
131D GLU* 1.3 63.5 + - + +
133D VAL* 3.4 5.7 - - - +
134D LYS* 3.4 45.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 131 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C GLU* 5.6 1.6 - - - +
127D PRO 3.0 12.3 + - - +
128D GLU* 3.7 10.1 - - + +
129D ALA 3.2 0.2 - - - -
130D ILE* 1.3 76.1 - - + +
132D GLU* 1.3 54.5 + - - +
134D LYS* 3.0 16.1 + - - +
135D ASN* 2.7 57.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 132 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B LYS* 3.3 17.9 + - - +
128D GLU* 3.1 27.0 + - + +
129D ALA 4.0 4.0 - - - +
130D ILE 3.5 0.2 - - - -
131D GLU* 1.3 75.3 - - + +
133D VAL* 1.3 61.7 + - - +
135D ASN* 2.8 31.7 + - - +
136D GLY 3.2 2.8 + - - -
137D GLY* 2.8 37.0 + - - +
138D TRP* 3.3 5.5 + - - -
145D TRP* 3.9 39.2 + - + +
146D LEU* 4.6 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 133 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C LEU* 4.9 7.5 - - + +
278C THR* 3.7 15.1 - - - +
283C LEU* 4.4 20.5 - - + +
290C ILE* 3.7 35.9 - - + +
291C LEU 4.3 0.4 - - - -
292C PRO* 3.6 29.4 - - + -
129D ALA 3.3 14.1 + - - +
130D ILE 3.4 9.2 - - - +
132D GLU* 1.3 80.6 - - - +
134D LYS* 1.3 64.3 + - + +
136D GLY* 3.9 0.9 + - - -
138D TRP* 3.6 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 134 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C THR* 3.4 20.8 - - - +
283C LEU* 3.8 38.3 + - + +
288C CYS 5.9 2.4 + - - -
130D ILE* 3.4 34.4 + - + +
131D GLU* 3.0 19.7 + - - +
133D VAL* 1.3 85.2 - - + +
135D ASN* 1.3 60.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 135 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B LYS* 3.6 8.9 + - - +
232B GLN* 5.4 7.4 + - - -
278C THR* 4.4 1.3 - - - -
131D GLU* 2.7 50.7 + - - +
132D GLU* 2.8 25.5 + - - +
134D LYS* 1.3 73.6 - - - +
136D GLY* 1.3 57.4 + - - +
137D GLY* 2.7 31.7 + - - -
----------------------------------------------------------
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