Contacts of the helix formed by residues 125 - 135 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B THR 3.3 1.9 + - - -
122B THR 3.1 17.1 + - - +
123B CYS 4.3 5.4 - - - +
124B ARG* 1.3 80.2 - - - +
126B LEU* 1.3 64.9 + - - +
127B PRO* 3.4 5.6 - - - -
128B GLU* 2.9 51.3 + - + +
129B ALA* 3.0 21.8 + - - +
146B LEU* 3.6 34.9 - - + +
147B CYS* 3.1 34.2 + - - +
148B GLY* 4.1 1.8 - - - -
149B TYR* 5.9 5.4 - - + -
286B LYS* 6.2 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LEU* 4.5 3.6 - - + -
117A SER* 3.6 26.0 - - - +
118A LEU* 4.3 3.8 - - - +
121A THR* 3.5 36.8 - - + +
291A LEU* 3.9 20.2 - - + -
294A ILE* 4.3 11.9 - - + -
120B LEU 4.7 0.4 - - - +
121B THR* 3.1 17.3 + - + +
124B ARG* 3.2 31.4 + - + +
125B ARG* 1.3 76.8 - - - +
127B PRO* 1.4 67.0 - - + +
129B ALA* 3.0 7.0 + - - +
130B ILE* 2.8 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ILE* 4.3 21.8 - - + -
134A LYS* 6.4 0.2 - - - +
121B THR* 3.4 29.8 - - + +
122B THR* 5.2 0.7 - - - -
125B ARG* 3.5 5.4 - - - -
126B LEU* 1.4 91.3 - - + +
128B GLU* 1.3 61.0 + - - +
130B ILE* 3.6 12.6 + - + +
131B GLU* 3.2 23.9 + - - +
286B LYS 6.1 1.3 - - - +
289B VAL* 4.0 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ARG* 2.9 56.8 + - + +
126B LEU 3.2 0.4 - - - -
127B PRO* 1.3 78.5 - - - +
129B ALA* 1.3 64.4 + - - +
131B GLU* 3.2 7.7 + - - +
132B GLU* 3.0 32.6 + - + +
146B LEU* 4.0 10.9 - - + +
286B LYS* 4.1 47.5 + - + +
287B ASN* 5.9 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A LEU* 3.8 3.8 - - + -
292A PRO* 3.5 23.9 - - + +
294A ILE* 3.7 21.1 - - + -
125B ARG 3.0 13.2 + - - +
126B LEU 3.0 7.8 + - - +
128B GLU* 1.3 73.0 - - - +
130B ILE* 1.3 65.3 + - - +
132B GLU* 3.1 13.2 + - - +
133B VAL* 3.2 16.5 + - - +
146B LEU* 4.0 19.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A THR* 5.7 2.5 - - + +
127A PRO* 3.9 25.8 - - + -
289A VAL* 3.8 23.8 - - + -
290A ILE 3.8 17.3 - - - +
291A LEU* 3.8 14.1 - - + +
126B LEU* 2.8 31.5 + - + +
127B PRO* 3.8 9.2 - - + +
129B ALA* 1.3 72.0 - - - +
131B GLU* 1.3 64.3 + - + +
133B VAL* 3.4 11.8 + - - +
134B LYS* 3.4 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B PRO 3.2 10.7 + - - +
128B GLU* 3.2 10.8 + - - +
129B ALA 3.2 0.6 - - - -
130B ILE* 1.3 82.2 - - + +
132B GLU* 1.3 52.9 + - - +
134B LYS* 3.0 19.0 + - + +
135B ASN* 2.7 59.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B GLU* 3.0 25.1 + - + +
129B ALA* 3.1 10.0 + - - +
131B GLU* 1.3 77.1 - - - +
133B VAL* 1.3 60.4 + - - +
135B ASN* 3.1 22.7 + - - +
136B GLY 3.6 0.2 + - - -
137B GLY* 2.8 46.5 + - - -
138B TRP* 3.0 10.2 + - - -
145B TRP* 3.7 35.6 + - + +
146B LEU* 4.4 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A LEU* 4.7 7.7 - - + +
278A THR* 3.3 19.4 - - - +
283A LEU* 3.8 34.4 - - + +
290A ILE* 3.6 29.6 - - + +
291A LEU 4.2 1.6 - - - -
292A PRO* 3.8 22.7 - - + -
129B ALA 3.2 17.5 - - - +
130B ILE 3.7 6.1 - - - +
131B GLU 3.2 0.2 - - - -
132B GLU* 1.3 76.4 - - - +
134B LYS* 1.3 66.5 + - + +
136B GLY* 4.0 0.5 + - - -
138B TRP* 4.0 21.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PRO* 6.3 1.2 - - - +
278A THR* 3.8 14.2 - - - +
283A LEU* 3.9 45.8 - - + +
285A LEU 5.9 1.4 + - - -
288A CYS 5.8 2.2 + - - -
130B ILE* 3.4 34.6 + - + +
131B GLU* 3.0 23.1 + - + +
133B VAL* 1.3 82.0 - - + +
135B ASN* 1.3 58.0 + - - +
136B GLY 3.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A THR* 4.5 1.1 - - - -
131B GLU* 2.7 38.3 + - - +
132B GLU* 3.1 27.1 + - - +
134B LYS* 1.3 75.4 - - - +
136B GLY* 1.3 56.0 + - - +
137B GLY* 2.7 22.3 + - - -
----------------------------------------------------------
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