Contacts of the strand formed by residues 31 - 37 (chain C) 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 TYR 31 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C THR 5.8 0.2 - - - -
30C PRO* 1.3 81.0 - - + +
32C LEU* 1.3 64.7 + - - +
33C PHE* 3.4 20.9 - + + -
49C TYR 4.1 7.0 - - - +
50C TYR* 3.5 48.9 - + + -
92C VAL* 3.3 6.6 - - - +
93C SER* 3.0 51.8 + - - -
97D GLY 4.1 16.8 - - - -
155I ARG* 2.7 41.4 + - - +
158I ALA* 5.6 2.3 - - - +
159I TYR* 6.0 0.7 - - - +
163I THR* 6.0 1.3 - - - -
3Q TYR* 4.7 3.5 - - - -
4Q LYS* 4.4 13.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C CYS* 6.4 0.2 - - - -
24C TYR* 4.0 18.4 - - + -
30C PRO* 3.8 13.5 - - + +
31C TYR* 1.3 83.3 - - - +
33C PHE* 1.3 66.2 + - - +
48C LYS* 4.2 1.6 - - - -
49C TYR* 3.3 58.3 + - + -
66C PHE* 3.8 16.8 - - + -
73C PHE* 3.3 48.8 - - + -
90C CYS* 6.0 1.6 - - - -
91C ALA 4.2 2.5 - - - -
92C VAL* 3.4 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C TYR* 3.4 35.0 - + + -
32C LEU* 1.3 80.0 - - - +
34C TRP* 1.3 65.5 + - - +
35C TYR* 4.2 27.1 - + + -
45C LEU* 5.0 6.1 - - + -
47C LEU 4.2 4.7 - - - -
48C LYS* 4.3 20.2 - - + -
49C TYR 6.0 0.4 - - - -
50C TYR* 4.8 4.0 - + - -
73C PHE* 4.6 0.2 - - - -
90C CYS* 3.2 9.8 - - - -
91C ALA* 3.0 46.2 + - + +
104C LEU* 3.5 30.7 - - + -
98D GLY* 2.8 44.9 - - - -
106D LEU* 5.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C GLN* 4.2 7.9 - - - -
20C LEU* 3.5 43.5 - - + -
21C ARG 4.5 0.2 - - - -
22C CYS* 3.3 25.6 - - + -
33C PHE* 1.3 71.7 - - - +
35C TYR* 1.3 65.7 + - - +
36C VAL* 5.7 0.4 - - + -
45C LEU* 4.1 4.2 - - - +
46C LEU* 3.7 31.2 + - + +
47C LEU* 3.9 19.5 + - + -
64C ALA* 3.8 13.2 - - + -
73C PHE* 3.0 47.4 + + - -
75C LEU* 3.5 32.0 - - + +
88C TYR* 3.7 14.4 - + + -
89C PHE 3.1 29.2 - - - -
90C CYS* 3.4 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C PHE* 4.3 29.8 - + + -
34C TRP* 1.3 75.7 - - - +
36C VAL* 1.3 66.9 + - - +
43C LEU* 3.5 32.5 - - + -
44C GLN* 2.9 30.5 - - - -
45C LEU* 3.5 34.3 - - + +
46C LEU* 5.7 0.2 - - - -
88C TYR* 4.4 0.3 - - - +
89C PHE* 2.7 53.5 + - + +
91C ALA* 5.9 0.7 - - + -
104C LEU* 4.4 11.0 - - + -
106C PHE* 4.3 20.0 - + + -
106D LEU* 3.6 35.1 + - + +
108D PHE* 5.1 1.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C TRP* 5.7 0.7 - - + -
35C TYR* 1.3 81.0 - - - +
37C GLN* 1.3 61.0 + - - +
38C TYR* 5.2 12.5 - - + +
42C GLY 4.7 1.2 - - - +
43C LEU* 4.4 2.7 - - - -
44C GLN* 3.9 28.5 + - + +
46C LEU* 4.2 26.2 - - + -
62C PHE* 6.1 2.2 - - + -
86C ALA* 4.9 7.9 - - + -
87C VAL 3.3 14.8 - - - +
88C TYR* 3.2 43.3 - - + -
89C PHE* 5.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C VAL* 1.3 76.2 - - - +
38C TYR* 1.3 87.4 + - - +
39C PRO* 4.3 1.4 - - - +
40C ARG* 5.1 2.6 - - - +
41C GLN* 3.5 2.8 - - - +
42C GLY* 2.5 55.4 + - - +
43C LEU* 3.8 13.5 - - + +
86C ALA* 3.7 9.0 - - - +
87C VAL* 3.1 33.7 + - + +
89C PHE* 5.8 3.9 - - + -
91D PHE* 4.1 26.6 - - + -
----------------------------------------------------------
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