Contacts of the strand formed by residues 153 - 158 (chain A) in PDB entry 2PWA
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 VAL 153 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A VAL* 4.6 3.6 - - + -
118A LYS* 3.7 26.5 - - + -
127A VAL* 3.4 16.8 - - + +
128A VAL 3.7 5.6 - - - -
129A ALA* 3.5 37.9 - - + +
148A LEU* 3.5 27.9 + - + +
149A GLN* 3.3 24.3 + - - +
151A SER* 3.7 10.3 - - - +
152A GLY* 1.3 81.1 - - - +
154A MET* 1.3 61.3 + - - +
155A VAL 3.2 7.4 + - - -
245A ALA* 3.9 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A VAL 2.9 16.3 + - - +
128A VAL* 3.3 16.5 - - + +
129A ALA 2.8 25.9 + - - +
149A GLN* 4.0 1.3 - - - +
153A VAL* 1.3 70.0 - - - +
155A VAL* 1.3 68.6 + - - +
156A ALA* 4.1 4.7 - - - -
178A CYS* 3.7 31.2 - - + -
230A VAL* 4.4 11.0 - - + -
231A ALA* 5.1 0.4 - - - -
234A ALA* 3.9 24.9 - - + -
238A MET* 4.3 1.6 - - - -
245A ALA* 3.5 24.2 - - - +
248A ALA* 3.7 19.7 - - + -
249A CYS* 3.9 20.6 - - + +
252A ILE* 4.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ALA 3.5 3.4 - - - -
131A LEU* 4.1 18.6 - - + -
145A ALA* 4.1 4.5 - - + +
148A LEU* 3.6 23.8 - - + -
149A GLN* 2.9 42.4 + - + +
153A VAL* 3.6 9.6 - - + +
154A MET* 1.3 75.6 - - - +
156A ALA* 1.3 61.1 + - - +
157A VAL* 3.7 23.3 - - + -
177A VAL* 3.7 15.2 - - + +
178A CYS* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ALA 2.9 11.3 + - - +
130A SER* 4.8 0.2 - - - -
131A LEU* 2.9 27.0 + - - +
154A MET* 3.8 9.6 + - - -
155A VAL* 1.3 72.3 - - - +
157A VAL* 1.3 63.7 + - - +
178A CYS* 3.3 8.7 - - + +
180A VAL* 4.5 1.1 - - + -
227A THR* 3.5 24.5 - - + +
230A VAL* 4.4 10.3 - - + -
231A ALA* 4.2 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU* 3.4 15.7 - - + +
145A ALA* 5.1 0.4 - - + -
155A VAL* 3.7 21.5 - - + -
156A ALA* 1.3 79.3 - - - +
158A ALA* 1.3 61.1 + - - +
171A PRO* 3.8 28.9 - - + +
172A ALA* 3.7 22.4 - - - -
177A VAL* 3.9 13.5 - - + -
178A CYS 2.8 8.4 + - - +
179A THR* 3.7 22.0 - - - +
180A VAL* 2.9 27.9 + - - +
227A THR* 3.5 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU 3.1 15.3 + - - +
132A SER* 4.2 5.4 - - - -
133A LEU 4.2 4.5 + - - +
157A VAL* 1.3 74.6 - - - +
159A ALA* 1.3 63.6 + - - +
160A GLY 3.4 0.3 + - - -
172A ALA* 3.4 17.1 + - - +
180A VAL 3.9 1.6 - - - -
223A THR* 3.5 9.2 - - - +
224A SER 4.1 0.7 - - - +
227A THR* 3.0 18.3 + - - +
2001A B2A 3.3 39.5 - - + +
----------------------------------------------------------
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