Contacts of the strand formed by residues 133 - 137 (chain B) in PDB entry 3UMO
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 ILE 133 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B VAL* 3.8 13.0 - - + -
3B ARG 3.0 9.9 + - - +
4B ILE* 3.5 7.0 - - + -
5B TYR* 2.8 36.2 + - - +
131B GLY 4.3 1.6 - - - +
132B ALA* 1.3 78.0 - - - +
134B LEU* 1.3 61.6 + - - +
135B VAL* 4.5 0.4 - - + -
161B ILE* 4.6 0.7 - - - -
162B ARG* 3.3 20.9 - - + +
164B ILE* 3.8 28.7 - - + -
263B THR* 4.0 14.8 - - + +
266B LEU* 3.6 22.9 - - + -
267B ALA* 3.6 39.7 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
5B TYR* 3.3 24.0 - - + +
6B THR 4.0 14.1 - - - +
7B LEU* 4.0 9.9 - - + +
58B ILE* 4.7 4.0 - - + -
125B VAL* 3.8 31.2 - - + -
128B ILE* 4.1 9.2 - - + -
133B ILE* 1.3 73.9 - - - +
135B VAL* 1.3 63.4 + - - +
136B ILE* 3.7 27.0 + - + +
152B LEU* 4.6 4.7 - - + -
156B ALA* 4.8 1.3 - - + -
161B ILE* 3.7 18.1 - - + +
162B ARG 2.8 10.0 + - - +
163B CYS* 3.4 12.9 - - - +
164B ILE 2.8 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 4.7 0.9 - - + -
5B TYR 2.8 17.6 + - - +
6B THR* 3.2 16.4 - - + -
7B LEU 2.8 29.8 + - - +
41B GLY* 4.7 0.5 - - - -
44B VAL* 4.2 10.1 - - + -
133B ILE* 4.5 1.3 - - + -
134B LEU* 1.3 74.2 - - - +
136B ILE* 1.3 58.8 + - - +
137B SER* 3.6 15.9 + - - -
164B ILE* 3.4 19.3 - - + +
166B ASP 5.6 1.1 - - - +
259B VAL* 3.8 24.9 - - + -
263B THR* 3.4 37.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.8 21.3 - - + +
9B LEU* 5.8 2.7 - - + -
134B LEU* 3.9 28.9 - - + +
135B VAL* 1.3 75.3 - - - +
137B SER* 1.3 60.0 + - - +
149B LEU* 4.3 20.0 - - + -
152B LEU* 4.4 7.4 - - + -
153B ILE* 3.5 35.2 - - + -
163B CYS* 4.6 10.1 - - + -
164B ILE 2.8 13.1 + - - +
165B VAL* 3.5 15.4 - - + +
166B ASP 3.0 24.6 + - - +
167B SER* 5.3 1.5 - - - -
175B ALA* 6.1 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU 3.2 15.5 + - - +
8B THR* 4.1 7.4 - - - +
9B LEU 5.1 0.9 + - - -
40B GLY* 3.3 18.0 + - - -
41B GLY* 3.1 33.0 + - - -
44B VAL* 4.2 4.0 - - - +
135B VAL* 3.6 13.1 + - - -
136B ILE* 1.3 77.4 - - - +
138B GLY* 1.3 61.3 + - - +
166B ASP* 3.2 24.2 + - - +
256B ASP* 4.0 8.3 + - - -
----------------------------------------------------------
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