Contacts of the strand formed by residues 133 - 137 (chain B) in PDB entry 3H2U
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 133 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B THR* 3.3 24.9 - - + +
131B ASP 3.1 8.3 + - - -
132B ALA* 1.3 70.8 - - - +
134B LEU* 1.3 69.8 + - - +
160B ARG* 3.9 25.8 - - + +
162B PHE* 5.8 2.5 - - + -
177B PHE* 3.8 23.6 - - + -
178B ALA 3.2 22.4 - - - +
179B GLU* 3.5 17.9 - - + -
207B TRP* 3.9 2.6 - - - -
208B THR* 2.9 55.0 + - + +
213B LEU* 4.3 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 1.3 73.5 - - - +
135B CYS* 1.3 62.7 + - - +
136B VAL* 4.1 7.2 - - + -
177B PHE* 3.2 12.2 - - - +
178B ALA* 2.8 41.2 + - + +
180B TYR* 4.5 4.7 - - + +
186B ALA* 3.5 33.4 - - + +
189B ALA* 3.7 13.2 - - + -
190B LYS* 3.5 16.6 - - + +
193B LEU* 5.3 1.3 - - + -
205B VAL* 3.8 21.1 - - + -
206B HIS 3.7 2.0 - - - -
207B TRP* 3.8 43.5 - - + +
208B THR* 4.7 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LEU* 1.3 73.3 - - - +
136B VAL* 1.3 62.3 + - - +
137B ALA 3.8 0.3 + - - -
175B TYR* 4.1 11.0 - - - -
176B GLY 3.4 13.7 - - - -
177B PHE* 3.9 19.7 - - + -
204B TYR 3.7 0.9 - - - +
205B VAL* 3.4 3.5 - - - -
206B HIS* 2.9 49.6 + - + +
208B THR* 4.7 1.1 - - - +
298B ALA* 3.2 29.8 - - - +
299B PRO* 3.8 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LEU* 4.8 9.6 - - + +
135B CYS* 1.3 74.8 - - - +
137B ALA* 1.3 61.2 + - - +
139B LEU* 3.8 23.0 - - + +
148B PHE* 4.0 13.0 - - + -
151B LEU* 4.5 6.1 - - + -
152B VAL* 4.0 23.8 - - + -
175B TYR* 3.2 4.4 - - - +
176B GLY 3.0 30.3 + - - -
178B ALA* 5.1 3.1 - - + -
193B LEU* 4.2 12.1 - - + -
203B LEU* 4.3 20.6 - - + -
204B TYR 3.4 9.2 - - - +
205B VAL* 4.5 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B CYS 3.8 0.4 + - - -
136B VAL* 1.3 75.7 - - - +
138B ASN* 1.3 74.4 + - - +
139B LEU 3.1 2.1 + - - -
174B GLY 3.7 0.4 - - - -
175B TYR* 3.6 18.2 - - + -
203B LEU* 3.6 6.8 - - - +
204B TYR* 2.8 36.7 + - + +
296B PHE 4.7 2.2 - - - +
297B CYS* 4.6 2.9 - - - -
298B ALA* 4.0 31.6 - - + +
----------------------------------------------------------
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