Contacts of the strand formed by residues 33 - 39 (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 SER 33 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLY 2.6 21.2 + - - -
31A GLN 3.2 1.4 + - - -
32A GLY* 1.3 80.1 + - - +
34A CYS* 1.3 69.1 - - - +
88A THR* 2.8 26.4 + - - -
89A GLN* 3.2 13.5 + - - +
125A LYS* 4.1 8.1 - - - -
126A GLY 3.4 12.3 - - - -
128A VAL* 5.7 1.1 - - - -
235A ALA* 3.4 27.8 - - - +
238A MET* 5.3 0.4 - - - -
239A THR* 3.6 10.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLY 4.9 0.7 - - - -
33A SER* 1.3 80.9 - - - +
35A VAL* 1.3 65.6 + - - +
36A TYR 4.2 0.2 - - - -
89A GLN* 3.3 15.3 - - - +
91A PHE* 3.6 24.9 - - + -
122A ASN 4.0 4.9 - - - -
123A CYS* 2.0 53.6 - - + -
126A GLY 3.0 6.8 + - - +
127A VAL* 3.3 9.4 - - + +
128A VAL* 2.9 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A CYS* 1.3 79.0 - - - +
36A TYR* 1.3 73.3 + - - +
37A VAL* 3.7 2.7 + - + +
77A VAL* 3.7 41.3 - - + -
88A THR* 3.6 14.8 - - - +
89A GLN 2.8 11.5 + - - +
90A LEU* 3.4 8.2 - - + +
91A PHE* 2.9 24.3 + - - +
128A VAL* 3.3 25.4 - - + +
130A SER* 4.3 7.2 - - - -
231A ALA* 4.4 1.8 - - + +
235A ALA* 3.8 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A CYS* 5.0 0.9 - - + -
35A VAL* 1.3 74.0 - - - +
37A VAL* 1.3 61.3 + - - +
38A ILE* 3.8 3.7 + - + -
56A VAL* 4.1 6.5 - - + -
91A PHE* 3.2 41.3 - + + -
93A VAL* 3.9 10.1 - - + -
113A PHE* 4.6 0.2 - + - -
114A VAL* 3.5 48.0 - - + -
117A ASP* 2.7 31.6 + - + -
118A LYS* 3.3 24.5 + - + -
121A ARG* 3.4 8.2 - - + +
123A CYS* 5.7 0.4 - - - -
127A VAL* 3.6 29.2 - - + -
128A VAL 2.8 12.0 + - - +
129A ALA* 3.3 5.0 - - + +
130A SER* 2.8 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A VAL* 4.2 9.9 - - + +
36A TYR* 1.3 74.1 - - - +
38A ILE* 1.3 60.9 + - - +
39A ASP* 3.6 15.9 + - + +
41A GLY 5.3 1.4 + - - +
42A ILE* 4.1 16.7 - - + +
70A GLY* 3.9 21.8 - - - +
73A CYS* 4.3 8.7 - - + -
74A ALA* 4.0 27.1 - - + +
77A VAL* 4.3 12.1 - - + -
90A LEU* 4.3 9.2 - - + -
91A PHE 2.8 7.7 + - - -
92A GLY* 3.7 2.8 - - - -
93A VAL 3.1 23.7 + - - +
130A SER* 3.8 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR 4.3 7.4 - - - +
37A VAL* 1.3 70.5 - - - +
39A ASP* 1.3 64.5 + - - +
93A VAL* 3.4 12.6 - - + +
95A VAL* 3.6 33.7 - - + -
107A ILE 5.1 3.8 - - - +
110A GLY 4.3 8.7 - - - +
111A MET* 4.4 7.0 - - + -
114A VAL* 3.8 29.8 - - + -
129A ALA* 4.2 7.6 - - + -
130A SER 3.1 18.1 + - - +
131A LEU* 3.7 29.3 - - + -
132A SER 4.3 0.2 + - - -
133A LEU* 3.4 23.2 - - + +
148A LEU* 4.3 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A VAL* 3.6 14.5 + - + +
38A ILE* 1.3 75.1 - - - +
40A THR* 1.3 74.7 + - - +
41A GLY 3.2 6.1 - - - +
69A HIS* 2.7 42.0 + - - -
70A GLY* 3.1 22.8 + - - -
73A CYS* 3.8 5.3 - - - +
93A VAL 2.9 7.3 + - - -
94A LYS* 3.2 3.6 - - - -
95A VAL* 2.9 26.1 + - - +
96A LEU* 3.0 21.1 + - - +
130A SER 5.7 0.2 - - - +
132A SER* 3.6 17.5 + - - +
----------------------------------------------------------
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