Contacts of the strand formed by residues 157 - 160 (chain A) in PDB entry 3UXA
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 ALA 157 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 5.7 2.7 - - + -
108A LEU* 3.8 18.1 - - + +
129A THR* 4.1 1.6 + - + +
130A VAL 2.8 6.8 + - - +
131A GLY* 3.5 3.1 - - - -
132A LEU 2.8 31.0 + - - -
155A GLU 3.9 0.8 + - - -
156A PRO* 1.3 75.9 - - - +
158A ILE* 1.3 57.0 - - - +
159A VAL* 4.0 0.4 - - - -
176A ILE* 3.7 20.2 - - + +
178A ILE* 3.7 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LEU* 3.4 20.9 - - + +
134A VAL* 3.6 29.2 - - + -
142A LEU* 4.6 2.5 - - + -
146A LEU* 4.3 16.8 - - + -
156A PRO 4.2 7.9 - - - +
157A ALA* 1.3 79.4 - - - +
159A VAL* 1.3 58.0 + - - +
160A ILE* 3.8 1.4 + - + +
169A ALA* 3.8 18.6 - - + -
172A ILE* 4.0 22.9 - - + -
174A ALA* 3.7 22.7 - - + -
175A ARG 5.5 0.2 - - - +
176A ILE 3.1 16.9 + - - +
177A ILE* 3.4 6.4 - - + +
178A ILE 2.7 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A TRP* 4.2 24.7 - - + +
131A GLY* 4.8 10.1 - - - -
132A LEU 2.9 16.9 + - - +
133A ILE* 4.4 21.3 - - + +
134A VAL* 3.6 21.5 + - - +
135A LYS 5.1 0.2 + - - -
157A ALA 4.8 0.2 - - - +
158A ILE* 1.3 73.9 - - - +
160A ILE* 1.3 68.4 + - - +
161A ASN* 5.9 0.7 - - - +
165A ASP* 4.4 1.4 - - - +
178A ILE* 3.3 35.2 - - + +
180A SER* 4.5 17.3 - - - -
184A LEU* 6.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 4.1 7.4 - - + -
158A ILE* 4.2 7.0 - - + +
159A VAL* 1.3 81.9 - - - +
161A ASN* 1.3 63.1 + - - +
165A ASP* 3.5 33.4 - - + +
166A LEU* 3.6 34.1 - - + -
169A ALA* 4.3 8.7 - - + -
177A ILE* 3.6 21.3 - - + -
178A ILE 2.7 19.0 + - - +
179A ILE* 3.7 16.1 - - + +
180A SER* 2.9 32.9 + - - +
197A LEU* 4.2 11.4 - - + -
201A ILE* 4.4 2.0 - - + -
----------------------------------------------------------
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