Contacts of the strand formed by residues 31 - 37 (chain I) in PDB entry 1MWA
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 THR 31 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I TYR* 3.9 1.6 - - - -
28I VAL* 3.4 16.6 + - - +
29I ASP 3.0 7.6 + - - -
30I ASP* 1.3 76.7 - - - +
32I GLU* 1.3 73.6 + - - +
33I PHE* 3.4 5.4 + - - +
51I TRP* 5.6 6.3 - - + +
178I THR* 6.0 4.0 - - + -
179I LEU* 3.5 31.0 - - + +
209I TYR* 2.9 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 32 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I VAL* 3.1 11.6 - - + +
26I GLY 3.5 4.3 - - - +
27I TYR* 3.3 29.3 + - + -
30I ASP 3.3 7.3 + - - -
31I THR* 1.3 83.6 - - - +
33I PHE* 1.3 63.3 + - - +
34I VAL 4.0 7.4 - - - +
35I ARG* 2.4 48.1 + - - -
48I ARG* 3.1 45.1 + - + +
49I ALA* 5.0 1.0 - - - +
903I GOL 3.9 14.8 + - - -
55M SER* 4.1 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 33 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I LEU* 3.8 4.5 - - + -
7I TYR* 4.1 4.9 - - - -
26I GLY* 3.0 37.0 - - - -
27I TYR 3.8 0.7 - - - -
28I VAL* 3.6 18.4 - - + -
31I THR 4.0 3.4 - - - +
32I GLU* 1.3 74.9 - - - +
34I VAL* 1.3 77.3 + - + +
47I PRO 3.5 0.2 - - - -
48I ARG* 2.5 35.2 + - - +
51I TRP* 3.3 43.1 - + + -
52I MET* 3.1 28.2 - - + +
171I TYR* 3.3 53.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 34 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I TYR* 4.3 8.5 - - + +
25I VAL* 3.1 8.1 - - - +
26I GLY* 3.1 32.6 + - - +
32I GLU* 4.0 1.7 - - - +
33I PHE* 1.3 118.4 - - + +
35I ARG* 1.3 61.9 + - - +
45I TYR* 3.9 26.2 - - + -
46I GLU 3.6 5.8 - - - +
48I ARG* 3.4 2.6 - - - +
52I MET* 3.7 14.6 - - - -
59I TYR* 4.0 7.6 - - - +
60I TRP* 3.9 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 35 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I MET* 4.1 11.6 - - - -
24I GLU 3.0 16.2 - - - +
25I VAL* 2.9 16.2 - - - +
32I GLU* 2.4 39.0 + - - +
34I VAL* 1.3 74.6 - - - +
36I PHE* 1.3 69.4 + - - +
37I ASP* 4.9 5.4 - - + +
44I ARG 4.0 0.3 - - - +
45I TYR* 4.5 2.7 - - - -
46I GLU* 2.7 43.1 + - + +
48I ARG* 3.1 30.6 - - - +
53M ASP* 3.4 36.6 + - - +
54M MET 3.0 21.8 + - - +
55M SER* 3.2 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 36 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I TYR* 3.7 29.6 - + - -
23I MET* 2.8 5.2 - - - +
24I GLU* 2.5 38.9 + - + +
35I ARG* 1.3 76.3 - - - +
37I ASP* 1.3 64.4 + - - +
38I SER* 3.7 17.3 - - - -
43I PRO* 2.9 46.7 - - + -
44I ARG* 3.2 24.5 - - - -
45I TYR* 3.2 33.4 - + + -
64I THR* 4.8 3.6 - - + -
67I ALA* 3.7 23.6 - - + -
68I LYS* 3.8 13.9 - - + -
71I GLU* 5.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 37 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I ARG* 3.5 13.9 + - - -
22I TYR 2.7 20.6 - - - +
23I MET* 3.0 29.5 - - + +
35I ARG* 4.9 7.6 - - + +
36I PHE* 1.3 83.3 - - - +
38I SER* 1.3 52.5 + - - +
39I ASP* 2.5 41.8 + - - +
40I ALA* 2.8 29.8 + - + +
43I PRO* 3.8 5.9 - - - +
44I ARG 4.6 1.8 + - - +
53M ASP* 5.1 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