Contacts of the helix formed by residues 133 - 144 (chain B) in PDB entry 3O9Z
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 HIS 133 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLN 3.4 2.0 + - - +
130B LEU* 3.2 25.1 + - + +
131B ARG 3.6 0.2 - - - -
132B VAL* 1.3 76.7 - - - +
134B PRO* 1.3 77.7 - - + +
135B SER* 3.1 34.4 + - - -
136B LEU* 3.0 15.7 + - + +
137B LEU* 2.9 21.0 + - - +
255B GLU 5.3 0.2 - - - -
256B PHE* 3.2 34.5 + - + -
258B GLU* 3.0 28.2 + - + -
260B PHE* 4.7 3.6 - - - -
263B LEU* 3.8 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B VAL 3.3 9.4 - - - +
133B HIS* 1.3 92.9 - - + +
135B SER* 1.3 56.9 + - - +
137B LEU* 3.5 10.3 + - + +
138B ALA* 3.0 29.5 + - - +
263B LEU* 4.4 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B HIS* 3.1 24.0 + - - -
134B PRO* 1.3 79.5 - - - +
136B LEU* 1.3 59.1 + - - +
138B ALA* 3.5 6.5 + - - +
139B LEU* 3.0 25.6 + - - +
142B ARG* 4.6 3.1 + - - -
254B VAL* 3.9 25.2 - - - +
255B GLU 5.2 2.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LEU* 3.7 40.8 - - + +
133B HIS* 3.0 13.0 + - + +
135B SER* 1.3 76.7 - - - +
137B LEU* 1.3 59.9 + - - +
138B ALA 3.2 0.4 - - - -
139B LEU* 3.6 11.3 - - + +
140B LYS* 2.9 29.3 + - - +
189B LEU* 3.9 19.7 - - + -
192B TRP* 4.2 11.7 - - + -
193B LEU* 4.7 2.0 - - + +
247B ILE* 4.2 12.8 - - + -
254B VAL* 4.2 13.7 - - + -
256B PHE* 3.9 45.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ARG 3.5 18.4 - - - +
132B VAL* 3.9 29.8 - - + +
133B HIS 2.9 14.5 + - - +
134B PRO* 3.8 8.1 - - + +
136B LEU* 1.3 76.0 - - - +
138B ALA* 1.3 62.2 + - - +
140B LYS* 3.3 5.8 + - + +
141B GLU* 3.1 27.8 + - + +
192B TRP* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B PRO 3.0 18.6 + - - +
135B SER* 3.7 7.2 - - - +
137B LEU* 1.3 75.1 - - - +
139B LEU* 1.3 66.1 + - - +
141B GLU* 3.2 9.0 + - - +
142B ARG* 3.1 40.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B SER 3.0 18.4 + - - +
136B LEU* 3.3 15.9 + - + +
138B ALA* 1.3 76.5 - - - +
140B LYS* 1.3 65.9 + - - +
142B ARG* 3.1 12.8 + - - +
143B LEU* 2.8 53.3 + - + +
193B LEU* 4.5 5.8 - - + -
247B ILE* 3.7 39.9 - - + -
249B VAL* 4.1 8.7 - - + -
252B GLU* 3.6 34.8 - - + +
254B VAL* 4.3 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU 2.9 18.7 + - - +
137B LEU* 3.6 9.0 - - + +
138B ALA 3.2 0.2 - - - -
139B LEU* 1.3 77.1 - - - +
141B GLU* 1.3 75.5 + - - +
143B LEU* 3.4 4.4 + - + +
144B GLY* 3.1 19.4 + - - -
192B TRP* 3.5 63.1 - - + +
193B LEU* 3.5 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU 3.1 15.4 + - - +
138B ALA* 3.2 9.8 + - - +
140B LYS* 1.3 94.5 + - - +
142B ARG* 1.3 63.3 + - + +
144B GLY* 3.2 10.8 + - - -
145B GLN* 3.4 17.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B SER 4.6 2.2 + - - -
138B ALA* 3.1 32.4 + - - +
139B LEU* 3.6 28.2 - - + +
141B GLU* 1.3 75.7 - - + +
143B LEU* 1.3 61.5 + - + +
145B GLN* 3.1 20.7 + - - +
146B GLU* 3.2 18.2 - - - +
252B GLU* 2.8 45.0 + - - +
254B VAL* 4.0 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 2.8 51.5 + - + +
140B LYS* 3.9 4.0 - - - +
141B GLU 3.3 0.2 - - - -
142B ARG* 1.3 76.6 - - - +
144B GLY* 1.3 59.7 + - - +
145B GLN 3.1 1.3 + - - -
146B GLU* 3.3 26.2 + - - +
150B LYS* 3.3 33.5 + - - -
193B LEU* 4.4 13.7 - - + +
194B PHE* 3.7 32.8 - - + -
249B VAL* 4.1 10.3 - - + -
250B ASP* 3.9 13.2 - - + +
252B GLU* 5.1 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LYS 3.1 13.1 + - - -
141B GLU* 3.2 5.6 + - - -
142B ARG 3.2 0.8 - - - -
143B LEU* 1.3 75.2 - - - +
145B GLN* 1.3 66.8 + - - +
146B GLU 3.1 6.7 + - - +
----------------------------------------------------------
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